From pjotr.public14 at thebird.nl Sun Feb 5 16:37:31 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 5 Feb 2012 22:37:31 +0100 Subject: [BioRuby] JRuby going to be way faster than MRI Message-ID: <20120205213731.GB20253@thebird.nl> Today I attended an interesting talk by Charles Nutter of JRuby fame at FOSDEM 2012. The short of it is that much of the work on JRuby is on performance and low level access to C libraries (through FFI)... http://blog.thebird.nl/ Pj. From pjotr.public14 at thebird.nl Wed Feb 8 13:48:17 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 8 Feb 2012 19:48:17 +0100 Subject: [BioRuby] A question for BioRuby newbies Message-ID: <20120208184817.GA31948@thebird.nl> Hi All, This mailing list counts 180 subscribed readers. Which is impressive. Also since the introduction of http://biogems.info/ the number of BioRuby downloads has increased rapidly. You may also have noticed Ruby, in general, is making its mark in bioinformatics. More and more people are programming in Ruby, which I think rather delightful. And Biogems.info is proving to be cutting edge, and accelerating development. So here is a question to people who read the mailing list, but do not necessarily participate. What is needed to pull you in? At this point I have two ideas to increase participation. (1) First a race. I would like all readers to vote a few times a year on the most beautiful Biogem source code. We'll put up a few projects to choose from, and the winner will be highlighted on http://biogems.info/. Ruby is about beauty, and we are seeing some of that in the biogems. The other idea I got at FOSDEM this year from a convincing talk by Brian Ostergard, titled 'You are doing it all wrong' http://fosdem.org/2012/schedule/event/really_grow_community where he made a strong case to address inexperienced developers. And you know what, I believe he is right. So (2) We will look for ways to get inexperienced developers involved. One way is to define uncomplicated and moderately complicated tasks, feature requests and bug fixes. We are going to list these 'jobs' on http://biogems.info/. If anyone picks up a task he/she will get very *strong* support from the plugin owner, as well as the Biogem maintainers. You, the programmer, will get all the credit for the work. How does this sound? Does this appeal to you? Anyone of the less experienced, or even experienced, wants to voice his or her opinion? We may even turn some work into a Google Summer of Code project proposal. Pj. From mail at michaelbarton.me.uk Wed Feb 8 15:52:57 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Wed, 8 Feb 2012 15:52:57 -0500 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208184817.GA31948@thebird.nl> References: <20120208184817.GA31948@thebird.nl> Message-ID: <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> I think this is a very good idea. More public engagement would be a boon to the BioRuby project. I would be happy to help new developers work on my Scaffolder gem. Here are two additional suggestions from me for increasing BioRuby participation. First suggestion: I think the bioruby home page could be made simpler. A very rough estimate shows 80 links on the front page: curl http://bioruby.open-bio.org/ | tidy -i -q | grep href | wc -> 80 links Compare this with the Rails and Sinatra homepages: curl http://rubyonrails.org/ | tidy -i -q | grep href | wc -> 47 links curl http://www.sinatrarb.com/ | tidy -i -q | grep href | wc -> 20 links I think making the homepage simpler would be very beneficial. For instance I think the two most important links (Tutorial and Sample codes) pages should be given much greater prominence. These are the two pages which most beginners will want to get started with. Compare with the Sinatra page which has only six links on the front page pointing to the most significant parts of the project. I think the Tutorial and Sample codes pages could do with some love also. These pages do not match the visual layout of the bioruby home page, one is in a separate domain while the other is a wiki page. I think these pages deserve attention to make them simpler and more accessible. A common CSS theme also provides a unified front to the BioRuby project. Compare with the Sinatra intro and documentation pages: * http://www.sinatrarb.com/intro * http://www.sinatrarb.com/documentation My opinion is that the BioRuby website should head in this direction. I am not a web designer but I am happy to contribute effort to writing web copy and BioRuby recipes. I also think that bioruby should also have its own web address too. Second Suggestion: I think as BioRuby becomes more and more popular the code base will continue to increase in size. I think this will become a disadvantage as a larger code base is harder to navigate, harder to maintain, and more intimidating to make contributions to. Pjotr has addressed this with the BioGems project but I think we should follow the natural progression and consider splitting the Bio gem into smaller self-contained gems. I think this is already starting to happen with the replacement gff3 and 'faster' fasta gems. I think smaller gems would be easier to maintain and allow different development cycles. I think it also easier to create a gem for a new idea rather than find a place for it in a large pre-existing code base. Finally this would follow the smaller 'does just one thing' gem development philosophy in Ruby. Michael Barton On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: > Hi All, > > This mailing list counts 180 subscribed readers. > Which is impressive. Also since the introduction of > http://biogems.info/ the number of BioRuby downloads has > increased rapidly. > > You may also have noticed Ruby, in general, is making > its mark in bioinformatics. More and more people are > programming in Ruby, which I think rather delightful. > And Biogems.info is proving to be cutting edge, and > accelerating development. > > So here is a question to people who read the mailing list, > but do not necessarily participate. What is needed to pull > you in? > > At this point I have two ideas to increase participation. > > (1) First a race. I would like all readers to vote a few > times a year on the most beautiful Biogem source code. > We'll put up a few projects to choose from, and the winner > will be highlighted on http://biogems.info/. Ruby is about > beauty, and we are seeing some of that in the biogems. > > The other idea I got at FOSDEM this year from a convincing > talk by Brian Ostergard, titled 'You are doing it all > wrong' > > http://fosdem.org/2012/schedule/event/really_grow_commun > ity > > where he made a strong case to address inexperienced > developers. And you know what, I believe he is right. So > > (2) We will look for ways to get inexperienced developers > involved. One way is to define uncomplicated and > moderately complicated tasks, feature requests and bug > fixes. > > We are going to list these 'jobs' on http://biogems.info/. > If anyone picks up a task he/she will get very *strong* > support from the plugin owner, as well as the Biogem > maintainers. You, the programmer, will get all the credit > for the work. > > How does this sound? Does this appeal to you? Anyone of > the less experienced, or even experienced, wants to voice > his or her opinion? We may even turn some work into a > Google Summer of Code project proposal. > > Pj. _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mictadlo at gmail.com Wed Feb 8 17:38:08 2012 From: mictadlo at gmail.com (Mic) Date: Thu, 9 Feb 2012 08:38:08 +1000 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> Message-ID: Hi all, It would be great if BioRuby/Ruby would have: * a good BAM/tabix/vcf support * a gff3 support which doesn't read the whole file in the memory see http://biopython.org/wiki/GFF_Parsing#Limiting_to_features_of_interest * http://www.scipy.org/ * a powerful chart library like http://matplotlib.sourceforge.net/ * http://networkx.lanl.gov/ Maybe Google Summer of Code 2012 could help. On Thu, Feb 9, 2012 at 6:52 AM, Michael Barton wrote: > I think this is a very good idea. More public engagement > would be a boon to the BioRuby project. I would be happy to > help new developers work on my Scaffolder gem. Here are two > additional suggestions from me for increasing BioRuby > participation. > > First suggestion: > > I think the bioruby home page could be made simpler. A very > rough estimate shows 80 links on the front page: > > curl http://bioruby.open-bio.org/ | tidy -i -q | grep href | wc > -> 80 links > > Compare this with the Rails and Sinatra homepages: > > curl http://rubyonrails.org/ | tidy -i -q | grep href | wc > -> 47 links > > curl http://www.sinatrarb.com/ | tidy -i -q | grep href | wc > -> 20 links > > I think making the homepage simpler would be very > beneficial. For instance I think the two most important > links (Tutorial and Sample codes) pages should be given much > greater prominence. These are the two pages which most > beginners will want to get started with. Compare with the > Sinatra page which has only six links on the front page > pointing to the most significant parts of the project. > > I think the Tutorial and Sample codes pages could do with > some love also. These pages do not match the visual layout > of the bioruby home page, one is in a separate domain while > the other is a wiki page. I think these pages deserve > attention to make them simpler and more accessible. A common > CSS theme also provides a unified front to the BioRuby > project. > > Compare with the Sinatra intro and documentation pages: > * http://www.sinatrarb.com/intro > * http://www.sinatrarb.com/documentation > > My opinion is that the BioRuby website should head in this > direction. I am not a web designer but I am happy to > contribute effort to writing web copy and BioRuby recipes. I > also think that bioruby should also have its own web address > too. > > Second Suggestion: > > I think as BioRuby becomes more and more popular the code > base will continue to increase in size. I think this will > become a disadvantage as a larger code base is harder to > navigate, harder to maintain, and more intimidating to make > contributions to. > > Pjotr has addressed this with the BioGems project but I > think we should follow the natural progression and consider > splitting the Bio gem into smaller self-contained gems. I > think this is already starting to happen with the > replacement gff3 and 'faster' fasta gems. > > I think smaller gems would be easier to maintain and allow > different development cycles. I think it also easier to > create a gem for a new idea rather than find a place for it > in a large pre-existing code base. Finally this would follow > the smaller 'does just one thing' gem development philosophy > in Ruby. > > Michael Barton > > On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: > > > Hi All, > > > > This mailing list counts 180 subscribed readers. > > Which is impressive. Also since the introduction of > > http://biogems.info/ the number of BioRuby downloads has > > increased rapidly. > > > > You may also have noticed Ruby, in general, is making > > its mark in bioinformatics. More and more people are > > programming in Ruby, which I think rather delightful. > > And Biogems.info is proving to be cutting edge, and > > accelerating development. > > > > So here is a question to people who read the mailing list, > > but do not necessarily participate. What is needed to pull > > you in? > > > > At this point I have two ideas to increase participation. > > > > (1) First a race. I would like all readers to vote a few > > times a year on the most beautiful Biogem source code. > > We'll put up a few projects to choose from, and the winner > > will be highlighted on http://biogems.info/. Ruby is about > > beauty, and we are seeing some of that in the biogems. > > > > The other idea I got at FOSDEM this year from a convincing > > talk by Brian Ostergard, titled 'You are doing it all > > wrong' > > > > http://fosdem.org/2012/schedule/event/really_grow_commun > > ity > > > > where he made a strong case to address inexperienced > > developers. And you know what, I believe he is right. So > > > > (2) We will look for ways to get inexperienced developers > > involved. One way is to define uncomplicated and > > moderately complicated tasks, feature requests and bug > > fixes. > > > > We are going to list these 'jobs' on http://biogems.info/. > > If anyone picks up a task he/she will get very *strong* > > support from the plugin owner, as well as the Biogem > > maintainers. You, the programmer, will get all the credit > > for the work. > > > > How does this sound? Does this appeal to you? Anyone of > > the less experienced, or even experienced, wants to voice > > his or her opinion? We may even turn some work into a > > Google Summer of Code project proposal. > > > > Pj. _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > From mictadlo at gmail.com Wed Feb 8 18:01:21 2012 From: mictadlo at gmail.com (Mic) Date: Thu, 9 Feb 2012 09:01:21 +1000 Subject: [BioRuby] EU-codefest in July In-Reply-To: <20120126103423.GA10234@thebird.nl> References: <20120126103423.GA10234@thebird.nl> Message-ID: HI Pjotr, Will be any videos of the talks available or are there any videos from year before available? Cheers, On Thu, Jan 26, 2012 at 8:34 PM, Pjotr Prins wrote: > EU-codefest 2012 will be 19 and 20 July in Lodi Italy > > In coordination with the BOSC committee we are organising the first > EU-Codefest, a low-key event the week after BOSC 2012. > > http://www.open-bio.org/wiki/EU_Codefest_2012 > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Thu Feb 9 04:04:22 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 09 Feb 2012 10:04:22 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: Message-ID: Hi Mic, On 08/02/12 23.38, "Mic" wrote: > Hi all, > It would be great if BioRuby/Ruby would have: > * a good BAM/tabix/vcf support About BAM: https://rubygems.org/gems/bio-samtools but any suggestion contribute or idea is more than welcome > * http://www.scipy.org/ > * a powerful chart library like http://matplotlib.sourceforge.net/ https://github.com/SciRuby/sciruby The developers are very active and some of them are working in bioinformatics, but they want to keep it separated from BioRuby because SciRuby can be useful for other purposes other than bioinformatics. There was a graphic library http://rubyvis.rubyforge.org/ (there was a GSoC project bio-images) now called http://mbostock.github.com/d3/ and another library which uses SVG is http://raphaeljs.com/ > * http://networkx.lanl.gov/ About network I don't know. > > Maybe Google Summer of Code 2012 could help. > > On Thu, Feb 9, 2012 at 6:52 AM, Michael Barton > wrote: > >> I think this is a very good idea. More public engagement >> would be a boon to the BioRuby project. I would be happy to >> help new developers work on my Scaffolder gem. Here are two >> additional suggestions from me for increasing BioRuby >> participation. >> >> First suggestion: >> >> I think the bioruby home page could be made simpler. A very >> rough estimate shows 80 links on the front page: >> >> curl http://bioruby.open-bio.org/ | tidy -i -q | grep href | wc >> -> 80 links >> >> Compare this with the Rails and Sinatra homepages: >> >> curl http://rubyonrails.org/ | tidy -i -q | grep href | wc >> -> 47 links >> >> curl http://www.sinatrarb.com/ | tidy -i -q | grep href | wc >> -> 20 links >> >> I think making the homepage simpler would be very >> beneficial. For instance I think the two most important >> links (Tutorial and Sample codes) pages should be given much >> greater prominence. These are the two pages which most >> beginners will want to get started with. Compare with the >> Sinatra page which has only six links on the front page >> pointing to the most significant parts of the project. >> >> I think the Tutorial and Sample codes pages could do with >> some love also. These pages do not match the visual layout >> of the bioruby home page, one is in a separate domain while >> the other is a wiki page. I think these pages deserve >> attention to make them simpler and more accessible. A common >> CSS theme also provides a unified front to the BioRuby >> project. >> >> Compare with the Sinatra intro and documentation pages: >> * http://www.sinatrarb.com/intro >> * http://www.sinatrarb.com/documentation >> >> My opinion is that the BioRuby website should head in this >> direction. I am not a web designer but I am happy to >> contribute effort to writing web copy and BioRuby recipes. I >> also think that bioruby should also have its own web address >> too. >> >> Second Suggestion: >> >> I think as BioRuby becomes more and more popular the code >> base will continue to increase in size. I think this will >> become a disadvantage as a larger code base is harder to >> navigate, harder to maintain, and more intimidating to make >> contributions to. >> >> Pjotr has addressed this with the BioGems project but I >> think we should follow the natural progression and consider >> splitting the Bio gem into smaller self-contained gems. I >> think this is already starting to happen with the >> replacement gff3 and 'faster' fasta gems. >> >> I think smaller gems would be easier to maintain and allow >> different development cycles. I think it also easier to >> create a gem for a new idea rather than find a place for it >> in a large pre-existing code base. Finally this would follow >> the smaller 'does just one thing' gem development philosophy >> in Ruby. >> >> Michael Barton >> >> On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: >> >>> Hi All, >>> >>> This mailing list counts 180 subscribed readers. >>> Which is impressive. Also since the introduction of >>> http://biogems.info/ the number of BioRuby downloads has >>> increased rapidly. >>> >>> You may also have noticed Ruby, in general, is making >>> its mark in bioinformatics. More and more people are >>> programming in Ruby, which I think rather delightful. >>> And Biogems.info is proving to be cutting edge, and >>> accelerating development. >>> >>> So here is a question to people who read the mailing list, >>> but do not necessarily participate. What is needed to pull >>> you in? >>> >>> At this point I have two ideas to increase participation. >>> >>> (1) First a race. I would like all readers to vote a few >>> times a year on the most beautiful Biogem source code. >>> We'll put up a few projects to choose from, and the winner >>> will be highlighted on http://biogems.info/. Ruby is about >>> beauty, and we are seeing some of that in the biogems. >>> >>> The other idea I got at FOSDEM this year from a convincing >>> talk by Brian Ostergard, titled 'You are doing it all >>> wrong' >>> >>> http://fosdem.org/2012/schedule/event/really_grow_commun >>> ity >>> >>> where he made a strong case to address inexperienced >>> developers. And you know what, I believe he is right. So >>> >>> (2) We will look for ways to get inexperienced developers >>> involved. One way is to define uncomplicated and >>> moderately complicated tasks, feature requests and bug >>> fixes. >>> >>> We are going to list these 'jobs' on http://biogems.info/. >>> If anyone picks up a task he/she will get very *strong* >>> support from the plugin owner, as well as the Biogem >>> maintainers. You, the programmer, will get all the credit >>> for the work. >>> >>> How does this sound? Does this appeal to you? Anyone of >>> the less experienced, or even experienced, wants to voice >>> his or her opinion? We may even turn some work into a >>> Google Summer of Code project proposal. >>> >>> Pj. _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Thu Feb 9 04:22:28 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 9 Feb 2012 10:22:28 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> Message-ID: <20120209092228.GB7020@thebird.nl> Hi Mic, On Thu, Feb 09, 2012 at 08:38:08AM +1000, Mic wrote: > * a gff3 support which doesn't read the whole file in the memory > see [1]http://biopython.org/wiki/GFF_Parsing#Limiting_to_features_of_interest The current bio-gff3 biogem only loads an index into memory, which is not too costly, and caches records. The problem with the GFF3 standard is (potentially) deep references, which is not so relevant for 99% of real GFF3 data. I agree we can do better. Still, for most practical purposes, the bio-gff3-plugin gem delivers. You may want to use the lru,line,lazy 75m 75m 0m17 (0.8.6) 50K 730M version. See the explanation on https://github.com/pjotrp/bioruby-gff3-plugin It is a tad slow. About six times slower than the full memory version. Speed is the first improvement I would work on. Pj. From p.j.a.cock at googlemail.com Thu Feb 9 04:25:38 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 9 Feb 2012 09:25:38 +0000 Subject: [BioRuby] EU-codefest in July In-Reply-To: References: <20120126103423.GA10234@thebird.nl> Message-ID: On Wed, Feb 8, 2012 at 11:01 PM, Mic wrote: > HI Pjotr, > Will be any videos of the talks available or are there any > videos from year before available? > > Cheers, Hi Mic, The BOSC committee are looking into this possibility for 2012, and volunteers with technical expertise would be most helpful. We're not promising anything yet though ;) For BOSC 2011 some of the talks were recorded, but this was not pre-planned, and I don't have contact details for the participant who filmed this. If we can track him down, and he still has the files, and the speakers are OK with it, then perhaps we can share some BOSC videos from last year. Regards, Peter (One of the BOSC committee) From pjotr.public14 at thebird.nl Thu Feb 9 05:03:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 9 Feb 2012 11:03:54 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics Message-ID: <20120209100353.GA8686@thebird.nl> We would like to highlight a project which sets a shining example for using Ruby for bioinformatics. We will vote on that on this list. Hereby I invite everyone to have a look at the projects on http://biogems.info/ and pick out a code snippet you really like. Send it to the mailing list, and explain why you think you like it. You can put forward one of your own projects :) ~~~ As an example, I am going to propose an implementation feature in the biogem tool, which represents a bit of Ruby meta-programming. It is called opening classes, and can be useful in overriding BioRuby itself, something I'll show below. Biogem does not implement everything from scratch. It uses a library from the Jeweler project, which was never designed to be shared(!). I.e. Jeweler was subverted for our purposes. Raoul put this together. The code I refer to lives, for example, in my forked project: https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb what you see here is that Biogem reopens the Jeweler::Generator class with class Jeweler class Generator (...) next, it overrides methods in that class. Because the file (jeweler.rb) gets included *later* than the original class, the overridden methods get called. The original methods can be renamed, e.g. alias original_render_template render_template and can be called from the overriding method. This technique of reopening classes and overriding behaviour is used in Ruby on Rails (indeed), but also in bio-logger and the bio-alignment gems. In bio-alignment it is used to make the BioRuby Bio::Sequence object enumerable, see https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bioruby.rb Having Bio::Sequence enumerable allows you to use enumerable functional methods, such as 'map'. For example I can now write @seq.map { |codon| codon.to_s }.join(' ') There is a case to be made to have standard BioRuby use Enumerable. However BioRuby has to support Ruby 1.8, which differs in this area. By reopening the class I can make it look like it is part of BioRuby anyway. I think it is a very powerful feature, and Raoul did the right thing in making Jeweler work for Biogem. I think it is an impressive example of beautiful code. Pj From cjfields at illinois.edu Fri Feb 10 13:04:31 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 10 Feb 2012 18:04:31 +0000 Subject: [BioRuby] Google Summer of Code project ideas References: <4F355910.4060203@gmail.com> Message-ID: Hi all, I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due in a couple of weeks, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. So, for each of the OBF projects that wants to do GSoC again this year, please: a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2012 OBF GSoC Organization Admin From pjotr.public14 at thebird.nl Fri Feb 10 14:03:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 10 Feb 2012 20:03:35 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <4F355910.4060203@gmail.com> Message-ID: <20120210190335.GA20909@thebird.nl> Building out on the idea of involving newbies in easy projects, I would like to invite all plugin authors to come up with ideas on this list. Even the smallest idea will help. So think beyond SoC. Michael came up with gemifying, or componentizing BioRuby. And also upgrading our web presentation. Good ideas, any others? Francesco, what about bio-ngs? Pj. On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > Hi all, > > I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due in a couple of weeks, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. > > So, for each of the OBF projects that wants to do GSoC again this year, please: > > a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. > > b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > > c.) Let me know via email that you have done so and it's ready for Google to peruse. > > Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) > > Rob > > ---- > Robert Buels > (prospective) 2012 OBF GSoC Organization Admin > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Sat Feb 11 02:47:51 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 11 Feb 2012 08:47:51 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> Message-ID: <20120211074751.GA23063@thebird.nl> Dear Toshiaki and Naohisa, I believe Michael has a very valid point. How about defining a project (potentially SoC), where we lay out the functionality we want from such a web presence? Pj. On Wed, Feb 08, 2012 at 03:52:57PM -0500, Michael Barton wrote: > I think making the homepage simpler would be very > beneficial. For instance I think the two most important > links (Tutorial and Sample codes) pages should be given much > greater prominence. These are the two pages which most > beginners will want to get started with. Compare with the > Sinatra page which has only six links on the front page > pointing to the most significant parts of the project. > > I think the Tutorial and Sample codes pages could do with > some love also. These pages do not match the visual layout > of the bioruby home page, one is in a separate domain while > the other is a wiki page. I think these pages deserve > attention to make them simpler and more accessible. A common > CSS theme also provides a unified front to the BioRuby > project. > > Compare with the Sinatra intro and documentation pages: > * http://www.sinatrarb.com/intro > * http://www.sinatrarb.com/documentation > > My opinion is that the BioRuby website should head in this > direction. I am not a web designer but I am happy to > contribute effort to writing web copy and BioRuby recipes. I > also think that bioruby should also have its own web address > too. From pjotr.public14 at thebird.nl Sat Feb 11 12:46:16 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 11 Feb 2012 18:46:16 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120209100353.GA8686@thebird.nl> References: <20120209100353.GA8686@thebird.nl> Message-ID: <20120211174616.GA24074@thebird.nl> Correct me if I am wrong, but has everyone moved across to BioPython now? Or even to the dark side? Pj. On Thu, Feb 09, 2012 at 11:03:54AM +0100, Pjotr Prins wrote: > We would like to highlight a project which sets a shining example for > using Ruby for bioinformatics. We will vote on that on this list. > > Hereby I invite everyone to have a look at the projects on > http://biogems.info/ and pick out a code snippet you really like. > Send it to the mailing list, and explain why you think you like it. > > You can put forward one of your own projects :) > > ~~~ > > As an example, I am going to propose an implementation feature in the > biogem tool, which represents a bit of Ruby meta-programming. It is > called opening classes, and can be useful in overriding BioRuby > itself, something I'll show below. > > Biogem does not implement everything from scratch. It uses a library > from the Jeweler project, which was never designed to be shared(!). > I.e. Jeweler was subverted for our purposes. > > Raoul put this together. The code I refer to lives, for example, in my > forked project: > > https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb > > what you see here is that Biogem reopens the Jeweler::Generator class with > > class Jeweler > class Generator > > (...) > > next, it overrides methods in that class. Because the file > (jeweler.rb) gets included *later* than the original class, the > overridden methods get called. The original methods can be renamed, > e.g. > > alias original_render_template render_template > > and can be called from the overriding method. > > This technique of reopening classes and overriding behaviour is used > in Ruby on Rails (indeed), but also in bio-logger and the > bio-alignment gems. In bio-alignment it is used to make the BioRuby > Bio::Sequence object enumerable, see > > https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bioruby.rb > > Having Bio::Sequence enumerable allows you to use enumerable > functional methods, such as 'map'. For example I can now write > > @seq.map { |codon| codon.to_s }.join(' ') > > There is a case to be made to have standard BioRuby use Enumerable. > However BioRuby has to support Ruby 1.8, which differs in this area. > By reopening the class I can make it look like it is part of BioRuby > anyway. I think it is a very powerful feature, and Raoul did the > right thing in making Jeweler work for Biogem. I think it is an > impressive example of beautiful code. > > Pj > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Sat Feb 11 14:08:37 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 11 Feb 2012 19:08:37 +0000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? > > Pj. I haven't noticed any BioRuby developers posting on the Biopython mailing lists recently - but you'd be welcome ;) On a related topic, my first BioRuby pull request was merged, so there is a little direct cross project contribution going on :) https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d Peter From hlapp at drycafe.net Sat Feb 11 15:16:30 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 11 Feb 2012 15:16:30 -0500 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> On Feb 11, 2012, at 12:46 PM, Pjotr Prins wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? The dark side is already here. You, too, can haz perl. All your gem are belong to us. -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From bonnal at ingm.org Sat Feb 11 15:15:02 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 11 Feb 2012 21:15:02 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> Message-ID: LOL On 11/02/12 18.46, "Pjotr Prins" wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? > > Pj. > > On Thu, Feb 09, 2012 at 11:03:54AM +0100, Pjotr Prins wrote: >> We would like to highlight a project which sets a shining example for >> using Ruby for bioinformatics. We will vote on that on this list. >> >> Hereby I invite everyone to have a look at the projects on >> http://biogems.info/ and pick out a code snippet you really like. >> Send it to the mailing list, and explain why you think you like it. >> >> You can put forward one of your own projects :) >> >> ~~~ >> >> As an example, I am going to propose an implementation feature in the >> biogem tool, which represents a bit of Ruby meta-programming. It is >> called opening classes, and can be useful in overriding BioRuby >> itself, something I'll show below. >> >> Biogem does not implement everything from scratch. It uses a library >> from the Jeweler project, which was never designed to be shared(!). >> I.e. Jeweler was subverted for our purposes. >> >> Raoul put this together. The code I refer to lives, for example, in my >> forked project: >> >> >> https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb >> >> what you see here is that Biogem reopens the Jeweler::Generator class with >> >> class Jeweler >> class Generator >> >> (...) >> >> next, it overrides methods in that class. Because the file >> (jeweler.rb) gets included *later* than the original class, the >> overridden methods get called. The original methods can be renamed, >> e.g. >> >> alias original_render_template render_template >> >> and can be called from the overriding method. >> >> This technique of reopening classes and overriding behaviour is used >> in Ruby on Rails (indeed), but also in bio-logger and the >> bio-alignment gems. In bio-alignment it is used to make the BioRuby >> Bio::Sequence object enumerable, see >> >> >> https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bio >> ruby.rb >> >> Having Bio::Sequence enumerable allows you to use enumerable >> functional methods, such as 'map'. For example I can now write >> >> @seq.map { |codon| codon.to_s }.join(' ') >> >> There is a case to be made to have standard BioRuby use Enumerable. >> However BioRuby has to support Ruby 1.8, which differs in this area. >> By reopening the class I can make it look like it is part of BioRuby >> anyway. I think it is a very powerful feature, and Raoul did the >> right thing in making Jeweler work for Biogem. I think it is an >> impressive example of beautiful code. >> >> Pj >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From georgkam at gmail.com Sat Feb 11 15:27:44 2012 From: georgkam at gmail.com (George Githinji) Date: Sat, 11 Feb 2012 23:27:44 +0300 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: Hi All Beauty is in the eyes of the beholder! The Bio-Alignment plugin can read and interconvert a nucleotide alignment to an amino acid alignment. I liked the simplicity of how PJ has implemented the codon to amino acid conversion helper method while taking care of the gaps or undefined aa translations. # lazily convert to Amino acid (once only) def to_aa aa = translate if not aa if gap? return '-' elsif undefined? return 'X' else raise 'What?' end end aa end This method does not have any ruby 'magic' and is self documenting. The gap? and undefined? methods are implemented as simple one line standalone methods. Again I like this simple 'trick' of getting an array of codons from a sequence in the codonsequence class. seq.scan(/\S\S\S/) #gets an array of codons The longer alternative would be to create a bio::sequence::NA object and iterate seq = Bio::Sequence::NA.new("blahahahha") seq.window_search(3, 3) do |subseq| puts subseq end It seems more intuitive to represent a sequence as an array of codon objects. In this way the codons have some state and can carry 'luggage'. getting the string representation of the sequence is as simple as def to_s @seq.map { |codon| codon.to_s }.join(' ') end To be more DRY, the to_nt method in the same class could be aliased from the to_s method It seems the bio-plugins are a rich source of tricks and great learning.... ! On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock wrote: > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins wrote: >> Correct me if I am wrong, but has everyone moved across to BioPython >> now? Or even to the dark side? >> >> Pj. > > I haven't noticed any BioRuby developers posting on the Biopython > mailing lists recently - but you'd be welcome ;) > > On a related topic, my first BioRuby pull request was merged, so > there is a little direct cross project contribution going on :) > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From cjfields at illinois.edu Sat Feb 11 17:00:23 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sat, 11 Feb 2012 22:00:23 +0000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> Message-ID: <2927BD64-ACC7-4F9E-9B25-2FF82C329421@illinois.edu> On Feb 11, 2012, at 2:16 PM, Hilmar Lapp wrote: > On Feb 11, 2012, at 12:46 PM, Pjotr Prins wrote: > >> Correct me if I am wrong, but has everyone moved across to BioPython >> now? Or even to the dark side? > > The dark side is already here. You, too, can haz perl. All your gem are belong to us. :) chris From pjotr.public14 at thebird.nl Sun Feb 12 03:43:13 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 12 Feb 2012 09:43:13 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> Message-ID: <20120212084313.GB25607@thebird.nl> On Sat, Feb 11, 2012 at 03:16:30PM -0500, Hilmar Lapp wrote: > > On Feb 11, 2012, at 12:46 PM, Pjotr Prins wrote: > > > Correct me if I am wrong, but has everyone moved across to BioPython > > now? Or even to the dark side? > > The dark side is already here. You, too, can haz perl. All your gem are belong to us. We have HAL! Oh wait... something odd is happening, I don't feel right Pj. From bonnal at ingm.org Sun Feb 12 18:17:30 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 00:17:30 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120210190335.GA20909@thebird.nl> Message-ID: I agree with Pjotr, So please post your ideas here and update the wiki. It's time to re-start IRC meetings, what about Feb 16 around: 9:00 GMT 10:00 Italy 18:00 Japan 4:00 NewYork ( too early ? :-) About BioNGS, I think it's too complicated by itself, but I could have 2 students working on this project. On 10/02/12 20.03, "Pjotr Prins" wrote: > Building out on the idea of involving newbies in easy projects, I > would like to invite all plugin authors to come up with ideas on this > list. Even the smallest idea will help. So think beyond SoC. > > Michael came up with gemifying, or componentizing BioRuby. And also > upgrading our web presentation. Good ideas, any others? > > Francesco, what about bio-ngs? > > Pj. > > On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: >> Hi all, >> >> I'm going to be OBF project admin again this year for Google Summer of code. >> OBF's application is due in a couple of weeks, and we need to update our >> project ideas on the OBF wiki page and on each project's individual wiki >> pages. >> >> So, for each of the OBF projects that wants to do GSoC again this year, >> please: >> >> a.) Update the list of project ideas on your project's GSoC page (BioPython, >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been >> done or no longer relevant, etc. >> >> b.) Update the list of project ideas on the main OBF GSoC page >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. >> >> c.) Let me know via email that you have done so and it's ready for Google to >> peruse. >> >> Please have the updates done, if possible, by this Friday (March 11). The >> number and quality of the project ideas are part of the evaluation process >> for whether OBF is accepted as a Summer of Code organization again this year, >> so let's come up with some good ones. :-) >> >> Rob >> >> ---- >> Robert Buels >> (prospective) 2012 OBF GSoC Organization Admin >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnal at ingm.org Sun Feb 12 18:35:05 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 00:35:05 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> Message-ID: I like this idea and commenting or posting snipped code is the chance to discuss about Ruby and design patterns or obscure techniques. Pjotr commented the way I reopened a class -thanks!- and that is called Monkey Patch technique http://en.wikipedia.org/wiki/Monkey_patch ; Metaprogramming Ruby by Paolo Perrotta it's something every Ruby developer should read. So +1 to use this ml for basic/advanced ruby questions not only for bio stuffs and the talented/skilled coders will provide support for sure. PS: I'm studing D :-) On 11/02/12 18.46, "Pjotr Prins" wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? > > Pj. > > On Thu, Feb 09, 2012 at 11:03:54AM +0100, Pjotr Prins wrote: >> We would like to highlight a project which sets a shining example for >> using Ruby for bioinformatics. We will vote on that on this list. >> >> Hereby I invite everyone to have a look at the projects on >> http://biogems.info/ and pick out a code snippet you really like. >> Send it to the mailing list, and explain why you think you like it. >> >> You can put forward one of your own projects :) >> >> ~~~ >> >> As an example, I am going to propose an implementation feature in the >> biogem tool, which represents a bit of Ruby meta-programming. It is >> called opening classes, and can be useful in overriding BioRuby >> itself, something I'll show below. >> >> Biogem does not implement everything from scratch. It uses a library >> from the Jeweler project, which was never designed to be shared(!). >> I.e. Jeweler was subverted for our purposes. >> >> Raoul put this together. The code I refer to lives, for example, in my >> forked project: >> >> >> https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb >> >> what you see here is that Biogem reopens the Jeweler::Generator class with >> >> class Jeweler >> class Generator >> >> (...) >> >> next, it overrides methods in that class. Because the file >> (jeweler.rb) gets included *later* than the original class, the >> overridden methods get called. The original methods can be renamed, >> e.g. >> >> alias original_render_template render_template >> >> and can be called from the overriding method. >> >> This technique of reopening classes and overriding behaviour is used >> in Ruby on Rails (indeed), but also in bio-logger and the >> bio-alignment gems. In bio-alignment it is used to make the BioRuby >> Bio::Sequence object enumerable, see >> >> >> https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bio >> ruby.rb >> >> Having Bio::Sequence enumerable allows you to use enumerable >> functional methods, such as 'map'. For example I can now write >> >> @seq.map { |codon| codon.to_s }.join(' ') >> >> There is a case to be made to have standard BioRuby use Enumerable. >> However BioRuby has to support Ruby 1.8, which differs in this area. >> By reopening the class I can make it look like it is part of BioRuby >> anyway. I think it is a very powerful feature, and Raoul did the >> right thing in making Jeweler work for Biogem. I think it is an >> impressive example of beautiful code. >> >> Pj >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From russell.whitaker at gmail.com Sun Feb 12 19:02:26 2012 From: russell.whitaker at gmail.com (Russell Whitaker) Date: Sun, 12 Feb 2012 16:02:26 -0800 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120211174616.GA24074@thebird.nl> Message-ID: On Sun, Feb 12, 2012 at 3:35 PM, Raoul Bonnal wrote: >[SNIP] > PS: I'm studing D :-) > Do tell: what do you like about D? For that matter, have you evaluated Scala? I've been curious about both... -- Russell Whitaker http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ http://www.linkedin.com/pub/russell-whitaker/0/b86/329 From pjotr.public14 at thebird.nl Mon Feb 13 02:09:31 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 08:09:31 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120211174616.GA24074@thebird.nl> Message-ID: <20120213070931.GA31051@thebird.nl> I have written about D and Scala in 'Ruby is a pony, Scala is a thoroughbred, D is a dragon'. http://blog.thebird.nl/?p=93 There is more on Scala examples on that site too. I may add D stuff in the future. We all need to write more about software and programming. Over the last year I prefer to program in Ruby and D - they are at both ends at the convenience vs. performance spectrum ;). D natively links against C libraries, something I like a lot (saves a lot of data copying). There will be biogem examples of bindings soon. Also the LLVM version of D2 is doing well, D will become part of Fedora and Debian based systems. If the JVM complex 'ecosystem' is no big issue, JRuby and Scala are also a brilliant match. You can check out my BioScala code and documents on github. JRuby is a great performer, so that may come naturally to you. Ruby gems work really well on the JVM, even when written in C. The JRuby developers have done a remarkable job. Personally, I think it boils down to background and experience. C/C++ programmers I see taking to D like a fish to water. People with a Java background may well prefer the JVM. Even after the balanced choice for D, I really miss some of the niceties of Scala. I guess, if I were programming Scala, I would do less in Ruby. I would strongly suggest to buy and read both Andrei's D book and Martin's Scala book. They are both classics in their own right - and see what appeals to you most. D and Scala are both next generation (strongly typed) languages designed by geniuses. They both work well with Ruby. Pj. On Sun, Feb 12, 2012 at 04:02:26PM -0800, Russell Whitaker wrote: > On Sun, Feb 12, 2012 at 3:35 PM, Raoul Bonnal wrote: > >[SNIP] > > PS: I'm studing D :-) > > > > Do tell: what do you like about D? For that matter, have you evaluated Scala? > I've been curious about both... > > -- > Russell Whitaker > http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ > http://www.linkedin.com/pub/russell-whitaker/0/b86/329 > From bonnal at ingm.org Mon Feb 13 02:16:31 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 08:16:31 +0100 Subject: [BioRuby] Article Published Message-ID: Dear all, We are happy to announce another paper! This time on 'Biogem: an effective tool based approach for scaling up open source software development in bioinformatics'. This was a community paper where all early biogem authors contributed to the paper in its final form. http://bioinformatics.oxfordjournals.org/content/early/2012/02/12/bioinforma tics.bts080.short?rss=1 Enjoy, Ra & Pj. From bonnal at ingm.org Mon Feb 13 02:44:21 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 08:44:21 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213070931.GA31051@thebird.nl> Message-ID: I'm studing D because of Pjotr :-), next will be Scala. Actually I tried Scala 2 year ago but my feeling was not so good with that language, maybe it's me. I feel comfortable reading D book, and I find the language a bit natural to me. Pjotr is right, we as bioinformaticians should know both and try others. What now is impossible with Ruby and Python is writing parallel applications. I'm looking for the best way to write parallel code and use the resources efficiently without forgetting easiness. Obviously there are other techniques like Hadoop for processing "big data", so ... Nothing is decided and we should discuss more. I'm here and I want to hear about your experience/opinion/approach. PS: Scala and D, both have binding to OpenCL On 13/02/12 08.09, "Pjotr Prins" wrote: > I have written about D and Scala in 'Ruby is a pony, Scala is a > thoroughbred, D is a dragon'. > > http://blog.thebird.nl/?p=93 > > There is more on Scala examples on that site too. I may add D stuff in > the future. We all need to write more about software and programming. > > Over the last year I prefer to program in Ruby and D - they are at > both ends at the convenience vs. performance spectrum ;). D natively > links against C libraries, something I like a lot (saves a lot of data > copying). There will be biogem examples of bindings soon. Also the > LLVM version of D2 is doing well, D will become part of Fedora and > Debian based systems. > > If the JVM complex 'ecosystem' is no big issue, JRuby and Scala are > also a brilliant match. You can check out my BioScala code and > documents on github. JRuby is a great performer, so that may come > naturally to you. Ruby gems work really well on the JVM, even when > written in C. The JRuby developers have done a remarkable job. > > Personally, I think it boils down to background and experience. C/C++ > programmers I see taking to D like a fish to water. People with a Java > background may well prefer the JVM. Even after the balanced choice for > D, I really miss some of the niceties of Scala. I guess, if I were > programming Scala, I would do less in Ruby. > > I would strongly suggest to buy and read both Andrei's D book and > Martin's Scala book. They are both classics in their own right - and > see what appeals to you most. > > D and Scala are both next generation (strongly typed) languages > designed by geniuses. They both work well with Ruby. > > Pj. > > On Sun, Feb 12, 2012 at 04:02:26PM -0800, Russell Whitaker wrote: >> On Sun, Feb 12, 2012 at 3:35 PM, Raoul Bonnal wrote: >>> [SNIP] >>> PS: I'm studing D :-) >>> >> >> Do tell: what do you like about D? For that matter, have you evaluated Scala? >> I've been curious about both... >> >> -- >> Russell Whitaker >> http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ >> http://www.linkedin.com/pub/russell-whitaker/0/b86/329 >> From pjotr.public14 at thebird.nl Mon Feb 13 02:54:30 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 08:54:30 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: <20120213075430.GA1086@thebird.nl> OK, here another candidate for the price of beautiful code: https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb Trevor has implemented some hairy logic into the RE code. I mean hairy, that if it were done by someone else it would become spaghetti code (plenty of examples there in the real world!). You can see, that even when choosing sensible names, and explaining the code with good comments, it may still be hard to understand! But I think def add_cuts_from_cut_ranges(cut_ranges) pretty much sums it up :). Still, it is beautiful, because it is hard to think of doing it better. The Ruby code is short and self explanatory and RE library has almost become a DSL for cutting sequences using restriction enzymes. That is beautiful. Pj. On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > Hi All > Beauty is in the eyes of the beholder! > The Bio-Alignment plugin can read and interconvert a nucleotide > alignment to an amino acid alignment. I liked the simplicity of how > PJ has implemented the codon to amino acid conversion helper method > while taking care of the gaps or undefined aa translations. > > # lazily convert to Amino acid (once only) > def to_aa > aa = translate > if not aa > if gap? > return '-' > elsif undefined? > return 'X' > else > raise 'What?' > end > end > aa > end > > This method does not have any ruby 'magic' and is self documenting. > The gap? and undefined? methods are implemented as simple one line > standalone methods. > > Again I like this simple 'trick' of getting an array of codons from a > sequence in the codonsequence class. > > seq.scan(/\S\S\S/) #gets an array of codons > > The longer alternative would be to create a bio::sequence::NA object > and iterate > seq = Bio::Sequence::NA.new("blahahahha") > seq.window_search(3, 3) do |subseq| > puts subseq > end > > It seems more intuitive to represent a sequence as an array of codon > objects. In this way the codons have some state and can carry > 'luggage'. getting the string representation of the sequence is as > simple as > def to_s > @seq.map { |codon| codon.to_s }.join(' ') > end > > To be more DRY, the to_nt method in the same class could be aliased > from the to_s method > > It seems the bio-plugins are a rich source of tricks and great learning.... ! > > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock wrote: > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins wrote: > >> Correct me if I am wrong, but has everyone moved across to BioPython > >> now? Or even to the dark side? > >> > >> Pj. > > > > I haven't noticed any BioRuby developers posting on the Biopython > > mailing lists recently - but you'd be welcome ;) > > > > On a related topic, my first BioRuby pull request was merged, so > > there is a little direct cross project contribution going on :) > > > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > > > Peter > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://biorelated.wordpress.com/ > Twitter: http://twitter.com/#!/george_l > From francesco.strozzi at gmail.com Mon Feb 13 05:06:03 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 13 Feb 2012 11:06:03 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213075430.GA1086@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <20120213075430.GA1086@thebird.nl> Message-ID: Some code I particularly liked comes from the BioNGS Wrapper library (by Raoul). The gem is in development and I'm contributing to it so I could look at the code from a very close perspective! https://gist.github.com/1815501 What is interesting is the use of an internal DSL which makes the code particularly expressive and readable, and writing a wrapper becomes only a matter of defining the options that the command line binary expects. The library is quite large and includes also methods to define aliases for the options. This module makes use also of the powerful Thor gem (used in Rails) to create and define tasks that can be used to launch the binaries and to include them in larger workflows and pipelines. Now let's say you want to turn your freshly new wrapped binary into a mighty Thor taks, all you need to do is: https://gist.github.com/1815523 The amazing part is that the parameters passed to the block works like arguments definition for the Thor task itself. The code that makes this possible behind the scenes is here: https://gist.github.com/1815481 It checks also if the number of arguments passed are equal to the arguments of the block. If not, it raises an error to the user as he/she is calling the task with the wrong number of arguments. To understand every part you need to know a bit the way the Thor library defines tasks (more here: https://github.com/wycats/thor) but the code here in BioNGS definitely worth a look! P.S. I'm diving into Scala too :-). I took the Odersky book few months ago and now I'm about to start looking in details at this new programming language. Easy and powerful parallelism is the new goal we need to achieve to keep up with the big data era. Cheers On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: > OK, here another candidate for the price of beautiful code: > > > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb > > Trevor has implemented some hairy logic into the RE code. I mean > hairy, that if it were done by someone else it would become spaghetti > code (plenty of examples there in the real world!). You can see, that > even when choosing sensible names, and explaining the code with good > comments, it may still be hard to understand! But I think > > def add_cuts_from_cut_ranges(cut_ranges) > > pretty much sums it up :). Still, it is beautiful, because it is hard > to think of doing it better. The Ruby code is short and self > explanatory and RE library has almost become a DSL for cutting > sequences using restriction enzymes. That is beautiful. > > Pj. > > On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > > Hi All > > Beauty is in the eyes of the beholder! > > The Bio-Alignment plugin can read and interconvert a nucleotide > > alignment to an amino acid alignment. I liked the simplicity of how > > PJ has implemented the codon to amino acid conversion helper method > > while taking care of the gaps or undefined aa translations. > > > > # lazily convert to Amino acid (once only) > > def to_aa > > aa = translate > > if not aa > > if gap? > > return '-' > > elsif undefined? > > return 'X' > > else > > raise 'What?' > > end > > end > > aa > > end > > > > This method does not have any ruby 'magic' and is self documenting. > > The gap? and undefined? methods are implemented as simple one line > > standalone methods. > > > > Again I like this simple 'trick' of getting an array of codons from a > > sequence in the codonsequence class. > > > > seq.scan(/\S\S\S/) #gets an array of codons > > > > The longer alternative would be to create a bio::sequence::NA object > > and iterate > > seq = Bio::Sequence::NA.new("blahahahha") > > seq.window_search(3, 3) do |subseq| > > puts subseq > > end > > > > It seems more intuitive to represent a sequence as an array of codon > > objects. In this way the codons have some state and can carry > > 'luggage'. getting the string representation of the sequence is as > > simple as > > def to_s > > @seq.map { |codon| codon.to_s }.join(' ') > > end > > > > To be more DRY, the to_nt method in the same class could be aliased > > from the to_s method > > > > It seems the bio-plugins are a rich source of tricks and great > learning.... ! > > > > > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock > wrote: > > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > pjotr.public14 at thebird.nl> wrote: > > >> Correct me if I am wrong, but has everyone moved across to BioPython > > >> now? Or even to the dark side? > > >> > > >> Pj. > > > > > > I haven't noticed any BioRuby developers posting on the Biopython > > > mailing lists recently - but you'd be welcome ;) > > > > > > On a related topic, my first BioRuby pull request was merged, so > > > there is a little direct cross project contribution going on :) > > > > > > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > > > > > Peter > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > -- > > --------------- > > Sincerely > > George > > Skype: george_g2 > > Blog: http://biorelated.wordpress.com/ > > Twitter: http://twitter.com/#!/george_l > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From pjotr.public14 at thebird.nl Mon Feb 13 05:34:08 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 11:34:08 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <20120213075430.GA1086@thebird.nl> Message-ID: <20120213103408.GA4358@thebird.nl> Excellent. May I propose that at least the other half of the authors of the Biogem paper send in an example of beautiful code? We can compile these snippets on a special page on one of the websites (or both). That will help courses, 'newbies' and even 'die hard' Perl users, such as Yoda, to see what this Ruby thing is about. Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh herh herh. Pj. On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: > Some code I particularly liked comes from the BioNGS Wrapper library (by > Raoul). The gem is in development and I'm contributing to it so I could > look at the code from a very close perspective! > > https://gist.github.com/1815501 > > What is interesting is the use of an internal DSL which makes the code > particularly expressive and readable, and writing a wrapper becomes only a > matter of defining the options that the command line binary expects. The > library is quite large and includes also methods to define aliases for the > options. > This module makes use also of the powerful Thor gem (used in Rails) to > create and define tasks that can be used to launch the binaries and to > include them in larger workflows and pipelines. > Now let's say you want to turn your freshly new wrapped binary into a > mighty Thor taks, all you need to do is: > > https://gist.github.com/1815523 > > The amazing part is that the parameters passed to the block works like > arguments definition for the Thor task itself. The code that makes this > possible behind the scenes is here: > > https://gist.github.com/1815481 > > It checks also if the number of arguments passed are equal to the arguments > of the block. If not, it raises an error to the user as he/she is calling > the task with the wrong number of arguments. To understand every part you > need to know a bit the way the Thor library defines tasks (more here: > https://github.com/wycats/thor) but the code here in BioNGS definitely > worth a look! > > P.S. I'm diving into Scala too :-). I took the Odersky book few months ago > and now I'm about to start looking in details at this new programming > language. Easy and powerful parallelism is the new goal we need to achieve > to keep up with the big data era. > > Cheers > > On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: > > > OK, here another candidate for the price of beautiful code: > > > > > > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb > > > > Trevor has implemented some hairy logic into the RE code. I mean > > hairy, that if it were done by someone else it would become spaghetti > > code (plenty of examples there in the real world!). You can see, that > > even when choosing sensible names, and explaining the code with good > > comments, it may still be hard to understand! But I think > > > > def add_cuts_from_cut_ranges(cut_ranges) > > > > pretty much sums it up :). Still, it is beautiful, because it is hard > > to think of doing it better. The Ruby code is short and self > > explanatory and RE library has almost become a DSL for cutting > > sequences using restriction enzymes. That is beautiful. > > > > Pj. > > > > On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > > > Hi All > > > Beauty is in the eyes of the beholder! > > > The Bio-Alignment plugin can read and interconvert a nucleotide > > > alignment to an amino acid alignment. I liked the simplicity of how > > > PJ has implemented the codon to amino acid conversion helper method > > > while taking care of the gaps or undefined aa translations. > > > > > > # lazily convert to Amino acid (once only) > > > def to_aa > > > aa = translate > > > if not aa > > > if gap? > > > return '-' > > > elsif undefined? > > > return 'X' > > > else > > > raise 'What?' > > > end > > > end > > > aa > > > end > > > > > > This method does not have any ruby 'magic' and is self documenting. > > > The gap? and undefined? methods are implemented as simple one line > > > standalone methods. > > > > > > Again I like this simple 'trick' of getting an array of codons from a > > > sequence in the codonsequence class. > > > > > > seq.scan(/\S\S\S/) #gets an array of codons > > > > > > The longer alternative would be to create a bio::sequence::NA object > > > and iterate > > > seq = Bio::Sequence::NA.new("blahahahha") > > > seq.window_search(3, 3) do |subseq| > > > puts subseq > > > end > > > > > > It seems more intuitive to represent a sequence as an array of codon > > > objects. In this way the codons have some state and can carry > > > 'luggage'. getting the string representation of the sequence is as > > > simple as > > > def to_s > > > @seq.map { |codon| codon.to_s }.join(' ') > > > end > > > > > > To be more DRY, the to_nt method in the same class could be aliased > > > from the to_s method > > > > > > It seems the bio-plugins are a rich source of tricks and great > > learning.... ! > > > > > > > > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock > > wrote: > > > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > > pjotr.public14 at thebird.nl> wrote: > > > >> Correct me if I am wrong, but has everyone moved across to BioPython > > > >> now? Or even to the dark side? > > > >> > > > >> Pj. > > > > > > > > I haven't noticed any BioRuby developers posting on the Biopython > > > > mailing lists recently - but you'd be welcome ;) > > > > > > > > On a related topic, my first BioRuby pull request was merged, so > > > > there is a little direct cross project contribution going on :) > > > > > > > > > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > > > > > > > Peter > > > > _______________________________________________ > > > > BioRuby Project - http://www.bioruby.org/ > > > > BioRuby mailing list > > > > BioRuby at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > > > > > -- > > > --------------- > > > Sincerely > > > George > > > Skype: george_g2 > > > Blog: http://biorelated.wordpress.com/ > > > Twitter: http://twitter.com/#!/george_l > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From georgkam at gmail.com Mon Feb 13 05:36:25 2012 From: georgkam at gmail.com (George Githinji) Date: Mon, 13 Feb 2012 13:36:25 +0300 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213103408.GA4358@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <20120213075430.GA1086@thebird.nl> <20120213103408.GA4358@thebird.nl> Message-ID: Good idea PJ! On Mon, Feb 13, 2012 at 1:34 PM, Pjotr Prins wrote: > Excellent. > > May I propose that at least the other half of the authors of the > Biogem paper send in an example of beautiful code? We can compile > these snippets on a special page on one of the websites (or both). > That will help courses, 'newbies' and even 'die hard' Perl users, such > as Yoda, to see what this Ruby thing is about. > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > herh herh. > > Pj. > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: >> Some code I particularly liked comes from the BioNGS Wrapper library (by >> Raoul). The gem is in development and I'm contributing to it so I could >> look at the code from a very close perspective! >> >> https://gist.github.com/1815501 >> >> What is interesting is the use of an internal DSL which makes the code >> particularly expressive and readable, and writing a wrapper becomes only a >> matter of defining the options that the command line binary expects. The >> library is quite large and includes also methods to define aliases for the >> options. >> This module makes use also of the powerful Thor gem (used in Rails) to >> create and define tasks that can be used to launch the binaries and to >> include them in larger workflows and pipelines. >> Now let's say you want to turn your freshly new wrapped binary into a >> mighty Thor taks, all you need to do is: >> >> https://gist.github.com/1815523 >> >> The amazing part is that the parameters passed to the block works like >> arguments definition for the Thor task itself. The code that makes this >> possible behind the scenes is here: >> >> https://gist.github.com/1815481 >> >> It checks also if the number of arguments passed are equal to the arguments >> of the block. If not, it raises an error to the user as he/she is calling >> the task with the wrong number of arguments. To understand every part you >> need to know a bit the way the Thor library defines tasks (more here: >> https://github.com/wycats/thor) but the code here in BioNGS definitely >> worth a look! >> >> P.S. I'm diving into Scala too :-). I took the Odersky book few months ago >> and now I'm about to start looking in details at this new programming >> language. Easy and powerful parallelism is the new goal we need to achieve >> to keep up with the big data era. >> >> Cheers >> >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: >> >> > OK, here another candidate for the price of beautiful code: >> > >> > >> > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb >> > >> > Trevor has implemented some hairy logic into the RE code. I mean >> > hairy, that if it were done by someone else it would become spaghetti >> > code (plenty of examples there in the real world!). You can see, that >> > even when choosing sensible names, and explaining the code with good >> > comments, it may still be hard to understand! But I think >> > >> > ?def add_cuts_from_cut_ranges(cut_ranges) >> > >> > pretty much sums it up :). Still, it is beautiful, because it is hard >> > to think of doing it better. The Ruby code is short and self >> > explanatory and RE library has almost become a DSL for cutting >> > sequences using restriction enzymes. That is beautiful. >> > >> > Pj. >> > >> > On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: >> > > Hi All >> > > Beauty is in the eyes of the beholder! >> > > The Bio-Alignment plugin can ?read and interconvert a nucleotide >> > > alignment to an amino acid alignment. ?I liked the simplicity of how >> > > PJ has implemented the codon to amino acid conversion helper method >> > > while taking care of the gaps or undefined aa translations. >> > > >> > > ? ? ? # lazily convert to Amino acid (once only) >> > > ? ? ? def to_aa >> > > ? ? ? ? aa = translate >> > > ? ? ? ? if not aa >> > > ? ? ? ? ? if gap? >> > > ? ? ? ? ? ? return '-' >> > > ? ? ? ? ? elsif undefined? >> > > ? ? ? ? ? ? return 'X' >> > > ? ? ? ? ? else >> > > ? ? ? ? ? ? raise 'What?' >> > > ? ? ? ? ? end >> > > ? ? ? ? end >> > > ? ? ? ? aa >> > > ? ? ? end >> > > >> > > This method does not have any ruby 'magic' and is self documenting. >> > > The gap? and undefined? methods are implemented as simple one line >> > > standalone methods. >> > > >> > > Again I like this simple 'trick' of getting an array of codons from a >> > > sequence in the codonsequence class. >> > > >> > > seq.scan(/\S\S\S/) #gets an array of codons >> > > >> > > The longer alternative would be to create a bio::sequence::NA object >> > > and iterate >> > > seq = Bio::Sequence::NA.new("blahahahha") >> > > seq.window_search(3, 3) do |subseq| >> > > ? puts subseq >> > > end >> > > >> > > It seems more intuitive to represent a sequence as an array of codon >> > > objects. In this way the codons have some state and can carry >> > > 'luggage'. getting the string representation of the sequence is as >> > > simple as >> > > def to_s >> > > ?@seq.map { |codon| codon.to_s }.join(' ') >> > > end >> > > >> > > To be more DRY, the to_nt method in the same class could be aliased >> > > from the to_s method >> > > >> > > It seems the bio-plugins are a rich source of tricks and great >> > learning.... ! >> > > >> > > >> > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock >> > wrote: >> > > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < >> > pjotr.public14 at thebird.nl> wrote: >> > > >> Correct me if I am wrong, but has everyone moved across to BioPython >> > > >> now? Or even to the dark side? >> > > >> >> > > >> Pj. >> > > > >> > > > I haven't noticed any BioRuby developers posting on the Biopython >> > > > mailing lists recently - but you'd be welcome ;) >> > > > >> > > > On a related topic, my first BioRuby pull request was merged, so >> > > > there is a little direct cross project contribution going on :) >> > > > >> > > > >> > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d >> > > > >> > > > Peter >> > > > _______________________________________________ >> > > > BioRuby Project - http://www.bioruby.org/ >> > > > BioRuby mailing list >> > > > BioRuby at lists.open-bio.org >> > > > http://lists.open-bio.org/mailman/listinfo/bioruby >> > > >> > > >> > > >> > > -- >> > > --------------- >> > > Sincerely >> > > George >> > > Skype: george_g2 >> > > Blog: http://biorelated.wordpress.com/ >> > > Twitter: http://twitter.com/#!/george_l >> > > >> > _______________________________________________ >> > BioRuby Project - http://www.bioruby.org/ >> > BioRuby mailing list >> > BioRuby at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioruby >> > >> >> >> >> -- >> >> Francesco >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From bonnal at ingm.org Mon Feb 13 05:37:20 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 11:37:20 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: Message-ID: Thanks Francesco, You have cute code in BioNGS as well. I like the piece of code which saves in an history file the commands executed by the user: https://github.com/helios/bioruby-ngs/blob/master/lib/bio/ngs/task.rb Every time the user runs biongs the command line is cached, the original idea was to save the commands to create a workflow on the fly. It is another example of Monkey Patching with injection of new code. On 13/02/12 11.06, "Francesco Strozzi" wrote: > Some code I particularly liked comes from the BioNGS Wrapper library (by > Raoul). The gem is in development and I'm contributing to it so I could > look at the code from a very close perspective! > > https://gist.github.com/1815501 > > What is interesting is the use of an internal DSL which makes the code > particularly expressive and readable, and writing a wrapper becomes only a > matter of defining the options that the command line binary expects. The > library is quite large and includes also methods to define aliases for the > options. > This module makes use also of the powerful Thor gem (used in Rails) to > create and define tasks that can be used to launch the binaries and to > include them in larger workflows and pipelines. > Now let's say you want to turn your freshly new wrapped binary into a > mighty Thor taks, all you need to do is: > > https://gist.github.com/1815523 > > The amazing part is that the parameters passed to the block works like > arguments definition for the Thor task itself. The code that makes this > possible behind the scenes is here: > > https://gist.github.com/1815481 > > It checks also if the number of arguments passed are equal to the arguments > of the block. If not, it raises an error to the user as he/she is calling > the task with the wrong number of arguments. To understand every part you > need to know a bit the way the Thor library defines tasks (more here: > https://github.com/wycats/thor) but the code here in BioNGS definitely > worth a look! > > P.S. I'm diving into Scala too :-). I took the Odersky book few months ago > and now I'm about to start looking in details at this new programming > language. Easy and powerful parallelism is the new goal we need to achieve > to keep up with the big data era. > > Cheers > > On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: > >> OK, here another candidate for the price of beautiful code: >> >> >> https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util >> /restriction_enzyme/range/sequence_range/calculated_cuts.rb >> >> Trevor has implemented some hairy logic into the RE code. I mean >> hairy, that if it were done by someone else it would become spaghetti >> code (plenty of examples there in the real world!). You can see, that >> even when choosing sensible names, and explaining the code with good >> comments, it may still be hard to understand! But I think >> >> def add_cuts_from_cut_ranges(cut_ranges) >> >> pretty much sums it up :). Still, it is beautiful, because it is hard >> to think of doing it better. The Ruby code is short and self >> explanatory and RE library has almost become a DSL for cutting >> sequences using restriction enzymes. That is beautiful. >> >> Pj. >> >> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: >>> Hi All >>> Beauty is in the eyes of the beholder! >>> The Bio-Alignment plugin can read and interconvert a nucleotide >>> alignment to an amino acid alignment. I liked the simplicity of how >>> PJ has implemented the codon to amino acid conversion helper method >>> while taking care of the gaps or undefined aa translations. >>> >>> # lazily convert to Amino acid (once only) >>> def to_aa >>> aa = translate >>> if not aa >>> if gap? >>> return '-' >>> elsif undefined? >>> return 'X' >>> else >>> raise 'What?' >>> end >>> end >>> aa >>> end >>> >>> This method does not have any ruby 'magic' and is self documenting. >>> The gap? and undefined? methods are implemented as simple one line >>> standalone methods. >>> >>> Again I like this simple 'trick' of getting an array of codons from a >>> sequence in the codonsequence class. >>> >>> seq.scan(/\S\S\S/) #gets an array of codons >>> >>> The longer alternative would be to create a bio::sequence::NA object >>> and iterate >>> seq = Bio::Sequence::NA.new("blahahahha") >>> seq.window_search(3, 3) do |subseq| >>> puts subseq >>> end >>> >>> It seems more intuitive to represent a sequence as an array of codon >>> objects. In this way the codons have some state and can carry >>> 'luggage'. getting the string representation of the sequence is as >>> simple as >>> def to_s >>> @seq.map { |codon| codon.to_s }.join(' ') >>> end >>> >>> To be more DRY, the to_nt method in the same class could be aliased >>> from the to_s method >>> >>> It seems the bio-plugins are a rich source of tricks and great >> learning.... ! >>> >>> >>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock >> wrote: >>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < >> pjotr.public14 at thebird.nl> wrote: >>>>> Correct me if I am wrong, but has everyone moved across to BioPython >>>>> now? Or even to the dark side? >>>>> >>>>> Pj. >>>> >>>> I haven't noticed any BioRuby developers posting on the Biopython >>>> mailing lists recently - but you'd be welcome ;) >>>> >>>> On a related topic, my first BioRuby pull request was merged, so >>>> there is a little direct cross project contribution going on :) >>>> >>>> >> https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd0 >> 94c5d >>>> >>>> Peter >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> >>> >>> -- >>> --------------- >>> Sincerely >>> George >>> Skype: george_g2 >>> Blog: http://biorelated.wordpress.com/ >>> Twitter: http://twitter.com/#!/george_l >>> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > > From bonnal at ingm.org Mon Feb 13 05:46:26 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 11:46:26 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213103408.GA4358@thebird.nl> Message-ID: Yeah, I was thinking the exact same thing. This kind of documentation will be of great help!!! I'm thinking about teaching Ruby @ Uni. What I missed from the previous email is: Beautiful code come from coders but that is not enough, working with people in this ML I found that the quality of code and its beauty increase only if you chat/talk with people and you are available to accept critics and contributes. Another tab ? ;-) On 13/02/12 11.34, "Pjotr Prins" wrote: > Excellent. > > May I propose that at least the other half of the authors of the > Biogem paper send in an example of beautiful code? We can compile > these snippets on a special page on one of the websites (or both). > That will help courses, 'newbies' and even 'die hard' Perl users, such > as Yoda, to see what this Ruby thing is about. > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > herh herh. > > Pj. > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: >> Some code I particularly liked comes from the BioNGS Wrapper library (by >> Raoul). The gem is in development and I'm contributing to it so I could >> look at the code from a very close perspective! >> >> https://gist.github.com/1815501 >> >> What is interesting is the use of an internal DSL which makes the code >> particularly expressive and readable, and writing a wrapper becomes only a >> matter of defining the options that the command line binary expects. The >> library is quite large and includes also methods to define aliases for the >> options. >> This module makes use also of the powerful Thor gem (used in Rails) to >> create and define tasks that can be used to launch the binaries and to >> include them in larger workflows and pipelines. >> Now let's say you want to turn your freshly new wrapped binary into a >> mighty Thor taks, all you need to do is: >> >> https://gist.github.com/1815523 >> >> The amazing part is that the parameters passed to the block works like >> arguments definition for the Thor task itself. The code that makes this >> possible behind the scenes is here: >> >> https://gist.github.com/1815481 >> >> It checks also if the number of arguments passed are equal to the arguments >> of the block. If not, it raises an error to the user as he/she is calling >> the task with the wrong number of arguments. To understand every part you >> need to know a bit the way the Thor library defines tasks (more here: >> https://github.com/wycats/thor) but the code here in BioNGS definitely >> worth a look! >> >> P.S. I'm diving into Scala too :-). I took the Odersky book few months ago >> and now I'm about to start looking in details at this new programming >> language. Easy and powerful parallelism is the new goal we need to achieve >> to keep up with the big data era. >> >> Cheers >> >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: >> >>> OK, here another candidate for the price of beautiful code: >>> >>> >>> https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti >>> l/restriction_enzyme/range/sequence_range/calculated_cuts.rb >>> >>> Trevor has implemented some hairy logic into the RE code. I mean >>> hairy, that if it were done by someone else it would become spaghetti >>> code (plenty of examples there in the real world!). You can see, that >>> even when choosing sensible names, and explaining the code with good >>> comments, it may still be hard to understand! But I think >>> >>> def add_cuts_from_cut_ranges(cut_ranges) >>> >>> pretty much sums it up :). Still, it is beautiful, because it is hard >>> to think of doing it better. The Ruby code is short and self >>> explanatory and RE library has almost become a DSL for cutting >>> sequences using restriction enzymes. That is beautiful. >>> >>> Pj. >>> >>> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: >>>> Hi All >>>> Beauty is in the eyes of the beholder! >>>> The Bio-Alignment plugin can read and interconvert a nucleotide >>>> alignment to an amino acid alignment. I liked the simplicity of how >>>> PJ has implemented the codon to amino acid conversion helper method >>>> while taking care of the gaps or undefined aa translations. >>>> >>>> # lazily convert to Amino acid (once only) >>>> def to_aa >>>> aa = translate >>>> if not aa >>>> if gap? >>>> return '-' >>>> elsif undefined? >>>> return 'X' >>>> else >>>> raise 'What?' >>>> end >>>> end >>>> aa >>>> end >>>> >>>> This method does not have any ruby 'magic' and is self documenting. >>>> The gap? and undefined? methods are implemented as simple one line >>>> standalone methods. >>>> >>>> Again I like this simple 'trick' of getting an array of codons from a >>>> sequence in the codonsequence class. >>>> >>>> seq.scan(/\S\S\S/) #gets an array of codons >>>> >>>> The longer alternative would be to create a bio::sequence::NA object >>>> and iterate >>>> seq = Bio::Sequence::NA.new("blahahahha") >>>> seq.window_search(3, 3) do |subseq| >>>> puts subseq >>>> end >>>> >>>> It seems more intuitive to represent a sequence as an array of codon >>>> objects. In this way the codons have some state and can carry >>>> 'luggage'. getting the string representation of the sequence is as >>>> simple as >>>> def to_s >>>> @seq.map { |codon| codon.to_s }.join(' ') >>>> end >>>> >>>> To be more DRY, the to_nt method in the same class could be aliased >>>> from the to_s method >>>> >>>> It seems the bio-plugins are a rich source of tricks and great >>> learning.... ! >>>> >>>> >>>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock >>> wrote: >>>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < >>> pjotr.public14 at thebird.nl> wrote: >>>>>> Correct me if I am wrong, but has everyone moved across to BioPython >>>>>> now? Or even to the dark side? >>>>>> >>>>>> Pj. >>>>> >>>>> I haven't noticed any BioRuby developers posting on the Biopython >>>>> mailing lists recently - but you'd be welcome ;) >>>>> >>>>> On a related topic, my first BioRuby pull request was merged, so >>>>> there is a little direct cross project contribution going on :) >>>>> >>>>> >>> https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd >>> 094c5d >>>>> >>>>> Peter >>>>> _______________________________________________ >>>>> BioRuby Project - http://www.bioruby.org/ >>>>> BioRuby mailing list >>>>> BioRuby at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >>>> >>>> >>>> -- >>>> --------------- >>>> Sincerely >>>> George >>>> Skype: george_g2 >>>> Blog: http://biorelated.wordpress.com/ >>>> Twitter: http://twitter.com/#!/george_l >>>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >> >> >> >> -- >> >> Francesco >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Mon Feb 13 05:50:28 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 11:50:28 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120210190335.GA20909@thebird.nl> Message-ID: <20120213105028.GA5237@thebird.nl> I am pretty hopeless with IRC. But I guess we should discuss possibilities for GSoC. Also, if anyone is interested, I could talk about Scala and D using Google Hangout. On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: > I agree with Pjotr, > So please post your ideas here and update the wiki. > It's time to re-start IRC meetings, what about Feb 16 around: > 9:00 GMT > 10:00 Italy > 18:00 Japan > 4:00 NewYork ( too early ? :-) > > About BioNGS, I think it's too complicated by itself, but I could have 2 > students working on this project. > > On 10/02/12 20.03, "Pjotr Prins" wrote: > > > Building out on the idea of involving newbies in easy projects, I > > would like to invite all plugin authors to come up with ideas on this > > list. Even the smallest idea will help. So think beyond SoC. > > > > Michael came up with gemifying, or componentizing BioRuby. And also > > upgrading our web presentation. Good ideas, any others? > > > > Francesco, what about bio-ngs? > > > > Pj. > > > > On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > >> Hi all, > >> > >> I'm going to be OBF project admin again this year for Google Summer of code. > >> OBF's application is due in a couple of weeks, and we need to update our > >> project ideas on the OBF wiki page and on each project's individual wiki > >> pages. > >> > >> So, for each of the OBF projects that wants to do GSoC again this year, > >> please: > >> > >> a.) Update the list of project ideas on your project's GSoC page (BioPython, > >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been > >> done or no longer relevant, etc. > >> > >> b.) Update the list of project ideas on the main OBF GSoC page > >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > >> > >> c.) Let me know via email that you have done so and it's ready for Google to > >> peruse. > >> > >> Please have the updates done, if possible, by this Friday (March 11). The > >> number and quality of the project ideas are part of the evaluation process > >> for whether OBF is accepted as a Summer of Code organization again this year, > >> so let's come up with some good ones. :-) > >> > >> Rob > >> > >> ---- > >> Robert Buels > >> (prospective) 2012 OBF GSoC Organization Admin > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From bonnal at ingm.org Mon Feb 13 05:58:13 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 11:58:13 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120213105028.GA5237@thebird.nl> Message-ID: I know that :-) so, please post ideas in this ML. +1 for Scala/D over Google Hangout On 13/02/12 11.50, "Pjotr Prins" wrote: > I am pretty hopeless with IRC. But I guess we should discuss > possibilities for GSoC. Also, if anyone is interested, I could talk > about Scala and D using Google Hangout. > > On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: >> I agree with Pjotr, >> So please post your ideas here and update the wiki. >> It's time to re-start IRC meetings, what about Feb 16 around: >> 9:00 GMT >> 10:00 Italy >> 18:00 Japan >> 4:00 NewYork ( too early ? :-) >> >> About BioNGS, I think it's too complicated by itself, but I could have 2 >> students working on this project. >> >> On 10/02/12 20.03, "Pjotr Prins" wrote: >> >>> Building out on the idea of involving newbies in easy projects, I >>> would like to invite all plugin authors to come up with ideas on this >>> list. Even the smallest idea will help. So think beyond SoC. >>> >>> Michael came up with gemifying, or componentizing BioRuby. And also >>> upgrading our web presentation. Good ideas, any others? >>> >>> Francesco, what about bio-ngs? >>> >>> Pj. >>> >>> On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: >>>> Hi all, >>>> >>>> I'm going to be OBF project admin again this year for Google Summer of >>>> code. >>>> OBF's application is due in a couple of weeks, and we need to update our >>>> project ideas on the OBF wiki page and on each project's individual wiki >>>> pages. >>>> >>>> So, for each of the OBF projects that wants to do GSoC again this year, >>>> please: >>>> >>>> a.) Update the list of project ideas on your project's GSoC page >>>> (BioPython, >>>> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been >>>> done or no longer relevant, etc. >>>> >>>> b.) Update the list of project ideas on the main OBF GSoC page >>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. >>>> >>>> c.) Let me know via email that you have done so and it's ready for Google >>>> to >>>> peruse. >>>> >>>> Please have the updates done, if possible, by this Friday (March 11). The >>>> number and quality of the project ideas are part of the evaluation process >>>> for whether OBF is accepted as a Summer of Code organization again this >>>> year, >>>> so let's come up with some good ones. :-) >>>> >>>> Rob >>>> >>>> ---- >>>> Robert Buels >>>> (prospective) 2012 OBF GSoC Organization Admin >>>> >>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> From cjfields at illinois.edu Mon Feb 13 09:17:06 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 13 Feb 2012 14:17:06 +0000 Subject: [BioRuby] Article Published In-Reply-To: References: Message-ID: <5D185D71-962B-4C4E-A1B5-D1AC1D7D190B@illinois.edu> congrats to everyone involved! chris On Feb 13, 2012, at 1:16 AM, Raoul Bonnal wrote: > Dear all, > > We are happy to announce another paper! This time on 'Biogem: an > effective tool based approach for scaling up open source software > development in bioinformatics'. This was a community paper where all > early biogem authors contributed to the paper in its final form. > > http://bioinformatics.oxfordjournals.org/content/early/2012/02/12/bioinforma > tics.bts080.short?rss=1 > > Enjoy, > > Ra & Pj. > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From francesco.strozzi at gmail.com Mon Feb 13 09:42:28 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 13 Feb 2012 15:42:28 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120213105028.GA5237@thebird.nl> Message-ID: Ok for me too about IRC meetings. And also about Google Hangouts with Scala / D. Cheers On Mon, Feb 13, 2012 at 11:58, Raoul Bonnal wrote: > > I know that :-) so, please post ideas in this ML. > > +1 for Scala/D over Google Hangout > > On 13/02/12 11.50, "Pjotr Prins" wrote: > > > I am pretty hopeless with IRC. But I guess we should discuss > > possibilities for GSoC. Also, if anyone is interested, I could talk > > about Scala and D using Google Hangout. > > > > On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: > >> I agree with Pjotr, > >> So please post your ideas here and update the wiki. > >> It's time to re-start IRC meetings, what about Feb 16 around: > >> 9:00 GMT > >> 10:00 Italy > >> 18:00 Japan > >> 4:00 NewYork ( too early ? :-) > >> > >> About BioNGS, I think it's too complicated by itself, but I could have 2 > >> students working on this project. > >> > >> On 10/02/12 20.03, "Pjotr Prins" wrote: > >> > >>> Building out on the idea of involving newbies in easy projects, I > >>> would like to invite all plugin authors to come up with ideas on this > >>> list. Even the smallest idea will help. So think beyond SoC. > >>> > >>> Michael came up with gemifying, or componentizing BioRuby. And also > >>> upgrading our web presentation. Good ideas, any others? > >>> > >>> Francesco, what about bio-ngs? > >>> > >>> Pj. > >>> > >>> On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > >>>> Hi all, > >>>> > >>>> I'm going to be OBF project admin again this year for Google Summer of > >>>> code. > >>>> OBF's application is due in a couple of weeks, and we need to update > our > >>>> project ideas on the OBF wiki page and on each project's individual > wiki > >>>> pages. > >>>> > >>>> So, for each of the OBF projects that wants to do GSoC again this > year, > >>>> please: > >>>> > >>>> a.) Update the list of project ideas on your project's GSoC page > >>>> (BioPython, > >>>> BioPerl, BioRuby, etc). Add new ones, remove ones that have already > been > >>>> done or no longer relevant, etc. > >>>> > >>>> b.) Update the list of project ideas on the main OBF GSoC page > >>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > >>>> > >>>> c.) Let me know via email that you have done so and it's ready for > Google > >>>> to > >>>> peruse. > >>>> > >>>> Please have the updates done, if possible, by this Friday (March 11). > The > >>>> number and quality of the project ideas are part of the evaluation > process > >>>> for whether OBF is accepted as a Summer of Code organization again > this > >>>> year, > >>>> so let's come up with some good ones. :-) > >>>> > >>>> Rob > >>>> > >>>> ---- > >>>> Robert Buels > >>>> (prospective) 2012 OBF GSoC Organization Admin > >>>> > >>>> > >>>> _______________________________________________ > >>>> BioRuby Project - http://www.bioruby.org/ > >>>> BioRuby mailing list > >>>> BioRuby at lists.open-bio.org > >>>> http://lists.open-bio.org/mailman/listinfo/bioruby > >>>> > >>> _______________________________________________ > >>> BioRuby Project - http://www.bioruby.org/ > >>> BioRuby mailing list > >>> BioRuby at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From mictadlo at gmail.com Mon Feb 13 23:33:04 2012 From: mictadlo at gmail.com (Mic) Date: Tue, 14 Feb 2012 14:33:04 +1000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> Message-ID: Hi, Did anyone try out * GO: http://en.wikipedia.org/wiki/Go_(programming_language) * Rust: http://en.wikipedia.org/wiki/Rust_(programming_language) * Vala: http://en.wikipedia.org/wiki/Vala_(programming_language) On Mon, Feb 13, 2012 at 8:46 PM, Raoul Bonnal wrote: > Yeah, I was thinking the exact same thing. > > This kind of documentation will be of great help!!! I'm thinking about > teaching Ruby @ Uni. > > What I missed from the previous email is: > Beautiful code come from coders but that is not enough, working with people > in this ML I found that the quality of code and its beauty increase only if > you chat/talk with people and you are available to accept critics and > contributes. > > Another tab ? ;-) > > > On 13/02/12 11.34, "Pjotr Prins" wrote: > > > Excellent. > > > > May I propose that at least the other half of the authors of the > > Biogem paper send in an example of beautiful code? We can compile > > these snippets on a special page on one of the websites (or both). > > That will help courses, 'newbies' and even 'die hard' Perl users, such > > as Yoda, to see what this Ruby thing is about. > > > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > > herh herh. > > > > Pj. > > > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: > >> Some code I particularly liked comes from the BioNGS Wrapper library (by > >> Raoul). The gem is in development and I'm contributing to it so I could > >> look at the code from a very close perspective! > >> > >> https://gist.github.com/1815501 > >> > >> What is interesting is the use of an internal DSL which makes the code > >> particularly expressive and readable, and writing a wrapper becomes > only a > >> matter of defining the options that the command line binary expects. The > >> library is quite large and includes also methods to define aliases for > the > >> options. > >> This module makes use also of the powerful Thor gem (used in Rails) to > >> create and define tasks that can be used to launch the binaries and to > >> include them in larger workflows and pipelines. > >> Now let's say you want to turn your freshly new wrapped binary into a > >> mighty Thor taks, all you need to do is: > >> > >> https://gist.github.com/1815523 > >> > >> The amazing part is that the parameters passed to the block works like > >> arguments definition for the Thor task itself. The code that makes this > >> possible behind the scenes is here: > >> > >> https://gist.github.com/1815481 > >> > >> It checks also if the number of arguments passed are equal to the > arguments > >> of the block. If not, it raises an error to the user as he/she is > calling > >> the task with the wrong number of arguments. To understand every part > you > >> need to know a bit the way the Thor library defines tasks (more here: > >> https://github.com/wycats/thor) but the code here in BioNGS definitely > >> worth a look! > >> > >> P.S. I'm diving into Scala too :-). I took the Odersky book few months > ago > >> and now I'm about to start looking in details at this new programming > >> language. Easy and powerful parallelism is the new goal we need to > achieve > >> to keep up with the big data era. > >> > >> Cheers > >> > >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins >wrote: > >> > >>> OK, here another candidate for the price of beautiful code: > >>> > >>> > >>> > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti > >>> l/restriction_enzyme/range/sequence_range/calculated_cuts.rb > >>> > >>> Trevor has implemented some hairy logic into the RE code. I mean > >>> hairy, that if it were done by someone else it would become spaghetti > >>> code (plenty of examples there in the real world!). You can see, that > >>> even when choosing sensible names, and explaining the code with good > >>> comments, it may still be hard to understand! But I think > >>> > >>> def add_cuts_from_cut_ranges(cut_ranges) > >>> > >>> pretty much sums it up :). Still, it is beautiful, because it is hard > >>> to think of doing it better. The Ruby code is short and self > >>> explanatory and RE library has almost become a DSL for cutting > >>> sequences using restriction enzymes. That is beautiful. > >>> > >>> Pj. > >>> > >>> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > >>>> Hi All > >>>> Beauty is in the eyes of the beholder! > >>>> The Bio-Alignment plugin can read and interconvert a nucleotide > >>>> alignment to an amino acid alignment. I liked the simplicity of how > >>>> PJ has implemented the codon to amino acid conversion helper method > >>>> while taking care of the gaps or undefined aa translations. > >>>> > >>>> # lazily convert to Amino acid (once only) > >>>> def to_aa > >>>> aa = translate > >>>> if not aa > >>>> if gap? > >>>> return '-' > >>>> elsif undefined? > >>>> return 'X' > >>>> else > >>>> raise 'What?' > >>>> end > >>>> end > >>>> aa > >>>> end > >>>> > >>>> This method does not have any ruby 'magic' and is self documenting. > >>>> The gap? and undefined? methods are implemented as simple one line > >>>> standalone methods. > >>>> > >>>> Again I like this simple 'trick' of getting an array of codons from a > >>>> sequence in the codonsequence class. > >>>> > >>>> seq.scan(/\S\S\S/) #gets an array of codons > >>>> > >>>> The longer alternative would be to create a bio::sequence::NA object > >>>> and iterate > >>>> seq = Bio::Sequence::NA.new("blahahahha") > >>>> seq.window_search(3, 3) do |subseq| > >>>> puts subseq > >>>> end > >>>> > >>>> It seems more intuitive to represent a sequence as an array of codon > >>>> objects. In this way the codons have some state and can carry > >>>> 'luggage'. getting the string representation of the sequence is as > >>>> simple as > >>>> def to_s > >>>> @seq.map { |codon| codon.to_s }.join(' ') > >>>> end > >>>> > >>>> To be more DRY, the to_nt method in the same class could be aliased > >>>> from the to_s method > >>>> > >>>> It seems the bio-plugins are a rich source of tricks and great > >>> learning.... ! > >>>> > >>>> > >>>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock < > p.j.a.cock at googlemail.com> > >>> wrote: > >>>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > >>> pjotr.public14 at thebird.nl> wrote: > >>>>>> Correct me if I am wrong, but has everyone moved across to BioPython > >>>>>> now? Or even to the dark side? > >>>>>> > >>>>>> Pj. > >>>>> > >>>>> I haven't noticed any BioRuby developers posting on the Biopython > >>>>> mailing lists recently - but you'd be welcome ;) > >>>>> > >>>>> On a related topic, my first BioRuby pull request was merged, so > >>>>> there is a little direct cross project contribution going on :) > >>>>> > >>>>> > >>> > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd > >>> 094c5d > >>>>> > >>>>> Peter > >>>>> _______________________________________________ > >>>>> BioRuby Project - http://www.bioruby.org/ > >>>>> BioRuby mailing list > >>>>> BioRuby at lists.open-bio.org > >>>>> http://lists.open-bio.org/mailman/listinfo/bioruby > >>>> > >>>> > >>>> > >>>> -- > >>>> --------------- > >>>> Sincerely > >>>> George > >>>> Skype: george_g2 > >>>> Blog: http://biorelated.wordpress.com/ > >>>> Twitter: http://twitter.com/#!/george_l > >>>> > >>> _______________________________________________ > >>> BioRuby Project - http://www.bioruby.org/ > >>> BioRuby mailing list > >>> BioRuby at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioruby > >>> > >> > >> > >> > >> -- > >> > >> Francesco > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Feb 14 02:19:50 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 08:19:50 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> Message-ID: <20120214071950.GA11317@thebird.nl> New programming languages are great. It is a form of evolution :). You should try to learn a language every year. The Clojure fan-boys have been quiet here - that is another one. Personally I looked a Go, and did not like it that much (apart from Go-routines). It is a bit over its hype now, so we can see what happens. Programming languages, nevertheless, do not solve the problem of programming. Never believe the person who tells you that all problems will be solved by programming language X. I know people who stick with C++ and are extremely productive, mostly because they have very rich libraries. I think they could do better with D, in the really long term. But who am I to suggest that? And I know people who are extremely productive with Ruby. Go figure. Pj. On Tue, Feb 14, 2012 at 02:33:04PM +1000, Mic wrote: > Hi, > Did anyone try out > * GO: [1]http://en.wikipedia.org/wiki/Go_(programming_language) > * Rust: [2]http://en.wikipedia.org/wiki/Rust_(programming_language) > * Vala: [3]http://en.wikipedia.org/wiki/Vala_(programming_language) > > On Mon, Feb 13, 2012 at 8:46 PM, Raoul Bonnal <[4]bonnal at ingm.org> wrote: > > Yeah, I was thinking the exact same thing. > > This kind of documentation will be of great help!!! I'm thinking about > teaching Ruby @ Uni. > > What I missed from the previous email is: > Beautiful code come from coders but that is not enough, working with > people > in this ML I found that the quality of code and its beauty increase only > if > you chat/talk with people and you are available to accept critics and > contributes. > > Another tab ? ;-) > > On 13/02/12 11.34, "Pjotr Prins" <[5]pjotr.public14 at thebird.nl> wrote: > > > Excellent. > > > > May I propose that at least the other half of the authors of the > > Biogem paper send in an example of beautiful code? We can compile > > these snippets on a special page on one of the websites (or both). > > That will help courses, 'newbies' and even 'die hard' Perl users, such > > as Yoda, to see what this Ruby thing is about. > > > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > > herh herh. > > > > Pj. > > > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: > >> Some code I particularly liked comes from the BioNGS Wrapper library > (by > >> Raoul). The gem is in development and I'm contributing to it so I > could > >> look at the code from a very close perspective! > >> > >> [6]https://gist.github.com/1815501 > >> > >> What is interesting is the use of an internal DSL which makes the > code > >> particularly expressive and readable, and writing a wrapper becomes > only a > >> matter of defining the options that the command line binary expects. > The > >> library is quite large and includes also methods to define aliases > for the > >> options. > >> This module makes use also of the powerful Thor gem (used in Rails) > to > >> create and define tasks that can be used to launch the binaries and > to > >> include them in larger workflows and pipelines. > >> Now let's say you want to turn your freshly new wrapped binary into a > >> mighty Thor taks, all you need to do is: > >> > >> [7]https://gist.github.com/1815523 > >> > >> The amazing part is that the parameters passed to the block works > like > >> arguments definition for the Thor task itself. The code that makes > this > >> possible behind the scenes is here: > >> > >> [8]https://gist.github.com/1815481 > >> > >> It checks also if the number of arguments passed are equal to the > arguments > >> of the block. If not, it raises an error to the user as he/she is > calling > >> the task with the wrong number of arguments. To understand every part > you > >> need to know a bit the way the Thor library defines tasks (more here: > >> [9]https://github.com/wycats/thor) but the code here in BioNGS > definitely > >> worth a look! > >> > >> P.S. I'm diving into Scala too :-). I took the Odersky book few > months ago > >> and now I'm about to start looking in details at this new programming > >> language. Easy and powerful parallelism is the new goal we need to > achieve > >> to keep up with the big data era. > >> > >> Cheers > >> > >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins > <[10]pjotr.public14 at thebird.nl>wrote: > >> > >>> OK, here another candidate for the price of beautiful code: > >>> > >>> > >>> > [11]https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti > >>> l/restriction_enzyme/range/sequence_range/calculated_cuts.rb > >>> > >>> Trevor has implemented some hairy logic into the RE code. I mean > >>> hairy, that if it were done by someone else it would become > spaghetti > >>> code (plenty of examples there in the real world!). You can see, > that > >>> even when choosing sensible names, and explaining the code with good > >>> comments, it may still be hard to understand! But I think > >>> > >>> def add_cuts_from_cut_ranges(cut_ranges) > >>> > >>> pretty much sums it up :). Still, it is beautiful, because it is > hard > >>> to think of doing it better. The Ruby code is short and self > >>> explanatory and RE library has almost become a DSL for cutting > >>> sequences using restriction enzymes. That is beautiful. > >>> > >>> Pj. > >>> > >>> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > >>>> Hi All > >>>> Beauty is in the eyes of the beholder! > >>>> The Bio-Alignment plugin can read and interconvert a nucleotide > >>>> alignment to an amino acid alignment. I liked the simplicity of > how > >>>> PJ has implemented the codon to amino acid conversion helper method > >>>> while taking care of the gaps or undefined aa translations. > >>>> > >>>> # lazily convert to Amino acid (once only) > >>>> def to_aa > >>>> aa = translate > >>>> if not aa > >>>> if gap? > >>>> return '-' > >>>> elsif undefined? > >>>> return 'X' > >>>> else > >>>> raise 'What?' > >>>> end > >>>> end > >>>> aa > >>>> end > >>>> > >>>> This method does not have any ruby 'magic' and is self documenting. > >>>> The gap? and undefined? methods are implemented as simple one line > >>>> standalone methods. > >>>> > >>>> Again I like this simple 'trick' of getting an array of codons from > a > >>>> sequence in the codonsequence class. > >>>> > >>>> seq.scan(/\S\S\S/) #gets an array of codons > >>>> > >>>> The longer alternative would be to create a bio::sequence::NA > object > >>>> and iterate > >>>> seq = Bio::Sequence::NA.new("blahahahha") > >>>> seq.window_search(3, 3) do |subseq| > >>>> puts subseq > >>>> end > >>>> > >>>> It seems more intuitive to represent a sequence as an array of > codon > >>>> objects. In this way the codons have some state and can carry > >>>> 'luggage'. getting the string representation of the sequence is as > >>>> simple as > >>>> def to_s > >>>> @seq.map { |codon| codon.to_s }.join(' ') > >>>> end > >>>> > >>>> To be more DRY, the to_nt method in the same class could be aliased > >>>> from the to_s method > >>>> > >>>> It seems the bio-plugins are a rich source of tricks and great > >>> learning.... ! > >>>> > >>>> > >>>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock > <[12]p.j.a.cock at googlemail.com> > >>> wrote: > >>>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > >>> [13]pjotr.public14 at thebird.nl> wrote: > >>>>>> Correct me if I am wrong, but has everyone moved across to > BioPython > >>>>>> now? Or even to the dark side? > >>>>>> > >>>>>> Pj. > >>>>> > >>>>> I haven't noticed any BioRuby developers posting on the Biopython > >>>>> mailing lists recently - but you'd be welcome ;) > >>>>> > >>>>> On a related topic, my first BioRuby pull request was merged, so > >>>>> there is a little direct cross project contribution going on :) > >>>>> > >>>>> > >>> > [14]https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd > >>> 094c5d > >>>>> > >>>>> Peter > >>>>> _______________________________________________ > >>>>> BioRuby Project - [15]http://www.bioruby.org/ > >>>>> BioRuby mailing list > >>>>> [16]BioRuby at lists.open-bio.org > >>>>> [17]http://lists.open-bio.org/mailman/listinfo/bioruby > >>>> > >>>> > >>>> > >>>> -- > >>>> --------------- > >>>> Sincerely > >>>> George > >>>> Skype: george_g2 > >>>> Blog: [18]http://biorelated.wordpress.com/ > >>>> Twitter: [19]http://twitter.com/#!/george_l > >>>> > >>> _______________________________________________ > >>> BioRuby Project - [20]http://www.bioruby.org/ > >>> BioRuby mailing list > >>> [21]BioRuby at lists.open-bio.org > >>> [22]http://lists.open-bio.org/mailman/listinfo/bioruby > >>> > >> > >> > >> > >> -- > >> > >> Francesco > >> _______________________________________________ > >> BioRuby Project - [23]http://www.bioruby.org/ > >> BioRuby mailing list > >> [24]BioRuby at lists.open-bio.org > >> [25]http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - [26]http://www.bioruby.org/ > > BioRuby mailing list > > [27]BioRuby at lists.open-bio.org > > [28]http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby Project - [29]http://www.bioruby.org/ > BioRuby mailing list > [30]BioRuby at lists.open-bio.org > [31]http://lists.open-bio.org/mailman/listinfo/bioruby > > References > > Visible links > 1. http://en.wikipedia.org/wiki/Go_(programming_language) > 2. http://en.wikipedia.org/wiki/Rust_(programming_language) > 3. http://en.wikipedia.org/wiki/Vala_(programming_language) > 4. mailto:bonnal at ingm.org > 5. mailto:pjotr.public14 at thebird.nl > 6. https://gist.github.com/1815501 > 7. https://gist.github.com/1815523 > 8. https://gist.github.com/1815481 > 9. https://github.com/wycats/thor > 10. mailto:pjotr.public14 at thebird.nl > 11. https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti > 12. mailto:p.j.a.cock at googlemail.com > 13. mailto:pjotr.public14 at thebird.nl > 14. https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd > 15. http://www.bioruby.org/ > 16. mailto:BioRuby at lists.open-bio.org > 17. http://lists.open-bio.org/mailman/listinfo/bioruby > 18. http://biorelated.wordpress.com/ > 19. http://twitter.com/#!/george_l > 20. http://www.bioruby.org/ > 21. mailto:BioRuby at lists.open-bio.org > 22. http://lists.open-bio.org/mailman/listinfo/bioruby > 23. http://www.bioruby.org/ > 24. mailto:BioRuby at lists.open-bio.org > 25. http://lists.open-bio.org/mailman/listinfo/bioruby > 26. http://www.bioruby.org/ > 27. mailto:BioRuby at lists.open-bio.org > 28. http://lists.open-bio.org/mailman/listinfo/bioruby > 29. http://www.bioruby.org/ > 30. mailto:BioRuby at lists.open-bio.org > 31. http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Tue Feb 14 03:24:32 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 09:24:32 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> Message-ID: <20120214082432.GA12201@thebird.nl> On Mon, Feb 13, 2012 at 11:46:26AM +0100, Raoul Bonnal wrote: > in this ML I found that the quality of code and its beauty increase > only if you chat/talk with people and you are available to accept > critics and contributes. I feel we can keep the momentum going if we use this list as a more general outlet of our personal development. It may be a metamorphosis of the old style of ML. Bio* is no longer about specialized libraries, it is mainly about the problem of software development in biology. I feel Ruby attracts the right type of people - that is why we have 'beautiful code' in the subject ;). The ML is the first place to share information. This is what new potential recruits may find interesting. Have them find us. In that vein I am presenting another piece of beautiful code, the omnipresent FlatFile handler of BioRuby. See https://github.com/bioruby/bioruby/blob/master/sample/any2fasta.rb e.g. ARGV.each do | fn | ff = Bio::FlatFile.auto(fn) ff.each_entry do |entry| if regex != nil next if eval("entry.seq !~ #{regex}") end print entry.seq.to_fasta(entry.definition,70) end end which does a lot of work in a few lines, with remarkable flexibility! Including automatic data format checking and a runtime defined regex search. Nowadays we would probably do it a little different. The eval can be taken out of the loop and the regex compiled (in a Pythonesque way). Also both each_entry and the Sequence objects should be lazy (it is not underneath) and properly iterate to avoid loading everything in RAM and parsing too much. But hey, it is still a great example what what we can do with Ruby anyway! I wrote this simple example any2fasta.rb 6 years ago, but the FlatFile and Sequence code is not mine. It is mostly by Toshiaka and Naohisa going all the way back to 2002. So the beautiful code is really by those two geniuses who are at the heart of the BioRuby project. Pj. From ngoto at gen-info.osaka-u.ac.jp Tue Feb 14 03:49:21 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 14 Feb 2012 17:49:21 +0900 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120211074751.GA23063@thebird.nl> References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> <20120211074751.GA23063@thebird.nl> Message-ID: <20120214084921.C3C971CBC528@idnmail.gen-info.osaka-u.ac.jp> Hi Michael, Pjotr and all, I've put current website contents of http://bioruby.org to GitHub. (excluding archives directory) https://github.com/ngoto/bioruby.org-webpage Please send new web contents with your idea. Due to the server-side restrictions and mirroring to http://bioruby.open-bio.org/, only static files are allowed. (CGI and server-side dynamic contents cannot be used.) Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Sat, 11 Feb 2012 08:47:51 +0100 Pjotr Prins wrote: > Dear Toshiaki and Naohisa, > > I believe Michael has a very valid point. How about defining a > project (potentially SoC), where we lay out the functionality we want > from such a web presence? > > Pj. > > On Wed, Feb 08, 2012 at 03:52:57PM -0500, Michael Barton wrote: > > I think making the homepage simpler would be very > > beneficial. For instance I think the two most important > > links (Tutorial and Sample codes) pages should be given much > > greater prominence. These are the two pages which most > > beginners will want to get started with. Compare with the > > Sinatra page which has only six links on the front page > > pointing to the most significant parts of the project. > > > > I think the Tutorial and Sample codes pages could do with > > some love also. These pages do not match the visual layout > > of the bioruby home page, one is in a separate domain while > > the other is a wiki page. I think these pages deserve > > attention to make them simpler and more accessible. A common > > CSS theme also provides a unified front to the BioRuby > > project. > > > > Compare with the Sinatra intro and documentation pages: > > * http://www.sinatrarb.com/intro > > * http://www.sinatrarb.com/documentation > > > > My opinion is that the BioRuby website should head in this > > direction. I am not a web designer but I am happy to > > contribute effort to writing web copy and BioRuby recipes. I > > also think that bioruby should also have its own web address > > too. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnal at ingm.org Tue Feb 14 04:50:43 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 14 Feb 2012 10:50:43 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: Message-ID: Hi all, I updated http://bioruby.open-bio.org/wiki/Google_Summer_of_Code starting from this thread, fell free to modify (title?) fill, add text and other projects as well. By Feb 24 we must have our proposals ready to go. On 13/02/12 15.42, "Francesco Strozzi" wrote: > Ok for me too about IRC meetings. And also about Google Hangouts with Scala / > D. > > Cheers > > On Mon, Feb 13, 2012 at 11:58, Raoul Bonnal wrote: >> >> I know that :-) so, please post ideas in this ML. >> >> +1 for Scala/D over Google Hangout >> >> On 13/02/12 11.50, "Pjotr Prins" wrote: >> >>> > I am pretty hopeless with IRC. But I guess we should discuss >>> > possibilities for GSoC. Also, if anyone is interested, I could talk >>> > about Scala and D using Google Hangout. >>> > >>> > On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: >>>> >> I agree with Pjotr, >>>> >> So please post your ideas here and update the wiki. >>>> >> It's time to re-start IRC meetings, what about Feb 16 around: >>>> >> 9:00 GMT >>>> >> 10:00 Italy >>>> >> 18:00 Japan >>>> >> 4:00 ?NewYork ( too early ? :-) >>>> >> >>>> >> About BioNGS, I think it's too complicated by itself, but I could have 2 >>>> >> students working on this project. >>>> >> >>>> >> On 10/02/12 20.03, "Pjotr Prins" wrote: >>>> >> >>>>> >>> Building out on the idea of involving newbies in easy projects, I >>>>> >>> would like to invite all plugin authors to come up with ideas on this >>>>> >>> list. Even the smallest idea will help. So think beyond SoC. >>>>> >>> >>>>> >>> Michael came up with gemifying, or componentizing BioRuby. And also >>>>> >>> upgrading our web presentation. Good ideas, any others? >>>>> >>> >>>>> >>> Francesco, what about bio-ngs? >>>>> >>> >>>>> >>> Pj. >>>>> >>> >>>>> >>> On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: >>>>>> >>>> Hi all, >>>>>> >>>> >>>>>> >>>> I'm going to be OBF project admin again this year for Google Summer of >>>>>> >>>> code. >>>>>> >>>> OBF's application is due in a couple of weeks, and we need to update our >>>>>> >>>> project ideas on the OBF wiki page and on each project's individual wiki >>>>>> >>>> pages. >>>>>> >>>> >>>>>> >>>> So, for each of the OBF projects that wants to do GSoC again this >>>>>> year, >>>>>> >>>> please: >>>>>> >>>> >>>>>> >>>> a.) Update the list of project ideas on your project's GSoC page >>>>>> >>>> (BioPython, >>>>>> >>>> BioPerl, BioRuby, etc). ?Add new ones, remove ones that have already been >>>>>> >>>> done or no longer relevant, etc. >>>>>> >>>> >>>>>> >>>> b.) Update the list of project ideas on the main OBF GSoC page >>>>>> >>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. >>>>>> >>>> >>>>>> >>>> c.) Let me know via email that you have done so and it's ready for >>>>>> Google >>>>>> >>>> to >>>>>> >>>> peruse. >>>>>> >>>> >>>>>> >>>> Please have the updates done, if possible, by this Friday (March >>>>>> 11). The >>>>>> >>>> number and quality of the project ideas are part of the evaluation >>>>>> process >>>>>> >>>> for whether OBF is accepted as a Summer of Code organization again this >>>>>> >>>> year, >>>>>> >>>> so let's come up with some good ones. ?:-) >>>>>> >>>> >>>>>> >>>> Rob >>>>>> >>>> >>>>>> >>>> ---- >>>>>> >>>> Robert Buels >>>>>> >>>> (prospective) 2012 OBF GSoC Organization Admin >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> _______________________________________________ >>>>>> >>>> BioRuby Project - http://www.bioruby.org/ >>>>>> >>>> BioRuby mailing list >>>>>> >>>> BioRuby at lists.open-bio.org >>>>>> >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>>>> >>>> >>>>> >>> _______________________________________________ >>>>> >>> BioRuby Project - http://www.bioruby.org/ >>>>> >>> BioRuby mailing list >>>>> >>> BioRuby at lists.open-bio.org >>>>> >>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >> >>>> >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > From ngoto at gen-info.osaka-u.ac.jp Tue Feb 14 06:22:59 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 14 Feb 2012 20:22:59 +0900 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: Message-ID: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> Hi Raoul, I think "Restyling BioRuby.org" is very difficult for Google Summer of Code 2012 because the FAQ says that documentation-only work cannot be accepted. http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/faqs#documentation >> 12. Are proposals for documentation work eligible for Google Summer of Code? >> >> While we greatly appreciate the value of documentation, this program is an exercise in developing code; we can't accept proposals for documentation-only work at this time. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Tue, 14 Feb 2012 10:50:43 +0100 Raoul Bonnal wrote: > Hi all, > I updated http://bioruby.open-bio.org/wiki/Google_Summer_of_Code starting > from this thread, fell free to modify (title?) fill, add text and other > projects as well. > By Feb 24 we must have our proposals ready to go. > > > From bonnal at ingm.org Tue Feb 14 06:25:28 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 14 Feb 2012 12:25:28 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On 14/02/12 12.22, "Naohisa GOTO" wrote: > Hi Raoul, > > I think "Restyling BioRuby.org" is very difficult for > Google Summer of Code 2012 because the FAQ says that > documentation-only work cannot be accepted. Ok good to know. > > http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/ > faqs#documentation >>> 12. Are proposals for documentation work eligible for Google Summer of Code? >>> >>> While we greatly appreciate the value of documentation, this program is an >>> exercise in developing code; we can't accept proposals for >>> documentation-only work at this time. > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Tue, 14 Feb 2012 10:50:43 +0100 > Raoul Bonnal wrote: > >> Hi all, >> I updated http://bioruby.open-bio.org/wiki/Google_Summer_of_Code starting >> from this thread, fell free to modify (title?) fill, add text and other >> projects as well. >> By Feb 24 we must have our proposals ready to go. >> >> >> From pjotr.public14 at thebird.nl Tue Feb 14 06:35:23 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 12:35:23 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> References: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120214113523.GB17407@thebird.nl> On Tue, Feb 14, 2012 at 08:22:59PM +0900, Naohisa GOTO wrote: > I think "Restyling BioRuby.org" is very difficult for > Google Summer of Code 2012 because the FAQ says that > documentation-only work cannot be accepted. > > http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/faqs#documentation > >> 12. Are proposals for documentation work eligible for Google Summer of Code? > >> > >> While we greatly appreciate the value of documentation, this program is an exercise in developing code; we can't accept proposals for documentation-only work at this time. Depends on the programming component. If we use staticmatic and HAML to generate the site, with coffeescript to interact with github and others, I think it becomes a very interesting programming job. Also the 'documentation' could consist of real example scripts, which execute. Possibly showing results online. I don't think students should be documenting, but they can put software together to make creating tutorials easier. I realize bioruby.org needs to be static, but it does not mean we can not host other services elsewhere, and even use Ruby on Rails. GSoC students are supposed to learn to program and to contribute to the main project. That is the key. If a project aims to achieve that, it can be part of GSoC. Restyling the Bioruby.org goes much deeper than documentation, in my opinion. Pj. From marian.povolny at gmail.com Tue Feb 14 07:53:13 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Tue, 14 Feb 2012 13:53:13 +0100 Subject: [BioRuby] GSoC participation without biology knowledge? Message-ID: Hello everybody, I'm a prospective GSoC student and would like to ask a short question before properly introducing myself on the mailing list. I have no knowledge about biology whatsoever. Would I be able to contribute to the bioruby project anyway? From the project list, the following project seems to be a fit: "Support Next Generation Sequencing (NGS) in BioRuby". I do have experience with Bash, Linux and Rails, but like I said, I don't have any experience related to biology beyond primary school. However, I'm looking into ways to enter the field and this would be a great starting point, if possible, of course. Thx, Marjan From pjotr.public14 at thebird.nl Tue Feb 14 09:57:40 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 15:57:40 +0100 Subject: [BioRuby] GSoC participation without biology knowledge? In-Reply-To: References: Message-ID: <20120214145740.GB18873@thebird.nl> Hi Marjan, The idea is programming first. The biology we can help with, if needed :) Pj. On Tue, Feb 14, 2012 at 01:53:13PM +0100, Marjan Povolni wrote: > Hello everybody, > > I'm a prospective GSoC student and would like to ask a short question > before properly introducing myself on the mailing list. > > I have no knowledge about biology whatsoever. Would I be able to contribute > to the bioruby project anyway? From the project list, the following project > seems to be a fit: "Support Next Generation Sequencing (NGS) in BioRuby". I > do have experience with Bash, Linux and Rails, but like I said, I don't > have any experience related to biology beyond primary school. > > However, I'm looking into ways to enter the field and this would be a great > starting point, if possible, of course. > > Thx, > Marjan > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Tue Feb 14 11:50:56 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 14 Feb 2012 17:50:56 +0100 Subject: [BioRuby] MAF UCSC and intervals Message-ID: Dear all, Can we parse a .MAF file and extract a spliced alignment like http://biopython.org/wiki/Multiple_Alignment_Format#Retrieving_a_pre-spliced _alignment_over_a_given_set_of_exons ? Why this ? I?m looking for new coding transcripts and I want to use https://github.com/mlin/PhyloCSF/wiki but I must recreate a specific alignment for every new transcript I identified with cufflinks. -- Ra From bonnal at ingm.org Thu Feb 16 04:13:24 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 16 Feb 2012 10:13:24 +0100 Subject: [BioRuby] GSoC participation without biology knowledge? In-Reply-To: <20120214145740.GB18873@thebird.nl> Message-ID: Hi Marjna, Pjotr is right but I think it also important to understand which are your motivations and interests in Bioinformatics, and from your email it seems you are intrigued by this field. The general ideas is to have people contributing to the Bio* projects also after the end of GSoC. So please, introduce yourself and let's discuss about GSoC projects. On 14/02/12 15.57, "Pjotr Prins" wrote: > Hi Marjan, > > The idea is programming first. The biology we can help with, if > needed :) > > Pj. > > On Tue, Feb 14, 2012 at 01:53:13PM +0100, Marjan Povolni wrote: >> Hello everybody, >> >> I'm a prospective GSoC student and would like to ask a short question >> before properly introducing myself on the mailing list. >> >> I have no knowledge about biology whatsoever. Would I be able to contribute >> to the bioruby project anyway? From the project list, the following project >> seems to be a fit: "Support Next Generation Sequencing (NGS) in BioRuby". I >> do have experience with Bash, Linux and Rails, but like I said, I don't >> have any experience related to biology beyond primary school. >> >> However, I'm looking into ways to enter the field and this would be a great >> starting point, if possible, of course. >> >> Thx, >> Marjan >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Thu Feb 16 04:43:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 10:43:35 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120210190335.GA20909@thebird.nl> Message-ID: <20120216094335.GA32160@thebird.nl> We are on IRC today: irc.freenode.net join #bioruby the channel logs are here (thanks to Toshiaki): http://irc.bioruby.org On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: > I agree with Pjotr, > So please post your ideas here and update the wiki. > It's time to re-start IRC meetings, what about Feb 16 around: > 9:00 GMT > 10:00 Italy > 18:00 Japan > 4:00 NewYork ( too early ? :-) > > About BioNGS, I think it's too complicated by itself, but I could have 2 > students working on this project. > > On 10/02/12 20.03, "Pjotr Prins" wrote: > > > Building out on the idea of involving newbies in easy projects, I > > would like to invite all plugin authors to come up with ideas on this > > list. Even the smallest idea will help. So think beyond SoC. > > > > Michael came up with gemifying, or componentizing BioRuby. And also > > upgrading our web presentation. Good ideas, any others? > > > > Francesco, what about bio-ngs? > > > > Pj. > > > > On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > >> Hi all, > >> > >> I'm going to be OBF project admin again this year for Google Summer of code. > >> OBF's application is due in a couple of weeks, and we need to update our > >> project ideas on the OBF wiki page and on each project's individual wiki > >> pages. > >> > >> So, for each of the OBF projects that wants to do GSoC again this year, > >> please: > >> > >> a.) Update the list of project ideas on your project's GSoC page (BioPython, > >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been > >> done or no longer relevant, etc. > >> > >> b.) Update the list of project ideas on the main OBF GSoC page > >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > >> > >> c.) Let me know via email that you have done so and it's ready for Google to > >> peruse. > >> > >> Please have the updates done, if possible, by this Friday (March 11). The > >> number and quality of the project ideas are part of the evaluation process > >> for whether OBF is accepted as a Summer of Code organization again this year, > >> so let's come up with some good ones. :-) > >> > >> Rob > >> > >> ---- > >> Robert Buels > >> (prospective) 2012 OBF GSoC Organization Admin > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From marian.povolny at gmail.com Thu Feb 16 05:28:03 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Thu, 16 Feb 2012 11:28:03 +0100 Subject: [BioRuby] My proper GSoC introduction Message-ID: Hello once again, My name is Marjan Povolni, I'm 27 years old and currently wrapping up my Masters in CS. My dissertation project will be done in a weeks time, but due to some bureaucracy requirements I won't be graduating until April. I saw that the requirement for GSoC is to be enrolled in an academic institution on April 23rd, so that fits me well. I also have some 5 years of professional experience working for a local outsourcing company, working with lots of technologies. If someone's interested in details, you can take a look at my LinkedIn page: http://rs.linkedin.com/in/mpovolni. I'm very curious, want to learn new stuff and get better at what I'm doing, and that seemed always to be to the contrary of what was required of me at that company, so... ...currently I'm switching to freelancing as a Rails developer and have an offer to be a TA and a Ph.D. student at the University of Novi Sad, at the systems lab, but that's starting in October. They're mainly doing research on operating systems, compilers and parallel programming, but as is the case for most labs in our country (Serbia), they have no funded projects, so I will be pretty much free to choose what I'm going to work on. Currently I'm looking into specializing in CUDA/OpenCL, and parallel algorithms and their use in bioinformatics. Those are my plans, a GSoC project would be of great help to me, but even if it doesn't work out, I'm still determined to continue with them ;) Best regards, Marjan From pjotr.public14 at thebird.nl Thu Feb 16 06:00:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 12:00:54 +0100 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: References: Message-ID: <20120216110054.GA32635@thebird.nl> Hi Marjan, Thanks for the intro. Looks to me we ought to set you a right challenge :). With you in mind we are going to propose to write the worlds fastest GFF3/GTF parser using parallel D actors, and provide bindings for Ruby (and later Python). The parser ought to iterate through the data files, possibly handling information back through a simple filter. How does that sound? Parsing GFF3/GTF in seconds, rather than hours. Would be a true open-bio Bio* project. Peter, you like this? Pj. On Thu, Feb 16, 2012 at 11:28:03AM +0100, Marjan Povolni wrote: > Hello once again, > > My name is Marjan Povolni, I'm 27 years old and currently wrapping up my > Masters in CS. My dissertation project will be done in a weeks time, but > due to some bureaucracy requirements I won't be graduating until April. I > saw that the requirement for GSoC is to be enrolled in an academic > institution on April 23rd, so that fits me well. > > I also have some 5 years of professional experience working for a local > outsourcing company, working with lots of technologies. If someone's > interested in details, you can take a look at my LinkedIn page: > http://rs.linkedin.com/in/mpovolni. I'm very curious, want to learn new > stuff and get better at what I'm doing, and that seemed always to be to the > contrary of what was required of me at that company, so... > > ...currently I'm switching to freelancing as a Rails developer and have an > offer to be a TA and a Ph.D. student at the University of Novi Sad, at the > systems lab, but that's starting in October. They're mainly doing research > on operating systems, compilers and parallel programming, but as is the > case for most labs in our country (Serbia), they have no funded projects, > so I will be pretty much free to choose what I'm going to work on. > Currently I'm looking into specializing in CUDA/OpenCL, and parallel > algorithms and their use in bioinformatics. > > Those are my plans, a GSoC project would be of great help to me, but even > if it doesn't work out, I'm still determined to continue with them ;) > > Best regards, > Marjan > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Thu Feb 16 06:33:49 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 16 Feb 2012 11:33:49 +0000 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: <20120216110054.GA32635@thebird.nl> References: <20120216110054.GA32635@thebird.nl> Message-ID: On Thu, Feb 16, 2012 at 11:00 AM, Pjotr Prins wrote: > Hi Marjan, > > Thanks for the intro. > > Looks to me we ought to set you a right challenge :). With you in mind > we are going to propose to write the worlds fastest GFF3/GTF parser > using parallel D actors, and provide bindings for Ruby (and later > Python). The parser ought to iterate through the data files, possibly > handling information back through a simple filter. > > How does that sound? Parsing GFF3/GTF in seconds, rather than hours. > > Would be a true open-bio Bio* project. Peter, you like this? > > Pj. We'd want Brad involved for Biopython + GFF, but it certainly sounds like an interesting project. The D dependency might make for some interesting build dependencies, but that is a different matter. Peter From pjotr.public14 at thebird.nl Thu Feb 16 06:42:56 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 12:42:56 +0100 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: References: <20120216110054.GA32635@thebird.nl> Message-ID: <20120216114256.GA914@thebird.nl> On Thu, Feb 16, 2012 at 11:33:49AM +0000, Peter Cock wrote: > We'd want Brad involved for Biopython + GFF Good point. > but it certainly sounds like an interesting project. The D > dependency might make for some interesting build dependencies, but > that is a different matter. D2 is getting to be part of standard distro's (Fedora, Debian). For Windows binary DLL's can be distributed. So, that covers much of the community. Only OSX loses out again, but then Apple still ships Ruby 1.8.7! So, for the FFI, one needs to build the interface using a pre-installed D compiler. Not too bad. If people want that speed... For the GSoC task I don't think the deployment problem is too much of a concern. But we do want a working library. I actually started on that parser, last year at BOSC. But somehow there is too much on my plate :/ Pj. From bonnal at ingm.org Thu Feb 16 06:42:54 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 16 Feb 2012 12:42:54 +0100 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: Message-ID: We can create a gem/plugins which downloads and compiles the lib in a sandbox, biongs works in that way. In case the machine is a biolinux we can skip the sandbox. On 16/02/12 12.33, "Peter Cock" wrote: > On Thu, Feb 16, 2012 at 11:00 AM, Pjotr Prins > wrote: >> Hi Marjan, >> >> Thanks for the intro. >> >> Looks to me we ought to set you a right challenge :). With you in mind >> we are going to propose to write the worlds fastest GFF3/GTF parser >> using parallel D actors, and provide bindings for Ruby (and later >> Python). The parser ought to iterate through the data files, possibly >> handling information back through a simple filter. >> >> How does that sound? Parsing GFF3/GTF in seconds, rather than hours. >> >> Would be a true open-bio Bio* project. Peter, you like this? >> >> Pj. > > We'd want Brad involved for Biopython + GFF, but it certainly > sounds like an interesting project. The D dependency might > make for some interesting build dependencies, but that is a > different matter. > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Thu Feb 16 08:16:22 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 14:16:22 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208184817.GA31948@thebird.nl> References: <20120208184817.GA31948@thebird.nl> Message-ID: <20120216131622.GA2318@thebird.nl> Following up on the E-mail on addressing newbies, I have the following suggestion using Github issues and Cucumber features: Any biogem hosted on github can create a feature request. The feature should be written out in cucumber, with accompanying test cases. For example I wrote the following feature: Feature: Alignment editing, the bridge rule Remove columns that contain too many gaps Drop all bridges in less than 'min_bridges_fraction' (default 1/3 or 33%). The dropped columns are tracked by the table columns. Scenario: Apply the bridge rule to an amino acid alignment Given I have an alignment """ ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV -------------IFHAVR-TC-HP----------------- """ When I apply rule 3 with max_gap_size 4 Then it should have removed 4 bridges """ SNSFSRPTIIFSGCSTACSGKSELVCGFRSFMLSDV SNSFSRPTIIFSGCSTACSGKSEQVCGFR---LSDV SNSFSRPTIIFSGCSTACSGKSEQVCGFR---LSDV PKLFSRPTIIFSGCSTACSGKSEPVCGFRSFMLSDV ------PTIIFSGCSKACSGKSELVCGFRSFMLSDV ------PTIIFSGCSKACSGK---FRSFRSFMLSAV ------PTIIFSGCSKACSGK---VCGIFHAVRSFM ------PTIIFSGCSKACSGKSELVCGFRSFMLSAV ---------IFHAVR-TC-HP--------------- """ Then I should be able to track removed columns This was the most important step. Now we need to announce the feature request. I propose to raise an issue through github, e.g. https://github.com/pjotrp/bioruby-alignment/issues/1 the issue should contain a link to the feature, i.e https://github.com/pjotrp/bioruby-alignment/blob/master/features/edit/del_bridges.feature and be marked with the 'Newbie' label. We can also introduce more labels, such as 'Experienced', 'Advanced' and targets, such as 'Rails' and 'FFI'. This is enough information to automatically create a consolidated list on the bioruby or biogems website(s). And this list can be used by people who want to try a contribution or bug fix. We should define a number of such tasks for newbies. Bug fixes are also possible, as long as it is written out as a feature (note that features are automatically tests!). What do you think? Pj. On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: > Hi All, > > This mailing list counts 180 subscribed readers. Which is impressive. > Also since the introduction of http://biogems.info/ the number of > BioRuby downloads has increased rapidly. > > You may also have noticed Ruby, in general, is making its mark in > bioinformatics. More and more people are programming in Ruby, which I > think rather delightful. And Biogems.info is proving to be cutting > edge, and accelerating development. > > So here is a question to people who read the mailing list, but do not > necessarily participate. What is needed to pull you in? > > At this point I have two ideas to increase participation. > > (1) First a race. I would like all readers to vote a few times a year on > the most beautiful Biogem source code. We'll put up a few projects to > choose from, and the winner will be highlighted on > http://biogems.info/. Ruby is about beauty, and we are seeing > some of that in the biogems. > > The other idea I got at FOSDEM this year from a convincing talk by Brian > Ostergard, titled 'You are doing it all wrong' > > http://fosdem.org/2012/schedule/event/really_grow_community > > where he made a strong case to address inexperienced developers. And > you know what, I believe he is right. So > > (2) We will look for ways to get inexperienced developers involved. > One way is to define uncomplicated and moderately complicated tasks, > feature requests and bug fixes. > > We are going to list these 'jobs' on http://biogems.info/. If anyone > picks up a task he/she will get very *strong* support from the plugin > owner, as well as the Biogem maintainers. You, the programmer, > will get all the credit for the work. > > How does this sound? Does this appeal to you? Anyone of the less > experienced, or even experienced, wants to voice his or her opinion? > We may even turn some work into a Google Summer of Code project > proposal. > > Pj. > From pjotr.public14 at thebird.nl Thu Feb 16 09:31:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 15:31:35 +0100 Subject: [BioRuby] Feature request: Gblocks implementation in Ruby Message-ID: <20120216143135.GA3760@thebird.nl> Feature: GBlocks implementation in Ruby https://github.com/pjotrp/bioruby-alignment/issues/2 (another example of a newbie assignment). From pjotr.public14 at thebird.nl Thu Feb 16 09:35:02 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 15:35:02 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120216131622.GA2318@thebird.nl> References: <20120208184817.GA31948@thebird.nl> <20120216131622.GA2318@thebird.nl> Message-ID: <20120216143502.GA3876@thebird.nl> On Thu, Feb 16, 2012 at 02:16:22PM +0100, Pjotr Prins wrote: > Following up on the E-mail on addressing newbies, I have the > following suggestion using Github issues and Cucumber features: Next to listing the features/tasks/assignment on biogems.info and bioruby.org would be to show who fixed it - giving credit to newcomers is important. Pj. From pjotr.public14 at thebird.nl Thu Feb 16 10:46:12 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 16:46:12 +0100 Subject: [BioRuby] A question for teachers In-Reply-To: <20120216143502.GA3876@thebird.nl> References: <20120208184817.GA31948@thebird.nl> <20120216131622.GA2318@thebird.nl> <20120216143502.GA3876@thebird.nl> Message-ID: <20120216154612.GB5276@thebird.nl> Some of you must be teaching students bioinformatics. Does this idea of creating feature requests look useful to you? From bonnal at ingm.org Thu Feb 16 10:53:05 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 16 Feb 2012 16:53:05 +0100 Subject: [BioRuby] A question for teachers In-Reply-To: <20120216154612.GB5276@thebird.nl> Message-ID: I'm not teaching but it's a very interesting approach. On 16/02/12 16.46, "Pjotr Prins" wrote: > Some of you must be teaching students bioinformatics. Does this idea > of creating feature requests look useful to you? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mail at michaelbarton.me.uk Thu Feb 16 11:14:51 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Thu, 16 Feb 2012 11:14:51 -0500 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120214113523.GB17407@thebird.nl> References: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> <20120214113523.GB17407@thebird.nl> Message-ID: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> Excuse my late reply to your emails Pjotr and Naohisa. I wanted to find the time to reply in detail. > > I think "Restyling BioRuby.org" is very difficult for > > Google Summer of Code 2012 because the FAQ says that > > documentation-only work cannot be accepted. I agree with this. I think if our aim is to attract new people to BioRuby then giving out tasks to update documentation is not very exciting. I would like to offer a suggestion that BiorUby GSOC projects could also push scientific problems with new ruby code. As we are scientists in addition to coders we could coach on the scientific investigative side as well as on coding. I also think encouraging GSOC students to publish their projects, such as a bioinformatics application note could be a good way demonstrate the success of BioRuby GSOC projects as a concrete outcome. I think this would demonstrate BioRuby is an exciting community where "open source work leads to publications" which I think is primary barrier to scientists committing time. I speak for myself in this case as I'm at the point in my career where publications are becoming critical to finding a new position when my current one ends. I've never been involved in a GSOC project however so please correct my ignorance if I am wrong. Perhaps somewhere on the redesigned site we could list publications that have directly come form BioRuby projects. Concretely, rather than "we used BioRuby in this project" it would be "I wrote this for BioRuby and published it." I think recent BioGems paper is a good example of this. > Depends on the programming component. If we use > staticmatic and HAML to generate the site, with > coffeescript to interact with github and others, I think > it becomes a very interesting programming job. I've used nanoc to generate the scaffolder documentation here: http://next.gs. The github repo for the site is here: https://github.com/scaffolder/scaffolder-website. The static site generator "stasis" also looks interesting and follows a rails centric theme: http://stasis.me. As Pjotr wrote these could generate the static HTML which is uploaded to BioRuby.org. > Also the 'documentation' could consist of real example > scripts, which execute. Possibly showing results online. I > don't think students should be documenting, but they can > put software together to make creating tutorials easier. I strongly agree with this. Documentation code should be executable to ensure that it works as expected. I've read somewhere in the past about gems that allow this. Mike From mictadlo at gmail.com Fri Feb 17 01:22:03 2012 From: mictadlo at gmail.com (Mic) Date: Fri, 17 Feb 2012 16:22:03 +1000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120214082432.GA12201@thebird.nl> References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> Message-ID: Hi all D currently has some problems, because many projects http://www.dsource.org/projects/ are no any more in active developed. The other problem is that Tango has also stooped. On other hand it sounds good, because you can access C, C++ and it is native language. Therefore it should uses less memory compare to Java eg. http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-a-huge-fastq-file . The Qt people think that they have removed all pitfalls in C++. Whether is true or not and how efficient the code with Qt is I do not know. I worked with Scala for a while, but I have found the language quite difficult to learn and also other people complain about it too. The other problem with Scala is that it is not possible to copy a little Java code in to Scala. Then I discover Groovy a very similar language to Ruby and easier to learn compare to Scala. The advantage of Groovy is that it is possible to copy Java code without to modefing it to Groovy. I have not tried out Groovy++ which is as fast as Java. Unfortunately, I run few month back with Groovy in to problems see http://jira.codehaus.org/browse/GROOVY-4851. Other Ruby like static language which I discover is http://www.mirah.org/wiki/MirahFeatures . Cheers, On Tue, Feb 14, 2012 at 6:24 PM, Pjotr Prins wrote: > On Mon, Feb 13, 2012 at 11:46:26AM +0100, Raoul Bonnal wrote: > > in this ML I found that the quality of code and its beauty increase > > only if you chat/talk with people and you are available to accept > > critics and contributes. > > I feel we can keep the momentum going if we use this list as a more > general outlet of our personal development. It may be a metamorphosis > of the old style of ML. Bio* is no longer about specialized libraries, > it is mainly about the problem of software development in biology. I > feel Ruby attracts the right type of people - that is why we have > 'beautiful code' in the subject ;). > > The ML is the first place to share information. This is what new > potential recruits may find interesting. Have them find us. > > In that vein I am presenting another piece of beautiful code, the > omnipresent FlatFile handler of BioRuby. See > > https://github.com/bioruby/bioruby/blob/master/sample/any2fasta.rb > > e.g. > > ARGV.each do | fn | > ff = Bio::FlatFile.auto(fn) > ff.each_entry do |entry| > if regex != nil > next if eval("entry.seq !~ #{regex}") > end > print entry.seq.to_fasta(entry.definition,70) > end > end > > which does a lot of work in a few lines, with remarkable flexibility! > Including automatic data format checking and a runtime defined regex > search. > > Nowadays we would probably do it a little different. The eval can be > taken out of the loop and the regex compiled (in a Pythonesque way). > Also both each_entry and the Sequence objects should be lazy (it is > not underneath) and properly iterate to avoid loading everything in > RAM and parsing too much. But hey, it is still a great example what > what we can do with Ruby anyway! > > I wrote this simple example any2fasta.rb 6 years ago, but the FlatFile > and Sequence code is not mine. It is mostly by Toshiaka and Naohisa > going all the way back to 2002. So the beautiful code is really by > those two geniuses who are at the heart of the BioRuby project. > > Pj. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From georgkam at gmail.com Fri Feb 17 02:32:38 2012 From: georgkam at gmail.com (George Githinji) Date: Fri, 17 Feb 2012 10:32:38 +0300 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> Message-ID: Hi Mic, > D currently has some problems, because many projects > http://www.dsource.org/projects/ are no any more in active developed. The > other problem is that Tango has also stooped. Phobos (http://dlang.org/phobos/index.html) is the standard runtime library that comes with the D language compiler thus Tango is more of an auxiliary library for those that want to do things different. Tango development might not have stopped and tango has now been ported to D2 see this announcement http://forum.dlang.org/thread/jgagrl$1ta5$1 at digitalmars.com I found this comparison table useful to evaluate the language features. http://dlang.org/comparison.html It seems most D community concerns are about syntax breaks and worry on stability. With the recent release they have fixed a lot of bugs(http://forum.dlang.org/thread/jhfdcu$iht$1 at digitalmars.com) . This reddit discussion highlights some of the community concerns (http://www.reddit.com/r/programming/comments/pqft5/d_reference_compiler_2058_is_out_15_new_features/) You might find it useful. Again these are personal opinions :) -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From pjotr.public14 at thebird.nl Fri Feb 17 03:38:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 17 Feb 2012 09:38:54 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> Message-ID: <20120217083854.GA11837@thebird.nl> On Fri, Feb 17, 2012 at 10:32:38AM +0300, George Githinji wrote: > Tango development might not have stopped and tango has now been ported > to D2 see this announcement > http://forum.dlang.org/thread/jgagrl$1ta5$1 at digitalmars.com Indeed. Even if Tango had been dropped, it would not be a good reason to say D has 'issues'. Saying that software libraries are not maintained is rubbish - how many Ruby modules do you think are not maintained? Much about the D1 schism is FUD. As I wrote in my blog ''Finally some things that keep cropping up when I bring up D. First, the licensing issues. D, for historical reasons was closed source. That is changing now, with D2 compilers getting part of Fedora and Debian to follow. Second the schism and negativism of D1 users caused by an the move to D2. That you'll find on the Internet. D2 is not compatible with D1, and that has caused grief. D2 was reinvented as the language designers progressed their ideas.'' http://blog.thebird.nl/?p=93 : I realise this is is not an appropriate mailing list to really vent opinions about programming languages. Clojure, Groovy, and many more, are fine languages. If anyone suggests that a language is superior over another, I would like to point out that there must be a lot of dumb people out there :). Every language has its pros and cons, and there is only one way to find out - that is by trying them yourself. So let us refrain from a flaming discussion on this ML. This list is about Ruby. We are using other languages to bind against Ruby, and the mechanisms for binding are universal. You can select pretty much any computer language, and try that with Ruby (or not). This means we can all gain, as long as the system can be deployed. With all languages mentioned here, that is possible. It is a good thing to experiment. I believe multi-language programming is necessary for big data analysis. The reason is parallel computing and efficient data structures. You may want to read our book chapter on language bindings in Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies by Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields and Toshiaki Katayama chapter 21 in Evolutionary Genomics: statistical and computational methods, ed. Anisimova M. within Meth. Mol. Biol. Series of Humana-Springer 2012 coming out in a month from now :). Notice the authors are from Perl, Python, Java and Ruby communities. Pj. From bonnal at ingm.org Fri Feb 17 07:07:11 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 17 Feb 2012 13:07:11 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> Message-ID: Quick update. I added some new project, MAF parser and BioImage * Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI * Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser (FFI?) * Testing framework for biogem plugins * Restyling BioRuby.org * Update bio-images a plugin to represent bio-object with cool images I'm thinking about biongs but I need to figure out and "easy" task for a student. As usual, please login and make contributes to all of them, do not hesitate to propose new projects. There is something you miss in BioRuby ? Propose a a project for a new Biogem (BioRuby plugin)! http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Proposal_2012 -- Ra From pjotr.public14 at thebird.nl Fri Feb 17 12:21:03 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 17 Feb 2012 18:21:03 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> Message-ID: <20120217172103.GA16813@thebird.nl> Thanks Raoul. I added: Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI Rationale GFF3/GTF parsers are used by genome browsers and next-gen sequencing tools. Current parsers are slow and use a lot of memory. A fast low-memory parser would be beneficial to many bio-medical projects Approach Based on existing implementation we can design a fast parser using the D programming language. D provides capabilities for hand-crafting high-performance parsers. If required, parallelization of records can be introduced by using Actors. D can compile libraries which can be bound to Ruby using a C-style interface. This means the GFF3/GTF parser can be used from Ruby. The design will focus on iterating records and feeding them back to the Ruby environment. The library will also be useful for Python, Perl and the JVM. Difficulty and needed skills This is a challenging project. Advanced programming concepts, concurrency, foreign language bindings. The project requires An interest in high performance computing. Some affinity with coding in C and one or more interpreted languages Mentors Pjotr Prins (author of bio-gff3), Raoul Bonnal Other interested parties Naohisa Goto (author BioRuby's GFF3 parser), Brad Chapman (author Biopython's GFF3 parser) and Peter Cock (Biopython), Chris Fields (BioPerl). On Fri, Feb 17, 2012 at 01:07:11PM +0100, Raoul Bonnal wrote: > Quick update. I added some new project, MAF parser and BioImage > * Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI > * Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser > (FFI?) > * Testing framework for biogem plugins > * Restyling BioRuby.org > * Update bio-images a plugin to represent bio-object with cool images > > I'm thinking about biongs but I need to figure out and "easy" task for a > student. > > As usual, please login and make contributes to all of them, do not hesitate > to propose new projects. There is something you miss in BioRuby ? Propose a > a project for a new Biogem (BioRuby plugin)! > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Proposal_2012 > > > -- > Ra > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Fri Feb 17 12:25:18 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 17 Feb 2012 18:25:18 +0100 Subject: [BioRuby] Restyling BioRuby.org Message-ID: <20120217172518.GB16813@thebird.nl> A question for everyone: What would you like to a fresh BioRuby.org to be? Myself, I am thinking we need to retool the site for inexperienced programmers. That means accentuating Tutorials and examples, as Michael Barton suggested. What do you think? And please, also let some respond that have not mailed to this list before! We are here to hear you! From cjfields at illinois.edu Fri Feb 17 12:26:32 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 17 Feb 2012 17:26:32 +0000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120217083854.GA11837@thebird.nl> References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> <20120217083854.GA11837@thebird.nl> Message-ID: <491E0F71-F8C9-40C6-9074-E0E7F566D52D@illinois.edu> I think understanding concepts in classic and modern programming languages, and their advantages and disadvantages, is considerably more important than the language itself. VM's like JVM, Mono, Parrot, etc allow one to cross over from one language to another (sometimes within the same module space), so the adage about which lang is best seems very trite now. Anyway, anytime I see someone pipe up (on SO, reddit, etc) with a big trolly 'lang A is better than lang B' thread, I invariably find the most interesting responses are from those who can clearly point out the advantages and disadvantages of both languages. Inevitably the conclusion is every language has its flaws, the choice is very much based on one's opinions, and that concepts and specifications are way more important to know than specific implementations of them (and knowledge of such allows one to migrate more effortlessly between languages). (my rant for the day, sorry, need coffee) chris On Feb 17, 2012, at 2:38 AM, Pjotr Prins wrote: > On Fri, Feb 17, 2012 at 10:32:38AM +0300, George Githinji wrote: >> Tango development might not have stopped and tango has now been ported >> to D2 see this announcement >> http://forum.dlang.org/thread/jgagrl$1ta5$1 at digitalmars.com > > Indeed. Even if Tango had been dropped, it would not be a good reason > to say D has 'issues'. Saying that software libraries are not > maintained is rubbish - how many Ruby modules do you think are not > maintained? > > ... > I believe multi-language programming is necessary for big data > analysis. The reason is parallel computing and efficient data > structures. You may want to read our book chapter on language > bindings in > > Sharing programming resources between Bio* projects through remote > procedure call and native call stack strategies > > by Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter > Willis, Christopher Fields and Toshiaki Katayama > > chapter 21 in Evolutionary Genomics: statistical and computational > methods, ed. Anisimova M. within Meth. Mol. Biol. Series of > Humana-Springer 2012 > > coming out in a month from now :). Notice the authors are from Perl, Python, > Java and Ruby communities. > > Pj. From p.j.a.cock at googlemail.com Fri Feb 17 17:40:29 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 17 Feb 2012 22:40:29 +0000 Subject: [BioRuby] Fwd: [Utilities-announce] NCBI E-Utilities Update In-Reply-To: References: Message-ID: Hi all, Just FYI, the following was also changed in this week's Entrez update to EFetch 2.0 (see forwarded email below). This was breaking some Biopython scripts - depending on how they passed in the id parameters. It turns out we relied on the undocumented and now withdrawn form in one of our examples, so some users had copied this style. Biopython 1.59 will solve this. I know BioJava is looking at the more publicised changes to retmode - I don't know if BioPerl or BioRuby was affected. Regards, Peter ---------- Forwarded message ---------- From: Date: Fri, Feb 17, 2012 at 7:09 PM Subject: [Utilities-announce] NCBI E-Utilities Update To: NLM/NCBI List utilities-announce The most recent NCBI E-Utilities update includes a more stringent check for correct URL parameters. EFetch URLs with multiple IDs must be entered as: id=1,2,3 EFetch no longer accepts invalid URL parameters, e.g., id=1&id=2&id=3 Please see the online E-Utilities help for additional information: http://www.ncbi.nlm.nih.gov/books/NBK25500/ EFetch online help: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch Thank you. _______________________________________________ Utilities-announce mailing list http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce From cjfields at illinois.edu Fri Feb 17 21:54:44 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sat, 18 Feb 2012 02:54:44 +0000 Subject: [BioRuby] [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utilities Update In-Reply-To: References: Message-ID: On Feb 17, 2012, at 4:40 PM, Peter Cock wrote: > Hi all, > > Just FYI, the following was also changed in this week's Entrez > update to EFetch 2.0 (see forwarded email below). > > This was breaking some Biopython scripts - depending on how > they passed in the id parameters. It turns out we relied on the > undocumented and now withdrawn form in one of our examples, > so some users had copied this style. Biopython 1.59 will solve > this. > > I know BioJava is looking at the more publicised changes to > retmode - I don't know if BioPerl or BioRuby was affected. No, I checked the BioPerl modules against regression tests today after seeing the announcement. Seems everything is fine; the main issue on NCBI's end that seemed to break things was how multiple IDs were joined. > Regards, > > Peter chris From pjotr.public14 at thebird.nl Sun Feb 19 03:56:12 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 19 Feb 2012 09:56:12 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120217172518.GB16813@thebird.nl> References: <20120217172518.GB16813@thebird.nl> Message-ID: <20120219085612.GA29424@thebird.nl> On Fri, Feb 17, 2012 at 06:25:18PM +0100, Pjotr Prins wrote: > What would you like to a fresh BioRuby.org to be? > > Myself, I am thinking we need to retool the site for inexperienced > programmers. That means accentuating Tutorials and examples, as > Michael Barton suggested. > > What do you think? > > And please, also let some respond that have not mailed to this list > before! We are here to hear you! With an embarrassing 0 (zero) responses, I can conclude there is either no interest in this matter, or no one considers it his/her business. That is sad. Open source software matters. Web presence matters. So let me take you by the hand and draw a vision :). I think programming for Biology (which I call big B) is important for the future of humanity, and the broader world we live in. We are the ones that have to unlock the potential of big data. As I see it around me, scientists are generating data at an incredible rate. Now the data analysis is the bottle neck, there are plenty of indications. For example, we have a programming course here at our biology university which was never really popular. This year the attendance tripled, and includes a number of Ph.D. students! I.e. the research groups are feeling the pinch. There are not enough people to analyse the data. It gets worse. What I see is that the universities train people to the level they can script a bit, and use existing tools. For example for genome assembly. The problem is that these tools work for the general case. With different experimental design and setups the data may contain more valuable information, i.e. there is often opportunity for harvesting more information - which never gets done. And we do not scale. Each of us is too busy, even to write to a mailing list and participate in mentoring students in the Google Summer of Code (GSoC). Are we being responsible scientific citizens here? I think not. Are most of us true participants in Bio*. I think not. This ML and GSoC is about all Bio* projects (BioRuby, Biopython, BioPerl, Bioconductor...). The programming languages are tools that we should use to not only analyse our own data, but also to give back to others so we can maximize the scientific potential. You are using open source software (OSS). I bet you have benefited from Bio*. We are asking to give back some of your time. Everyone can do it in a different way. Ben Woodcroft has created many small plugins of his coding efforts. That is greatness in my opinion. Raoul spent many weeks of his free time to create the Biogems tool and make it possible for people to share code. That is greatness in my opinion. So how can you participate and be great? First by discussing ideas on the mailing list. Discuss what you want out of the BioRuby web presence. Any idea will do. An active mailing list will help young developers find us. Adding projects to GSoC will help young developers find us. I don't think mentoring GSoC students necessarily leads to long term committers, but that is not the point. The point is to move science as a whole forward. The universities train people to use tools and maybe script them together. We here, are the select crowd of real software afficiendos in Biology. I think there is only one conclusion possible, if we are not to sink in a cynical mire. If you understand and benefit from *our* OSS, don't go the way alone. Don't just take and not give. Help us materialize that potential of young developers. They are out there, and we need them to find us. I am asking: What do you think? How can we accommodate this goal using the tools we have. Pj. From pjotr.public14 at thebird.nl Sun Feb 19 04:31:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 19 Feb 2012 10:31:54 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120217172103.GA16813@thebird.nl> References: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> <20120217172103.GA16813@thebird.nl> Message-ID: <20120219093154.GA1030@thebird.nl> I added the following GSoC proposal: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Testing_framework_for_biogem_plugins Testing framework for biogem plugins Rationale Biogems are Ruby gems that are created by independent authors, see the publication. Designing an automated testing frame work for different versions of Ruby is critical for the successful use of Ruby in bioinformatics. Gems should be tested on release, but also when tagged on github Approach We integrate facilities of http://biogems.info/, http://rubygems.org/ and http://github.com/ to automatically test gems that get released in the public domain. We can make use of open-bio's testing framework to test individual gems, or crowd sourcing setups, such as http://test.rubygems.org/ to test gems in different setups. Next we program the http://biogems.info/ website to show the test results in easy way. Difficulty and needed skills Ruby scripting, and affinity for web integration, some web programming including Ruby, HTML (HAML), CSS and Javascript (Coffee) The project requires Mentors Pjotr Prins, Raoul Bonnal, Peter Cock (confirm) From pjotr.public14 at thebird.nl Sun Feb 19 04:45:21 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 19 Feb 2012 10:45:21 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120219093154.GA1030@thebird.nl> References: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> <20120217172103.GA16813@thebird.nl> <20120219093154.GA1030@thebird.nl> Message-ID: <20120219094521.GA1154@thebird.nl> Another one :) Restyling BioRuby.org Rationale BioRuby.org is a portal for getting appropriate information on Ruby-related software development to bioinformatics software developers. The current portal discourages both experienced and inexperienced software developers from digging deeper, and finding solutions to typical bioinformatics problems. Approach We want to restyle the portal so it becomes an interactive environment, encourages people to participate and put information in, and information gets easier to find. The restyling is about web design, and programming an interactive website in Ruby, using Ruby on Rails and other tools, such as markdown, haml, sass, staticmatic, etc. Also the idea is to use existing webservices, such has github gists, rubydoc.info, e.g. example, and embed them into the site - rather than recreating all these services from scratch. We would like to create a collection of code snippets and documentation that is easy to navigate and add to. It should be even less effort than maintaining a Wiki. Also code snippets should be able to run online - and prove they are correct. The total design should also be useful for other Bio* projectcs, such as BioPerl. It is possible to get a scientific paper out of this work. Difficulty and needed skills Affinity for web design, accessibility of information, web programming in Ruby. Perhaps Javascript and Coffeescript. The project requires Some Ruby experience, experience in web design Mentors Raoul Bonnal, Pjotr Prins, Toshiaki Katayama (confirm) http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Restyling_BioRuby.org From hlapp at drycafe.net Sun Feb 19 18:27:00 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 19 Feb 2012 18:27:00 -0500 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120219085612.GA29424@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> Message-ID: <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> On Feb 19, 2012, at 3:56 AM, Pjotr Prins wrote: > With an embarrassing 0 (zero) responses, I can conclude there is > either no interest in this matter, or no one considers it his/her > business. Or that nobody else has as much time on their hands :-) -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From pjotr.public14 at thebird.nl Mon Feb 20 04:51:29 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 20 Feb 2012 10:51:29 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> Message-ID: <20120220095129.GA10167@thebird.nl> On Sun, Feb 19, 2012 at 06:27:00PM -0500, Hilmar Lapp wrote: > > On Feb 19, 2012, at 3:56 AM, Pjotr Prins wrote: > > > With an embarrassing 0 (zero) responses, I can conclude there is > > either no interest in this matter, or no one considers it his/her > > business. > > Or that nobody else has as much time on their hands :-) Which somewhat proves my point. We need fresh blood. I must admit I have not been good at nurturing this myself, but now I have seen the light :). Questions that keep going through my mind are: 1. Where is our leadership? This is not unique to BioRuby. The other projects suffer similar problems. Perhaps, in bioinformatics (the small b), people get too busy too quickly, and sitting leadership starts being the cause of inertia. 2. Is this the time fork the BioRuby project? I have been thinking this for many years ;). Forking the code is one thing - as noted before, we can and should strip out modules into Biogems. Forking the project is not possible, unless the domain gets released. Do we want a bioruby2.org? 3. How are we going to revamp our web presence? With Biogems.info we show that a change in this can have real effect on contributions. Here we have raised that we can take the web presence to a new level. 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* projects? It is appears to me that sitting leadership is reluctant to give away their positions. I have discussed this with Chris Fields last year. We agreed that there are also few to take over the helm. So... 5. how do we nurture future leadership? I am old and cynical enough to know people mostly work for their own direct benefit (their itch, so tho speak) in OSS, or anywhere else. Still, I am going to poke and prod for some time, to see if we can make change. I believe Bio* projects are at fork in the road. Which one are we going to take? Should BioRuby exist as it is, or should we use it as a breeding ground for young developers. Same question really for BioPython and BioPerl. The BioRuby community is almost in a coma, I think. Despite 180 readers of the ML. I see the same people engaging, and interestingly, a significant number of messages from Biopython and BioPerl leadership. Thank you for that. BioRuby is just coming out of its shell, and you are helping. 6. What is needed to get BioRuby out of the comatose state? With BioRuby we have had lively discussions before, but they tend to peter out. We can reason about this, but I think it goes back to leadership again. Please note that I have no ambition in taking on a leadership role. That would also be too contentious ;). That is not what I am trying to achieve here. But I would certainly like to make the leadership more fluent, responsive, and rotating. Pj. From ngoto at gen-info.osaka-u.ac.jp Mon Feb 20 05:37:07 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 20 Feb 2012 19:37:07 +0900 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120219085612.GA29424@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> Message-ID: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Hi, On Sun, 19 Feb 2012 09:56:12 +0100 Pjotr Prins wrote: > With an embarrassing 0 (zero) responses, I can conclude there is > either no interest in this matter, or no one considers it his/her > business. That is sad. Open source software matters. Web presence > matters. I think requesting for writing responses for the mail posted on Friday night in the weekend is too hurry. I personally don't feel strong dissatisfaction with the current http://bioruby.org/ website, although I agree it is not the best ideal state, and I don't have strong motivation to discuss about the topic unless new website candidate is sent by someone. So, please send new site html contents. Current contents is now on th GitHub. https://github.com/ngoto/bioruby.org-webpage Writing new pages without using current contents is also welcomed. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From francesco.strozzi at gmail.com Mon Feb 20 06:22:23 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 20 Feb 2012 12:22:23 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: Hi all, coming back to the website restyle. If I could suggest a new look, I really like the layout of http://jruby.org . You have 3-4 main sections just at the first page, very clear and very visible. There we could place sections like "Why Ruby?" (as in JRuby) to show the pros and avantages of Ruby (or why we love it and use it in Bioinformatics). A second section like "Use it", with clear and coincise info on how to start using BioRuby and a reference to the most updated/most recent official documentation (e.g. point to github / wiki etc.). A last third section "Contribute" that describe the BioRuby code organization, the repository and the BioGems/plugins system. Just under these 3 main sections you can have one or two areas with "Recent news", Tweets that mention BioRuby and/or OpenBio projects in general, plus maybe a feed or even a calendar with conferences, events, hackathons where BioRuby and OpenBio people meets and presents stuff. This to show the community activity, plus also some links to point to the ML and IRC. That's my view so far, I think there is room for discussion. Cheers -- Francesco From pjotr.public14 at thebird.nl Mon Feb 20 06:40:06 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 20 Feb 2012 12:40:06 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120220114006.GA13746@thebird.nl> Hi Naohisa, > I personally don't feel strong dissatisfaction with the current > http://bioruby.org/ website, although I agree it is not the > best ideal state, Good. > and I don't have strong motivation to discuss about the topic unless > new website candidate is sent by someone. Bad. This is bad, because you are asking for someone to do (a lot of) work, without any guarantee that it will be used. Do you see why no one will respond to this query? Leadership sets the tone of things. What are your ideas, to start with? It is not a discussion per se. > So, please send new site html contents. > Current contents is now on th GitHub. > https://github.com/ngoto/bioruby.org-webpage > Writing new pages without using current contents is also welcomed. Better. Based on this response, my questions are: 1. Who is in charge of the website - is it You? So you are effectively Mr BioRuby now? 2. What is the process to get the new website approved? 3. Can it be a democratic process? I doubt you will approve of just any new website :) Pj. From ngoto at gen-info.osaka-u.ac.jp Mon Feb 20 08:49:47 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 20 Feb 2012 22:49:47 +0900 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220114006.GA13746@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> <20120220114006.GA13746@thebird.nl> Message-ID: <20120220134948.878861CBC4B1@idnmail.gen-info.osaka-u.ac.jp> Hi Pjotr, On Mon, 20 Feb 2012 12:40:06 +0100 Pjotr Prins wrote: > Bad. > > This is bad, because you are asking for someone to do (a lot of) > work, without any guarantee that it will be used. Do you see why no > one will respond to this query? I understand hard work (and/or money) would be needed for restyling bioruby.org. > Leadership sets the tone of things. What are your ideas, to start > with? It is not a discussion per se. I think there may be some starting points. * Edting current site gradually, accumulating small changes * Paying money to professional web designers * Waiting for someone to bring new website Indeed, I don't have enough motivation about all of the above. In my todo list, the priority is low. > > So, please send new site html contents. > > Current contents is now on th GitHub. > > https://github.com/ngoto/bioruby.org-webpage > > Writing new pages without using current contents is also welcomed. > > Better. > > Based on this response, my questions are: > > 1. Who is in charge of the website - is it You? So you are > effectively Mr BioRuby now? Currently, only Toshiaki can update the website. Usually I send him modified html files when releasing new version of bioruby. > 2. What is the process to get the new website approved? > > 3. Can it be a democratic process? Nothing decided. Maybe vote in this mailing list? > I doubt you will approve of just any new website :) Don't worry :) Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From hlapp at drycafe.net Mon Feb 20 13:01:30 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 20 Feb 2012 13:01:30 -0500 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220095129.GA10167@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> <20120220095129.GA10167@thebird.nl> Message-ID: <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> On Feb 20, 2012, at 4:51 AM, Pjotr Prins wrote: > 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* projects? How would the OBF do that? In the present relationship between the OBF umbrella and its member projects, the OBF takes a completely hands-off approach with respect to how each of the member projects organize themselves. The OBF doesn't meddle in matters of its member project communities that concern the respective member project. As a consequence, the OBF by definition neither encourages nor discourages inertia in its member projects. Instead the OBF leaves it to each member project how inert or not they want to be. I think this is different, for better or worse, from the relationship between the Apache Foundation and Apache projects, and we've had some of that discussion (such as, is it better or worse) as a result of Ross Gardler's talk at BOSC a while ago. Personally, I am open to OBF changing the nature of that relationship, but I think the drive to do that would have to come with very broad community support that cuts across our projects, rather than top-down. > It is appears to me that sitting leadership is reluctant to give away their positions. I'm not sure - I can imagine that Chris F would more than happily turn over release and other leadership to someone else if they stepped up. I think volunteers taking leadership and responsibility is fundamentally at odds with the loosey-goosey fork-patch-pull request micro-contribution model that reins supreme on Github. While that model has done lots of good in terms of lowering the barrier to contribution, we must not forget that taking leadership and responsibility is not a micro-contribution, and by nature not low-barrier. Hence, cultivating a large following of micro-contributors is by no means prone to give you an ample resource for future leadership. Sorry if that's not what you wanted to hear. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From mictadlo at gmail.com Tue Feb 21 00:41:07 2012 From: mictadlo at gmail.com (Mic) Date: Tue, 21 Feb 2012 15:41:07 +1000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> <20120220095129.GA10167@thebird.nl> <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> Message-ID: BioRuby must become faster in next generation sequence time. Some of the mailing list member like D very much. How about BioD or BioGO or BioVala instead of a BioRuby fork? On Tue, Feb 21, 2012 at 4:01 AM, Hilmar Lapp wrote: > > On Feb 20, 2012, at 4:51 AM, Pjotr Prins wrote: > > > 4. One for you Hilmar: does the OBF actually encourage inertia in the > Bio* projects? > > How would the OBF do that? > > In the present relationship between the OBF umbrella and its member > projects, the OBF takes a completely hands-off approach with respect to how > each of the member projects organize themselves. The OBF doesn't meddle in > matters of its member project communities that concern the respective > member project. As a consequence, the OBF by definition neither encourages > nor discourages inertia in its member projects. Instead the OBF leaves it > to each member project how inert or not they want to be. > > I think this is different, for better or worse, from the relationship > between the Apache Foundation and Apache projects, and we've had some of > that discussion (such as, is it better or worse) as a result of Ross > Gardler's talk at BOSC a while ago. Personally, I am open to OBF changing > the nature of that relationship, but I think the drive to do that would > have to come with very broad community support that cuts across our > projects, rather than top-down. > > > It is appears to me that sitting leadership is reluctant to give away > their positions. > > I'm not sure - I can imagine that Chris F would more than happily turn > over release and other leadership to someone else if they stepped up. I > think volunteers taking leadership and responsibility is fundamentally at > odds with the loosey-goosey fork-patch-pull request micro-contribution > model that reins supreme on Github. While that model has done lots of good > in terms of lowering the barrier to contribution, we must not forget that > taking leadership and responsibility is not a micro-contribution, and by > nature not low-barrier. Hence, cultivating a large following of > micro-contributors is by no means prone to give you an ample resource for > future leadership. > > Sorry if that's not what you wanted to hear. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Feb 21 03:52:29 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Feb 2012 09:52:29 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120221085229.GA21491@thebird.nl> Francesco, All valid points. I also like the design - very Ruby. Pj. On Mon, Feb 20, 2012 at 12:22:23PM +0100, Francesco Strozzi wrote: > Hi all, > coming back to the website restyle. If I could suggest a new look, I really > like the layout of http://jruby.org . You have 3-4 main sections just at > the first page, very clear and very visible. There we could place sections > like "Why Ruby?" (as in JRuby) to show the pros and avantages of Ruby (or > why we love it and use it in Bioinformatics). A second section like "Use > it", with clear and coincise info on how to start using BioRuby and a > reference to the most updated/most recent official documentation (e.g. > point to github / wiki etc.). A last third section "Contribute" that > describe the BioRuby code organization, the repository and the > BioGems/plugins system. > > Just under these 3 main sections you can have one or two areas with "Recent > news", Tweets that mention BioRuby and/or OpenBio projects in general, plus > maybe a feed or even a calendar with conferences, events, hackathons where > BioRuby and OpenBio people meets and presents stuff. This to show the > community activity, plus also some links to point to the ML and IRC. > > That's my view so far, I think there is room for discussion. > > Cheers > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Feb 21 04:04:52 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Feb 2012 10:04:52 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> <20120220095129.GA10167@thebird.nl> <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> Message-ID: <20120221090452.GB21491@thebird.nl> Hi Mic, On Tue, Feb 21, 2012 at 03:41:07PM +1000, Mic wrote: > BioRuby must become faster in next generation sequence time. > Some of the mailing list member like D very much. How about BioD or BioGO > or BioVala instead of a BioRuby fork? It is a very good idea to start a new project. Still we need to work on BioRuby too. If you look at all the Bio* projects, you can see that the statically typed languages don't do that well, including BioJava. Dynamically typed languages have a lower threshold, and give instant gratification. That is the key to understanding success in bioinformatics ;). We do, however, need fast back-end stuff. BioRuby needs to allow for that (and we do in biogems), so the broader user base only needs to know Ruby (or Python, or whatever). We'll see more bindings to these other languages. A new BioD project - I am sure someone will start - should aim to provide that. Focussing on D bioinformatics alone, however, will render you a small community. Check out the committers of BioJava, BioC, BioC++, etc. It is my experience with BioScala too. Not to stop anyone, just saying that Ruby, Python, Perl and R will remain mainstream for years to come. Pj. From bonnal at ingm.org Tue Feb 21 06:29:53 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 21 Feb 2012 12:29:53 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220095129.GA10167@thebird.nl> Message-ID: Hi Pjotr, Hilmar and others, On 20/02/12 10.51, "Pjotr Prins" wrote: > On Sun, Feb 19, 2012 at 06:27:00PM -0500, Hilmar Lapp wrote: > 1. Where is our leadership? > > This is not unique to BioRuby. The other projects suffer similar > problems. Perhaps, in bioinformatics (the small b), people get too > busy too quickly, and sitting leadership starts being the cause of > inertia. > > 2. Is this the time fork the BioRuby project? > > I have been thinking this for many years ;). Forking the code is one > thing - as noted before, we can and should strip out modules into > Biogems. Forking the project is not possible, unless the domain gets > released. Do we want a bioruby2.org? At this time forking is not a solution, like creating another Bio language (as suggested by Mic with D) which is just used by a niche of developers. Why is not a solution ? A) Because I supposed we have no time to support a whole library from zero. B) It's not a founded project, so I can not spend time on it. Now I can justify the effort because I use it daily or for specific tasks but if I must spend time supporting people on things which are not relevant to my own work, that would be a real problem. In Boston (BOSC) (Apache talk) we discussed about the chance to be founded, but I can imagine is not easy. C) I think that extending or hacking bioruby with plugins is a good way to introduce new concept/design keeping compatibility when needed and most importantly publishing papers to be cited = Ruby more widespread in bioinformatics. Unfortunately bioruby by itself is not enough so we must provide support and contribute to SciRuby (just an example). C.1) everyone will contribute to its own field and is normal. D) WE NEED A ROAD MAP (is connected to point 3) I would put a link ( Ruby for Science Alliance ) to friend projects like SciRuby :-) > 3. How are we going to revamp our web presence? > > With Biogems.info we show that a change in this can have real > effect on contributions. Here we have raised that we can take the > web presence to a new level. Publications, ML activities, IRC meetings, ROAD Map is the only way I see. So in a new BioRuby site, as Francesco suggested, calendar/events etc.. Is more than welcome. > 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* > projects? > > It is appears to me that sitting leadership is reluctant to > give away their positions. I have discussed this with Chris Fields > last year. We agreed that there are also few to take over the helm. > So... I don't see how OBF could push the projects, in case of founds they would be distributed equally? We are good people so we are working together promoting our language helping the others. During the last BioHackathon the most astonishing things was seeing Bio Perl/Ruby/Python/Java working (really) together, it was great. > 5. how do we nurture future leadership? > > I am old and cynical enough to know people mostly work for their own > direct benefit (their itch, so tho speak) in OSS, or anywhere else. > Still, I am going to poke and prod for some time, to see if we can > make change. I believe Bio* projects are at fork in the road. Which > one are we going to take? > Should BioRuby exist as it is, or should we > use it as a breeding ground for young developers. Same question really > for BioPython and BioPerl. Not very clear, at least to me. > The BioRuby community is almost in a coma, I think. Despite 180 > readers of the ML. I see the same people engaging, and interestingly, > a significant number of messages from Biopython and BioPerl > leadership. Thank you for that. BioRuby is just coming out of its > shell, and you are helping. > 6. What is needed to get BioRuby out of the comatose state? > > With BioRuby we have had lively discussions before, but they tend to > peter out. We can reason about this, but I think it goes back to > leadership again. I don't know how to solve this issue... The democratic process you suggested some time ago ? Which is the workload, which is the coding power we have ? Which are the languages we can rely on for performances (it means which is the knowledge of the people around here )? Do we want to support Jruby? Suppose we now need a new feature in BioRuby, which one ? Do we want to participate to GSoC ? YES and we MUST there is no doubt and we NEED to write good proposals but everything should be made as a community not only as a group of passionate developers. LANGUAGES: D or Scala, I don't know that I'm just curious and eager to learn. Most of my work is managing large scale data and interconnecting them extracting information etc... I would say, why not Hadoop ? We are just a piece of a bigger ecosystem, the problem is that most of the time "setting up" each piece is a pain in the ass. WEBSITE Proposals: Why not create and post images, an image per page. Is a usual approach for proposing new layouts. We are growing and this kind of discussions are a natural process. -- Ra From pjotr.public14 at thebird.nl Tue Feb 21 12:31:21 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Feb 2012 18:31:21 +0100 Subject: [BioRuby] Developing a VISION Message-ID: <20120221173121.GA28249@thebird.nl> I guess this is a good moment to work on a VISION for BioRuby. A VISION may lead to a ROADMAP. See if you like the following... # BioRuby Vision Here BioRuby is defined as the wider eco-system of Ruby in bioinformatics. This includes the BioRuby project, biogems, and external libraries and tools which can interoperate with Ruby. Note that for Ruby one can equally use Python or Perl. ## Challenges in Computational Biology At this point in time a number of challenges in computational biology are recognised: 1. Big data: bioinformatics software needs to address performance and efficiency required for TB analysis 2. Biological analysis: we need to find ways of making analysis software available to users not so proficient in programming software 3. Education: more biologists need to become software engineers, from entry level all the way to expert BioRuby is the natural place to look for a concerted drive in addressing these challenges, as it has a thriving community, software engineering expertise, and people working in all three areas of challenge. ## Vision statement: BioRuby should focus on inexperienced developers Experienced people tend to be very busy in their jobs. Experienced developers do not scale that well. Young people are less experienced, but have the time and energy to make a difference. Experienced developers were once inexperienced too. This leads to a natural conclusion that BioRuby should focus on inexperienced developers. Realisation: We need to find ways of making BioRuby cool (something RoR handles very well), we need to have young people engage with us, we need to pull them into BioRuby with a good web presence. Talented developers like challenges, so we should set challenges and make sure there is the proper guidance. Questions on the mailing list should be rapidly responded to, always in a positive fashion. Rapidly means within hours, not within days. The IRC channel should be monitored at all time. GSoC is an almost free way of attracting talent, and deserves the effort of mentoring GSoC students. ## Vision statement: BioRuby aims for distributed development Distributed development puts power into the hands of developers, and makes sure they get the credits. Dependencies are clear, and modules are easily replaced and upgraded. Realisation: We have Biogem, which is a powerful tool in making distributed development possible. Anyone can create a biogem. The current BioRuby source base, meanwhile, is bloated, and confusing to newcomers. The code base needs to be reduced, and modules have to be moved into biogems. These biogems may gain new ownership, or may disappear over time. RoR shows the way of reducing complexity, and striving for logical organisation of pluggable modules. External dependencies, such as FFI, need to be implemented in independent biogems. We will have biogems for the JVM and native Ruby. The core BioRuby gem itself should be platform independent. more to come... From cjfields at illinois.edu Tue Feb 21 13:54:00 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 21 Feb 2012 18:54:00 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: Message-ID: <8B427626-EEDB-4ED9-94DE-2F0D99F14866@illinois.edu> On Feb 21, 2012, at 5:29 AM, Raoul Bonnal wrote: > Hi Pjotr, Hilmar and others, > ... > >> 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* >> projects? >> >> It is appears to me that sitting leadership is reluctant to >> give away their positions. I have discussed this with Chris Fields >> last year. We agreed that there are also few to take over the helm. >> So... > I don't see how OBF could push the projects, in case of founds they would be > distributed equally? We are good people so we are working together promoting > our language helping the others. During the last BioHackathon the most > astonishing things was seeing Bio Perl/Ruby/Python/Java working (really) > together, it was great. Bioinformatics problems span languages >> 5. how do we nurture future leadership? >> >> I am old and cynical enough to know people mostly work for their own >> direct benefit (their itch, so tho speak) in OSS, or anywhere else. >> Still, I am going to poke and prod for some time, to see if we can >> make change. I believe Bio* projects are at fork in the road. Which >> one are we going to take? > >> Should BioRuby exist as it is, or should we >> use it as a breeding ground for young developers. Same question really >> for BioPython and BioPerl. > Not very clear, at least to me. > >> The BioRuby community is almost in a coma, I think. Despite 180 >> readers of the ML. I see the same people engaging, and interestingly, >> a significant number of messages from Biopython and BioPerl >> leadership. Thank you for that. BioRuby is just coming out of its >> shell, and you are helping. > > >> 6. What is needed to get BioRuby out of the comatose state? >> >> With BioRuby we have had lively discussions before, but they tend to >> peter out. We can reason about this, but I think it goes back to >> leadership again. > I don't know how to solve this issue... The democratic process you suggested > some time ago ? Which is the workload, which is the coding power we have ? > Which are the languages we can rely on for performances (it means which is > the knowledge of the people around here )? Do we want to support Jruby? > Suppose we now need a new feature in BioRuby, which one ? Do we want to > participate to GSoC ? YES and we MUST there is no doubt and we NEED to write > good proposals but everything should be made as a community not only as a > group of passionate developers. > > > LANGUAGES: > D or Scala, I don't know that I'm just curious and eager to learn. Most of > my work is managing large scale data and interconnecting them extracting > information etc... I would say, why not Hadoop ? > We are just a piece of a bigger ecosystem, the problem is that most of the > time "setting up" each piece is a pain in the ass. > > WEBSITE Proposals: > Why not create and post images, an image per page. Is a usual approach for > proposing new layouts. > > > We are growing and this kind of discussions are a natural process. > -- > Ra > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From cjfields at illinois.edu Tue Feb 21 14:10:41 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 21 Feb 2012 19:10:41 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <8B427626-EEDB-4ED9-94DE-2F0D99F14866@illinois.edu> References: <8B427626-EEDB-4ED9-94DE-2F0D99F14866@illinois.edu> Message-ID: <492B88CE-FC32-4AEE-B4A6-0F688DC50D85@illinois.edu> Um, that was sent a little early :P Saw a unicorn and distractedly hit the 'send'... On Feb 21, 2012, at 12:54 PM, Christopher Fields wrote: > On Feb 21, 2012, at 5:29 AM, Raoul Bonnal wrote: > >> Hi Pjotr, Hilmar and others, >> ... >> >>> 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* >>> projects? >>> >>> It is appears to me that sitting leadership is reluctant to >>> give away their positions. I have discussed this with Chris Fields >>> last year. We agreed that there are also few to take over the helm. >>> So... >> I don't see how OBF could push the projects, in case of founds they would be >> distributed equally? We are good people so we are working together promoting >> our language helping the others. During the last BioHackathon the most >> astonishing things was seeing Bio Perl/Ruby/Python/Java working (really) >> together, it was great. > > Bioinformatics problems span languages My point being, cross-pollination of projects with common problems makes sense. >>> 5. how do we nurture future leadership? >>> >>> I am old and cynical enough to know people mostly work for their own >>> direct benefit (their itch, so tho speak) in OSS, or anywhere else. >>> Still, I am going to poke and prod for some time, to see if we can >>> make change. I believe Bio* projects are at fork in the road. Which >>> one are we going to take? >> >>> Should BioRuby exist as it is, or should we >>> use it as a breeding ground for young developers. Same question really >>> for BioPython and BioPerl. >> Not very clear, at least to me. You can probably have it every way, make a toolkit that the community can use and have it be a means to bring in additional developers to attempt to add or improve upon functionality. That's how I got involved with bioperl. >>> The BioRuby community is almost in a coma, I think. Despite 180 >>> readers of the ML. I see the same people engaging, and interestingly, >>> a significant number of messages from Biopython and BioPerl >>> leadership. Thank you for that. BioRuby is just coming out of its >>> shell, and you are helping. There is a favorite term of mine that was coined back in the early Perl days, 'being Warnocked': http://en.wikipedia.org/wiki/Warnock's_dilemma Lack of a response to a question could mean a lot of things. If you absolutely need a response, an email thread may not be the best option (maybe a survey?) >>> 6. What is needed to get BioRuby out of the comatose state? >>> >>> With BioRuby we have had lively discussions before, but they tend to >>> peter out. We can reason about this, but I think it goes back to >>> leadership again. >> I don't know how to solve this issue... The democratic process you suggested >> some time ago ? Which is the workload, which is the coding power we have ? >> Which are the languages we can rely on for performances (it means which is >> the knowledge of the people around here )? Do we want to support Jruby? >> Suppose we now need a new feature in BioRuby, which one ? Do we want to >> participate to GSoC ? YES and we MUST there is no doubt and we NEED to write >> good proposals but everything should be made as a community not only as a >> group of passionate developers. Developers tend to work hard on projects they are passionate about; if the website project or others aren't gathering input, it's possibly b/c there isn't anyone passionate about it. Or as Naohisa indicated, there hasn't been enough time to adequately respond. As mentioned above, everyone has a day $job and can't dedicate a lot of time to discussions. >> LANGUAGES: >> D or Scala, I don't know that I'm just curious and eager to learn. Most of >> my work is managing large scale data and interconnecting them extracting >> information etc... I would say, why not Hadoop ? >> We are just a piece of a bigger ecosystem, the problem is that most of the >> time "setting up" each piece is a pain in the ass. >> >> WEBSITE Proposals: >> Why not create and post images, an image per page. Is a usual approach for >> proposing new layouts. >> >> >> We are growing and this kind of discussions are a natural process. >> -- >> Ra Yes, but I think you have to balance that with actual work (code). Theoreticals and pet projects work only up to a point, you have to both establish a project's usefulness to the community, and even then sometimes the community doesn't immediately pick it up. chris From p.j.a.cock at googlemail.com Wed Feb 22 08:27:22 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 22 Feb 2012 13:27:22 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Mon, Feb 20, 2012 at 10:37 AM, Naohisa GOTO wrote: > Hi, > > On Sun, 19 Feb 2012 09:56:12 +0100 > Pjotr Prins wrote: > >> With an embarrassing 0 (zero) responses, I can conclude there is >> either no interest in this matter, or no one considers it his/her >> business. That is sad. Open source software matters. Web presence >> matters. > > I think requesting for writing responses for the mail posted > on Friday night in the weekend is too hurry. +1 I'm sure some people wouldn't even have seen Pjotr's email until Monday. Personally I saw this thread but was tied up with a workshop on Monday & Tuesday so didn't reply immediately. > I personally don't feel strong dissatisfaction with the current > http://bioruby.org/ website, although I agree it is not the > best ideal state, and I don't have strong motivation to discuss > about the topic unless new website candidate is sent by someone. I quite like the style of the current BioRuby.org page - there are two issues here, style and content. Obviously they are linked and the technical side will restrain the style and things like the ability to embed Twitter feeds or RSS. In terms of style, most of the Bio* home pages are simply wiki pages - usually protected to prevent vandalism, while most of the Bio* wiki pages are able to be edited by any registered account. This made it easy for anyone to create an alternative home page for discussion, and for that to be adopted. That's how we did the last major restructuring of the Biopython home page on our wiki, http://biopython.org/wiki/Main_Page > So, please send new site html contents. > Current contents is now on th GitHub. > https://github.com/ngoto/bioruby.org-webpage > Writing new pages without using current contents is also welcomed. That is interesting - I know other major open source projects have or are moving their home pages to github like this. For developers this isn't a major barrier to contribution - you can fork it and build an alterative webpage proposal. Pjotr wrote: >> Myself, I am thinking we need to retool the site >> for inexperienced programmers. That means >> accentuating Tutorials and examples, as >> Michael Barton suggested. We had similar concerns with Biopython's homepage and the current rather minimal page is attempting to highlight this kind of thing and make it obvious. While tutorial links are on the BioPerl, BioJava and BioRuby home pages, and near the start, I personally I find they are lost in an overly full page. (Constructive criticism/feedback on the Biopython website is also welcome) Another issue is keeping the content fresh. I notice that the Biopython, BioPerl and BioRuby homepage all have an embedded news feed top right from the OBF news server (filtering on the project category). This is great but relies on regular content appearing on the news server. I've tried to write blog posts on new or forthcoming features for Biopython, and suggested this would be a nice thing for all our developers to do. Another idea is community updates posts, perhaps monthly - something BioPerl used to do by email some years ago. The trouble is you need someone keen and committed to keep this going - although they don't have to be a developer so this is a nice way of trying to broaden community participation, We might be able to embed a Twitter feed on the home pages too... Regards, Peter From p.j.a.cock at googlemail.com Wed Feb 22 08:33:18 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 22 Feb 2012 13:33:18 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock wrote: > > We might be able to embed a Twitter feed on the > home pages too... > Looks like you can get an RSS feed easily enough, e.g. http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby That can be embedded in MediaWiki but it isn't very pretty. Peter From pjotr.public14 at thebird.nl Wed Feb 22 11:56:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 22 Feb 2012 17:56:27 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120221173121.GA28249@thebird.nl> References: <20120221173121.GA28249@thebird.nl> Message-ID: <20120222165627.GA1210@thebird.nl> ## Vision statement: BioRuby is about beauty Ruby is a language that encourages writing 'beautiful code'. RoR is often praised for its solutions and minimalism. It is no accident that many new ideas in agile software development are quickly taken up, or even originate in the the Ruby community. For example Cucumber feature DSL is a typical Ruby idea. BioRuby, however, shows little of this excitement. Let us have more focus on beautiful code and taking up behaviour driven development. Realisation: We should show many examples on how to design software properly, and redesign BioRuby to match that expectation. From georgkam at gmail.com Wed Feb 22 12:37:18 2012 From: georgkam at gmail.com (George Githinji) Date: Wed, 22 Feb 2012 20:37:18 +0300 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: +1 On Wed, Feb 22, 2012 at 7:56 PM, Pjotr Prins wrote: > ## Vision statement: BioRuby is about beauty > > Ruby is a language that encourages writing 'beautiful code'. RoR is often > praised for its solutions and minimalism. It is no accident that many new ideas > in agile software development are quickly taken up, or even originate in the > the Ruby community. For example Cucumber feature DSL is a typical Ruby idea. > BioRuby, however, shows little of this excitement. Let us have more focus > on beautiful code and taking up behaviour driven development. > > Realisation: > > We should show many examples on how to design software properly, and redesign > BioRuby to match that expectation. > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From hlapp at drycafe.net Wed Feb 22 17:17:05 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 22 Feb 2012 17:17:05 -0500 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: <9340D5B7-C1E0-4965-B4A3-A9BC2AC4E1D2@drycafe.net> On Feb 22, 2012, at 11:56 AM, Pjotr Prins wrote: > ## Vision statement: BioRuby is about beauty Perl is, too, actually. The beauty of getting things done. Some beauty may be more difficult to see than another, but that doesn't make it any less beautiful :-) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From mictadlo at gmail.com Wed Feb 22 18:27:03 2012 From: mictadlo at gmail.com (Mic) Date: Thu, 23 Feb 2012 09:27:03 +1000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: I thought BioRuby would run with JRuby. How far is Rubinus and support for it? There is a Ruby like language on to of erlang http://reia-lang.org/ which support erlang's famous concurrent programming. On Wed, Feb 22, 2012 at 11:33 PM, Peter Cock wrote: > On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock > wrote: > > > > We might be able to embed a Twitter feed on the > > home pages too... > > > > Looks like you can get an RSS feed easily enough, e.g. > > http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython > > http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl > > http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby > > That can be embedded in MediaWiki but it isn't very pretty. > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From georgkam at gmail.com Thu Feb 23 00:41:29 2012 From: georgkam at gmail.com (George Githinji) Date: Thu, 23 Feb 2012 08:41:29 +0300 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: Now let us get discuss the issues regarding actually restyling the bioruby.org site. If we were to restyle bioruby.org., What is the community's preferred way of doing it? 1. Using an existing Ruby framework i) Rails ii) Sinatra iii) Others (specify) 2. Getting together some static pages without utilizing a framework. Some considerations: 1. Who hosts the Bioruby.org site This is important so as to access the nature and the ease of deployment. Also should bioruby.org be hosted on a cloud infrastructure like heroku? What are the pros and cons? 2. Who owns the bioruby.org domain name? aka who pays and registers this domain every year and why? Is this person willing to surrender the domain ownership to the community? Would he perform the registration on behalf of the community ? 3. For a while now, bioruby.org redirects to http://bioruby.open-bio.org/. Which of the two is the more appropriate 'home' url? On Thu, Feb 23, 2012 at 2:27 AM, Mic wrote: > I thought BioRuby would run with JRuby. How far is Rubinus and support for > it? There is a Ruby like language on to of erlang ?http://reia-lang.org/ which > support erlang's famous concurrent programming. > > On Wed, Feb 22, 2012 at 11:33 PM, Peter Cock wrote: > >> On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock >> wrote: >> > >> > We might be able to embed a Twitter feed on the >> > home pages too... >> > >> >> Looks like you can get an RSS feed easily enough, e.g. >> >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython >> >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl >> >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby >> >> That can be embedded in MediaWiki but it isn't very pretty. >> >> Peter >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From pjotr.public14 at thebird.nl Thu Feb 23 02:35:37 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 23 Feb 2012 08:35:37 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120223073537.GB4065@thebird.nl> Today we will be on IRC. Pj. On Thu, Feb 23, 2012 at 08:41:29AM +0300, George Githinji wrote: > Now let us get discuss the issues regarding actually restyling the > bioruby.org site. > > If we were to restyle bioruby.org., What is the community's preferred > way of doing it? > 1. Using an existing Ruby framework > i) Rails > ii) Sinatra > iii) Others (specify) > > 2. Getting together some static pages without utilizing a framework. > > Some considerations: > 1. Who hosts the Bioruby.org site > This is important so as to access the nature and the ease of > deployment. Also should bioruby.org be hosted on a cloud > infrastructure like heroku? What are the pros and cons? > > 2. Who owns the bioruby.org domain name? aka who pays and registers > this domain every year and why? > Is this person willing to surrender the domain ownership to the > community? Would he perform the registration on behalf of the > community ? > > 3. For a while now, bioruby.org redirects to > http://bioruby.open-bio.org/. Which of the two is the more > appropriate 'home' url? > > > > > > On Thu, Feb 23, 2012 at 2:27 AM, Mic wrote: > > I thought BioRuby would run with JRuby. How far is Rubinus and support for > > it? There is a Ruby like language on to of erlang ?http://reia-lang.org/ which > > support erlang's famous concurrent programming. > > > > On Wed, Feb 22, 2012 at 11:33 PM, Peter Cock wrote: > > > >> On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock > >> wrote: > >> > > >> > We might be able to embed a Twitter feed on the > >> > home pages too... > >> > > >> > >> Looks like you can get an RSS feed easily enough, e.g. > >> > >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython > >> > >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl > >> > >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby > >> > >> That can be embedded in MediaWiki but it isn't very pretty. > >> > >> Peter > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://biorelated.wordpress.com/ > Twitter: http://twitter.com/#!/george_l > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Thu Feb 23 03:40:14 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 23 Feb 2012 08:40:14 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <941C9523-3B11-434D-B04B-35BC170A209E@googlemail.com> Hi George, On 23 Feb 2012, at 05:41, George Githinji wrote: > Some considerations: > 1. Who hosts the Bioruby.org site > This is important so as to access the nature and the ease of > deployment. Also should bioruby.org be hosted on a cloud > infrastructure like heroku? What are the pros and cons? Currently most Bio* project homepages are hosted on an OBF server - see www.open-bio.org - with donated bandwidth. I understand that the BioRuby homepage is hosted on Github (see earlier in this thread). Some OBF machines are in the cloud, specifically the buildbot server runs on an Amazon instance. > 2. Who owns the bioruby.org domain name? aka who pays and registers > this domain every year and why? > Is this person willing to surrender the domain ownership to the > community? Would he perform the registration on behalf of the > community ? Currently the OBF (at least, they do for most of the Bio* projects) which is on behalf of the community. I assume the same applies to the BioRuby.org domain. > 3. For a while now, bioruby.org redirects to > http://bioruby.open-bio.org/. Which of the two is the more > appropriate 'home' url? Why exactly that happens I don't know, it doesn't happen for BioPerl.org or Biopython.org for instance. It could be linked to the GitHub hosting and domain records - it can probably be tweaked. Peter (Biopython, also OBF board member) From ngoto at gen-info.osaka-u.ac.jp Thu Feb 23 07:16:11 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Thu, 23 Feb 2012 21:16:11 +0900 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <941C9523-3B11-434D-B04B-35BC170A209E@googlemail.com> References: <941C9523-3B11-434D-B04B-35BC170A209E@googlemail.com> Message-ID: <20120223211611.6787.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > I understand that the BioRuby homepage is hosted on > Github (see earlier in this thread). No, not hosted on GitHub. The GitHub URL in the previous mail https://github.com/ngoto/bioruby.org-webpage is my personal copy of http://bioruby.org web contents. I've push them to GitHub for smooth collaboration. The contents should be copied to real servers by hand. http://bioruby.org/ is now redirection to http://bioruby.open-bio.org/, provided by a domain name registerer. Previously, http://bioruby.org/ was hosted on the University of Tokyo and http://bioruby.open-bio.org/ was a mirror site of http://bioruby.org/, but due to the machine replacement and administration changes in the university, it was changed to the redirection. We provided some server-side services in http://bioruby.org/ server, e.g. BioFetch service http://bioruby.org/cgi-bin/biofetch.rb. That was a reason why we could not migrate to OBF server and kept bioruby.open-bio.org as a mirror server. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Thu Feb 23 07:27:39 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 23 Feb 2012 13:27:39 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120223122739.GA7421@thebird.nl> On Thu, Feb 23, 2012 at 09:27:03AM +1000, Mic wrote: > I thought BioRuby would run with JRuby. How far is Rubinus and support for > it? There is a Ruby like language on to of erlang > [1]http://reia-lang.org/ which support erlang's famous concurrent > programming. Reia too different a dialect. Rubinius should work. Pj. From bonnal at ingm.org Thu Feb 23 09:50:01 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 23 Feb 2012 15:50:01 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120223122739.GA7421@thebird.nl> Message-ID: George have summarised some of the points raised during irc meeting: here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling About :" support example code snippets that can be run from the browser * it would be great if we had a set of tutorials that users can follow in the browser" A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I think Katayama did it. From marian.povolny at gmail.com Thu Feb 23 12:28:23 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Thu, 23 Feb 2012 18:28:23 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120223122739.GA7421@thebird.nl> Message-ID: Hi all, Looking at the "Audience" section on the http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling page, is there a real need for a separate treatment of Computer Science and Ruby background? What different paths would those two groups go to get into bioinformatics using BioRuby? Except for learning Ruby frirst :) And also, I think there is one category of audience missing: BioRuby developers :) -- Marjan Povolni On Thu, Feb 23, 2012 at 3:50 PM, Raoul Bonnal wrote: > George have summarised some of the points raised during irc meeting: > here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling > > About :" support example code snippets that can be run from the browser > * it would be great if we had a set of tutorials that users can follow in > the browser" > A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I > think Katayama did it. > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Thu Feb 23 12:38:56 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 23 Feb 2012 18:38:56 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: Message-ID: Actually no need, may be .... What about a kind of logo with: BioRuby boosted by FFI, that could be interesting for CS which can incorporate their algorithm written in C/C++ (whatever language) into Ruby. BioRuby developers could be ?redirected? to biogems.info/tutorial or incorporate it into the site. If I remember correctly Jan wrote guide lines on howto use git for developing bioruby, that kind of docs could be used as inspiration for the new docs. http://saaientist.blogspot.com/2008/06/bioruby-with-git-how-would-that-work. html http://nsaunders.wordpress.com/2011/08/05/bioruby-development-feedback-on-us ing-git/ http://lists.open-bio.org/pipermail/bioruby/2008-September/000700.html On 23/02/12 18.28, "Marjan Povolni" wrote: > Hi all, > > Looking at the "Audience" section on > the?http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling?page, is there a > real need for a separate treatment of Computer Science and Ruby background? > > > What different paths would those two groups go to get into bioinformatics > using BioRuby? Except for learning Ruby frirst :) > > And also, I think there is one category of audience missing: BioRuby > developers :) > > -- > Marjan Povolni > > On Thu, Feb 23, 2012 at 3:50 PM, Raoul Bonnal wrote: >> George have summarised some of the points raised during irc meeting: >> here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling >> >> About :" support example code snippets that can be run from the browser >> * it would be great if we had a set of tutorials that users can follow in >> the browser" >> A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, ?I >> think Katayama did it. >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > From pjotr.public14 at thebird.nl Thu Feb 23 13:37:51 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 23 Feb 2012 19:37:51 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: <20120223183751.GA10920@thebird.nl> ## Vision statement: BioRuby is for biologists Ruby is a language which shines in creating simple DSL's for end-users. Great examples are Cucumber, Chef and bio-ngs. BioRuby needs to build out this concept of creating 'simple' work flows in the form of DSLs. The other area is in creating web sites. Many papers publish simple web sites presenting some algorithm (some of these papers get embarrassingly high impact). BioRuby should present a quick way of building websites - probably on top of RoR. Realisation: Biogem has some facility for that, but it should be much easier and obvious. Combining RoR with DSL's could make BioRuby a preferred environment for both publications and education. From yannick.wurm at unil.ch Thu Feb 23 13:37:25 2012 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Thu, 23 Feb 2012 18:37:25 +0000 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: References: Message-ID: <11659791-F673-4D2B-B444-EB6A47ABB326@unil.ch> On 23 Feb 2012, at 17:00, bioruby-request at lists.open-bio.org wrote: > George have summarised some of the points raised during irc meeting: > here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling > > About :" support example code snippets that can be run from the browser > * it would be great if we had a set of tutorials that users can follow in > the browser" > A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I > think Katayama did it. Apologies for chiming in a bit late. I fully agree that having something along these lines set up can greatly facilitate bioruby adoption. * people should be able to test it without having to install anything. (I recently tried running the BioRubyOnRails & failed). * http://rubular.com/ (used for learning & testing regexps) provides good inspiration. * making it idiot-proof (e.g. having an "upload flatfile" button... and then autogenerating the appropriate file loading code) can help further... Cheers, yannick ---- Yannick Wurm Ants, Genomes & Evolution ? y.wurm at qmul.ac.uk ? skype:yannickwurm ? +44 207 882 3049 5.03A Fogg ? School of Biological & Chemical Sciences ? Queen Mary, University of London ? Mile End Road ? E1 4NX London ? UK From marian.povolny at gmail.com Thu Feb 23 15:03:53 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Thu, 23 Feb 2012 21:03:53 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: Message-ID: > > > BioRuby developers could be ?redirected? to biogems.info/tutorial or > incorporate it into the site. If I remember correctly Jan wrote guide lines > on howto use git for developing bioruby, that kind of docs could be used as > inspiration for the new docs. > > > http://saaientist.blogspot.com/2008/06/bioruby-with-git-how-would-that-work.html > > http://nsaunders.wordpress.com/2011/08/05/bioruby-development-feedback-on-using-git/ > http://lists.open-bio.org/pipermail/bioruby/2008-September/000700.html > > That sounds like a page for potential contributors, with instructions on how to contribute. That should definitely be a part of the new website. Is there anything else the active developers could use in their development effort, or maybe something to stay in touch with the community and what are others doing? Any ideas? Or is the ML doing a good job? I would also like to see a similar page like the GSoC page on wiki, but incorporated into the new site, maybe even with a link like "Need a challenge?" on the front page, or the page for contributors. The purpose would be to list feature descriptions that somebody would like to see implemented but has no time to do it, but still would be available for some mentoring. I can see myself handing out the link to my future students which would like to learn more, or get some experience while doing something useful. Would anybody in the developer community be interested in supporting something like this? Or would the mentoring part be too much work? -- Marjan Povolni From bonnal at ingm.org Fri Feb 24 02:37:50 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 24 Feb 2012 08:37:50 +0100 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: <11659791-F673-4D2B-B444-EB6A47ABB326@unil.ch> Message-ID: On 23/02/12 19.37, "Yannick Wurm" wrote: > On 23 Feb 2012, at 17:00, bioruby-request at lists.open-bio.org wrote: > George > have summarised some of the points raised during irc meeting: > here at > http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling > > About :" support > example code snippets that can be run from the browser > * it would be great > if we had a set of tutorials that users can follow in > the browser" > A > starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I > think > Katayama did it. Apologies for chiming in a bit late. I fully agree that > having something along these lines set up can greatly facilitate bioruby > adoption. * people should be able to test it without having to install > anything. (I recently tried running the BioRubyOnRails & failed). * It was developed a long time ago and Ror is great but life time cycle of each release is very short. >* making it idiot-proof (e.g. having an "upload flatfile" > button... and then autogenerating the appropriate file loading code) can help > further... Good point we could also present a set of tutorials/docs related with the file type uploaded: ok you uploaded this filetime and now the related docs is 1,2,3,4...n From bonnal at ingm.org Fri Feb 24 02:51:01 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 24 Feb 2012 08:51:01 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: Message-ID: +1 Mentoring is not too much work if the mentor has interest :-) I would call that page ?BioRuby Lab?. In this page I would rank the projects accomplished, these projects could be used by universities to offer stages for students (Francesco and Me, we are doing in this way) I?d like to have a page with the developers with an image and brief description of his/her research/interest with all contact information (twitter,email,irc,skype,G+). On 23/02/12 21.03, "Marjan Povolni" wrote: >> >> BioRuby developers could be ?redirected? to biogems.info/tutorial >> or incorporate it into the site. If I >> remember correctly Jan wrote guide lines on howto use git for developing >> bioruby, that kind of docs could be used as inspiration for the new docs. >> >> http://saaientist.blogspot.com/2008/06/bioruby-with-git-how-would-that-work.h >> tml >> http://nsaunders.wordpress.com/2011/08/05/bioruby-development-feedback-on-usi >> ng-git/ >> http://lists.open-bio.org/pipermail/bioruby/2008-September/000700.html >> > ? > That sounds like a page for potential contributors, with instructions on how > to contribute. That should definitely be a part of the new website. > > Is there anything else the active developers could use in their development > effort, or maybe something to stay in touch with the community and what are > others doing? Any ideas? Or is the ML doing a good job?? > > I would also like to see a similar page like the GSoC page on wiki, but > incorporated into the new site, maybe even with a link like "Need a > challenge?" on the front page, or the page for contributors. The purpose would > be to list feature descriptions that somebody would like to see implemented > but has no time to do it, but still would be available for some mentoring. I > can see myself handing out the link to my future students which would like to > learn more, or get some experience while doing something useful. Would anybody > in the developer community be interested in supporting something like this? Or > would the mentoring part be too much work? > > -- > Marjan Povolni > From bonnal at ingm.org Fri Feb 24 02:59:31 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 24 Feb 2012 08:59:31 +0100 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: <11659791-F673-4D2B-B444-EB6A47ABB326@unil.ch> Message-ID: ++1 On 23/02/12 19.37, "Yannick Wurm" wrote: > * making it idiot-proof This is a key point, user experience is everything. From pjotr.public14 at thebird.nl Fri Feb 24 11:11:11 2012 From: pjotr.public14 at thebird.nl (pjotr.public14 at thebird.nl) Date: Fri, 24 Feb 2012 17:11:11 +0100 Subject: [BioRuby] New age BioRuby Message-ID: <20120224161111.GB18826@thebird.nl> Hi everyone, We are happy to announce a new age BioRuby. This is BioRuby in the broadest sense, which includes gems and web presence. As a group, we have decided to take BioRuby into a new age, and change the way we approach community and newcomers. This we will do at four levels: (1) Democracy First of all, for new age BioRuby the decision making process will be transparent and democratic. To guard the democratic process we are forming a panel of active major BioRuby committers, including Pjotr, Raoul and Francesco. The panel will act as a monitor. Other active major BioRuby and biogem committers are welcome to join the panel. (2) Web presence The web presence needs to change to appeal to a new generation of coders. We are committed to changing that. (3) BioRuby gems The recently published Biogem system has introduced the plug-in approach and we think has a natural evolving process that BioRuby needs to be adapted for the new generation of tools. We will take on moving functionality into gems, creating a modular setup, and reducing the existing BioRuby source to a skeleton framework. The old BioRuby will continue to exist for reasons of backward compatibility. Until someone else is elected by the community, the panel will be responsible for the new BioRuby code base, and Pjotr will be in charge of coordinating the effort. (4) New talent The new age of BioRuby is really about nurturing new talent. This means giving away responsibilities to the next generation. We will rotate leadership for projects on a regular basis. To achieve our ends we will put together a VISION statement for BioRuby, as well as a road map. Pj, Ra & Fra From ktym at hgc.jp Fri Feb 24 17:34:48 2012 From: ktym at hgc.jp (Toshiaki Katayama) Date: Sat, 25 Feb 2012 07:34:48 +0900 Subject: [BioRuby] New age BioRuby In-Reply-To: <20120224161111.GB18826@thebird.nl> References: <20120224161111.GB18826@thebird.nl> Message-ID: <44451BFF-5016-4BAB-98F5-49166C57985C@hgc.jp> Hello Pjotr, I felt your recent statements sent to me and on this list were not fair. I believe everyone naturally has rights and freedom to try any changes on the code base. You can propose it when you implemented. You can also propose new web site candidate when it is ready. I have been a web maintainer for the historical reasons (as I paid for past 10 years and maintained the computer resources in my institution and on the open-bio.org). I tried to cover all aspects of the BioRuby related web resources when I designed the current site. I can admit we need to update the site and happy to see the alternative candidates, but I personally think what actually we need is not that superficial but the contents which kindly describes the usage of the BioRuby for scientific purposes (and future plans, maybe). The founder of the BioRuby had been responsible on the functionality and stability of the BioRuby over 10 years and have never been non-democratic. We welcomed contributors like you and gave privileges as a committer. However, you had never committed the process of the release management which actually is a hard and sometimes painful task. Dr. Goto has been done a great job on this as a release manager for many years as he understand all modules in the BioRuby code base so that he could pay careful attention to keep the library very stable and also to keep backward compatibilities. I respect him as he has been an only person who dedicated on this procedure because no one else have volunteered for the task until now. We invited you to Japan and discussed many aspects of the BioRuby which finally resulted as the Biogem system. Before we get there, we started from open CVS repository then moved to SVN but both still had some barrier to join the development process, therefore we moved to the GitHub so that everyone can fork and contribute without any privileges given in advance. (Other Open Bio* groups followed the same way.) This means real democracy had been maintained as much as we can. Finally, with Biogem, anyone can develop and release bioinformatics modules without bothered by the release cycle of the stable core. I believe that this system was a milestone where most democratic development process had been firstly introduced among the Open Bio* projects. Given said that, I don't intend to block your motivations to make the BioRuby better. Rather, I hope you to push your plans in a fruitful way. I just wish that people on this list won't misunderstand the founders of this project wrongly. We had paid tons of efforts to cross the chasm as innovators. We may already have reached the early majority stage with the help of early adopters like you and good others on this list. If so, now is the time to change the scene as you described. I may have missed several mails recently posted on this list or sent personally to me as I had been quite busy. Sorry about that. Despite the long message of this mail, it is easy for me to catch up with short e-mails, basically. Thanks. ;) P.S. I have several plans to develop (Bio)Ruby/Rails or Node.js based semantic DB applications starting from this spring. Is there anyone who are interested in to work with us in Japan? We may be able to employ some developers. Regards, Toshiaki Katayama On 2012/02/25, at 1:11, pjotr.public14 at thebird.nl wrote: > Hi everyone, > > We are happy to announce a new age BioRuby. This is BioRuby in the > broadest sense, which includes gems and web presence. As a group, we > have decided to take BioRuby into a new age, and change the way we > approach community and newcomers. This we will do at four levels: > > > (1) Democracy > > First of all, for new age BioRuby the decision making process will be > transparent and democratic. To guard the democratic process we are > forming a panel of active major BioRuby committers, including Pjotr, > Raoul and Francesco. The panel will act as a monitor. Other active > major BioRuby and biogem committers are welcome to join the panel. > > > (2) Web presence > > The web presence needs to change to appeal to a new generation of > coders. We are committed to changing that. > > > (3) BioRuby gems > > The recently published Biogem system has introduced the plug-in > approach and we think has a natural evolving process that BioRuby > needs to be adapted for the new generation of tools. We will take on > moving functionality into gems, creating a modular setup, and reducing > the existing BioRuby source to a skeleton framework. The old BioRuby > will continue to exist for reasons of backward compatibility. Until > someone else is elected by the community, the panel will be > responsible for the new BioRuby code base, and Pjotr will be in charge > of coordinating the effort. > > > (4) New talent > > The new age of BioRuby is really about nurturing new talent. This > means giving away responsibilities to the next generation. We will > rotate leadership for projects on a regular basis. > > To achieve our ends we will put together a VISION statement for > BioRuby, as well as a road map. > > > Pj, Ra & Fra > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Fri Feb 24 18:51:13 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 24 Feb 2012 23:51:13 +0000 Subject: [BioRuby] Nightly build testing Message-ID: Hello all, My apologies, the buildbot server has been offline over a week. It had run out of disk space (too many log files), solved now: http://testing.open-bio.org/bioruby/ I intend to setup a Windows XP (32bit) machine as another build slave next week - there was a permissions problem running the BioRuby tests under Windows but that was fixed. Regards, Peter P.S. Who should the failure emails be sent to? Initially at least there may be quite a few - so this mailing list does not seem appropriate: http://lists.open-bio.org/pipermail/bioruby/2011-December/001996.html From pjotr.public14 at thebird.nl Sat Feb 25 03:18:36 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 25 Feb 2012 09:18:36 +0100 Subject: [BioRuby] New age BioRuby In-Reply-To: <44451BFF-5016-4BAB-98F5-49166C57985C@hgc.jp> References: <20120224161111.GB18826@thebird.nl> <44451BFF-5016-4BAB-98F5-49166C57985C@hgc.jp> Message-ID: <20120225081836.GB24046@thebird.nl> On Sat, Feb 25, 2012 at 07:34:48AM +0900, Toshiaki Katayama wrote: > Hello Pjotr, > > I felt your recent statements sent to me and on this list were not > fair. I believe everyone naturally has rights and freedom to try > any changes on the code base. You can propose it when you > implemented. You can also propose new web site candidate when it is > ready. I have been a web maintainer for the historical reasons (as I > paid for past 10 years and maintained the computer resources in my > institution and on the open-bio.org). I tried to cover all aspects > of the BioRuby related web resources when I designed the current > site. I can admit we need to update the site and happy to see the > alternative candidates, but I personally think what actually we need > is not that superficial but the contents which kindly describes the > usage of the BioRuby for scientific purposes (and future plans, > maybe). > > The founder of the BioRuby had been responsible on the functionality > and stability of the BioRuby over 10 years and have never been > non-democratic. We welcomed contributors like you and gave > privileges as a committer. However, you had never committed the > process of the release management which actually is a hard and > sometimes painful task. Dr. Goto has been done a great job on this > as a release manager for many years as he understand all modules in > the BioRuby code base so that he could pay careful attention to keep > the library very stable and also to keep backward compatibilities. > I respect him as he has been an only person who dedicated on this > procedure because no one else have volunteered for the task until > now. > > We invited you to Japan and discussed many aspects of the BioRuby > which finally resulted as the Biogem system. Before we get there, we > started from open CVS repository then moved to SVN but both still > had some barrier to join the development process, therefore we moved > to the GitHub so that everyone can fork and contribute without any > privileges given in advance. (Other Open Bio* groups followed the > same way.) This means real democracy had been maintained as much as > we can. Finally, with Biogem, anyone can develop and release > bioinformatics modules without bothered by the release cycle of the > stable core. I believe that this system was a milestone where most > democratic development process had been firstly introduced among the > Open Bio* projects. > > Given said that, I don't intend to block your motivations to make > the BioRuby better. Rather, I hope you to push your plans in a > fruitful way. > > I just wish that people on this list won't misunderstand the > founders of this project wrongly. We had paid tons of efforts to > cross the chasm as innovators. I think no one on this list disagrees with the above. I would be the last one not to recognize your and Naohisa's inputs and achievements. I thank you for inviting us to Japan, for encouraging plugins. And basically I thank you for being you. I hope that is clear enough. > We may already have reached the early majority stage with the help > of early adopters like you and good others on this list. If so, now > is the time to change the scene as you described. We as BioRuby have been innovative, and attract some really good people. We should continue pushing for innovation, including the processes that encourage innovation. Also, it is very important that people who put in a lot of energy get the right credit for their work, and get encouraged to keep putting in a lot of work. We have erected a panel to ascertain that we continue the line of innovation, including total encouragement to new comers and old hands. That takes a lot of time and energy, and needs total commitment. By erecting the panel we have *committed* ourselves. Together with you we can define the exact remit of the panel. In fact, you should be on the panel. In my opinion the remit of the panel is to ascertain the code base, chosen technologies, website, web presence etc. represent the interests of the community. I am not saying it was not handled properly before, but I am saying it can be improved. By having a body of dedicated people, and open discussion, we can move forward. We also have to think about developing leadership. You have been doing this job for over 10 years. I don't expect you to think you will be project leader in another 10 year's time. Personally I think no one should be leading for a really long time. People get very busy - which is a natural progression in science. The panel should put the processes in place to nurture new leadership. The first job of the panel is to exactly define its remit for the coming years. We have made a start in that earlier announcement. Thanks for response Toshiaki. We all have the interest of BioRuby at heart, so let's keep on innovating and keep BioRuby going as the most exciting Bio* project! Pj. From pjotr.public14 at thebird.nl Sat Feb 25 03:42:00 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 25 Feb 2012 09:42:00 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: <20120225084200.GA28069@thebird.nl> ## Vision statement: BioRuby is agile The Ruby community is always working on agile processes. BioRuby can benefit from behaviour driven development (BDD), specifications, doctests and integration and unit testing. Realisation: In addition to unit testing we should concentrate on introducing Rspec, Cucumber, rubydoctests across the board. Also we should use the continuous integration testing by services such as travis-ci (I have a writeup on the latter soon) and perhaps use the OBF test services for stable plugins. From bonnal at ingm.org Sat Feb 25 04:16:21 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 25 Feb 2012 10:16:21 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120225084200.GA28069@thebird.nl> Message-ID: +1 On 25/02/12 09.42, "Pjotr Prins" wrote: > ## Vision statement: BioRuby is agile > > The Ruby community is always working on agile processes. BioRuby can > benefit from behaviour driven development (BDD), specifications, > doctests and integration and unit testing. > > Realisation: > > In addition to unit testing we should concentrate on introducing > Rspec, Cucumber, rubydoctests across the board. Also we should use the > continuous integration testing by services such as travis-ci (I have a > writeup on the latter soon) and perhaps use the OBF test services for > stable plugins. From p.j.a.cock at googlemail.com Sat Feb 25 04:35:31 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 25 Feb 2012 09:35:31 +0000 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120225084200.GA28069@thebird.nl> Message-ID: On Saturday, February 25, 2012, Raoul Bonnal wrote: > +1 > > > On 25/02/12 09.42, "Pjotr Prins" > > wrote: > > > ## Vision statement: BioRuby is agile > > > > The Ruby community is always working on agile processes. BioRuby can > > benefit from behaviour driven development (BDD), specifications, > > doctests and integration and unit testing. > > > > Realisation: > > > > In addition to unit testing we should concentrate on introducing > > Rspec, Cucumber, rubydoctests across the board. Also we should use the > > continuous integration testing by services such as travis-ci (I have a > > writeup on the latter soon) and perhaps use the OBF test services for > > stable plugins. > Without an extensive testing process like this, I struggle to see how a dynamic range of plugins from different authors can keep interoperability - so this sounds good. As we've discussed, the buildbot system as we're using it on the OBF testing service is more suited to testing one code base under a single repository. So another +1 for looking at automated testing of all the biogem packages. It will be a lot of work though... But should pay off :) Peter From georgkam at gmail.com Sat Feb 25 05:15:20 2012 From: georgkam at gmail.com (George Githinji) Date: Sat, 25 Feb 2012 13:15:20 +0300 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120225084200.GA28069@thebird.nl> Message-ID: +1 On Sat, Feb 25, 2012 at 12:35 PM, Peter Cock wrote: > On Saturday, February 25, 2012, Raoul Bonnal wrote: > >> +1 >> >> >> On 25/02/12 09.42, "Pjotr Prins" > >> wrote: >> >> > ## Vision statement: BioRuby is agile >> > >> > The Ruby community is always working on agile processes. BioRuby can >> > benefit from behaviour driven development (BDD), specifications, >> > doctests and integration and unit testing. >> > >> > Realisation: >> > >> > In addition to unit testing we should concentrate on introducing >> > Rspec, Cucumber, rubydoctests across the board. Also we should use the >> > continuous integration testing by services such as travis-ci (I have a >> > writeup on the latter soon) and perhaps use the OBF test services for >> > stable plugins. >> > > Without an extensive testing process like this, I struggle to see > how a dynamic range of plugins from different authors can keep > interoperability - so this sounds good. As we've discussed, the > buildbot system as we're using it on the OBF testing service is > more suited to testing one code base under a single repository. > > So another +1 for looking at automated testing of all the biogem > packages. It will be a lot of work though... But should pay off :) > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From bonnal at ingm.org Sat Feb 25 08:49:03 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 25 Feb 2012 14:49:03 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: Message-ID: Something we need and I need to figure out how to do is, check the plugins? interdependencies/dependencies and notify to the author, ml or the web site the need to update them; maybe would be useful to test the plugin with upgraded dependencies and let that know to the developers. This would be useful because gems are updated frequently and if the developer maintains a lot of plugins it?s a mess follow everything ( at least for me). PS: If you need to mirror the test bots I can see if there are machines available here, do they require a lot of resources ? On 25/02/12 10.35, "Peter Cock" wrote: > > > On Saturday, February 25, 2012, Raoul Bonnal wrote: >> +1 >> >> >> On 25/02/12 09.42, "Pjotr Prins" > >> wrote: >> >>> > ## Vision statement: BioRuby is agile >>> > >>> > The Ruby community is always working on agile processes. BioRuby can >>> > benefit from behaviour driven development (BDD), specifications, >>> > doctests and integration and unit testing. >>> > >>> > Realisation: >>> > >>> > In addition to unit testing we should concentrate on introducing >>> > Rspec, Cucumber, rubydoctests across the board. Also we should use the >>> > continuous integration testing by services such as travis-ci (I have a >>> > writeup on the latter soon) and perhaps use the OBF test services for >>> > stable plugins. > ? > Without an extensive testing process like this, I struggle to see > how a dynamic range of plugins from different authors can keep > interoperability - so this sounds good. As we've discussed, the > buildbot system as we're using it on the OBF testing service is > more?suited to testing one code base under a single repository. > > So another +1 for looking at automated testing of all the biogem > packages. It will be a lot of work though... But should pay off :) > > Peter > From bonnal at ingm.org Sat Feb 25 11:41:16 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 25 Feb 2012 17:41:16 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: Message-ID: Found a candidate https://gemnasium.com/ On 25/02/12 14.49, "Raoul Bonnal" wrote: > Something we need and I need to figure out how to do is, check the > plugins? interdependencies/dependencies and notify to the author, ml or the > web site the need to update them; maybe would be useful to test the plugin > with upgraded dependencies and let that know to the developers. This would > be useful because gems are updated frequently and if the developer maintains > a lot of plugins it?s a mess follow everything ( at least for me). > > PS: If you need to mirror the test bots I can see if there are machines > available here, do they require a lot of resources ? > > > On 25/02/12 10.35, "Peter Cock" wrote: > >> >> >> On Saturday, February 25, 2012, Raoul Bonnal wrote: >>> +1 >>> >>> >>> On 25/02/12 09.42, "Pjotr Prins" > >>> wrote: >>> >>>>> ## Vision statement: BioRuby is agile >>>>> >>>>> The Ruby community is always working on agile processes. BioRuby can >>>>> benefit from behaviour driven development (BDD), specifications, >>>>> doctests and integration and unit testing. >>>>> >>>>> Realisation: >>>>> >>>>> In addition to unit testing we should concentrate on introducing >>>>> Rspec, Cucumber, rubydoctests across the board. Also we should use the >>>>> continuous integration testing by services such as travis-ci (I have a >>>>> writeup on the latter soon) and perhaps use the OBF test services for >>>>> stable plugins. >> ? >> Without an extensive testing process like this, I struggle to see >> how a dynamic range of plugins from different authors can keep >> interoperability - so this sounds good. As we've discussed, the >> buildbot system as we're using it on the OBF testing service is >> more?suited to testing one code base under a single repository. >> >> So another +1 for looking at automated testing of all the biogem >> packages. It will be a lot of work though... But should pay off :) >> >> Peter >> > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From francesco.strozzi at gmail.com Sat Feb 25 12:43:23 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Sat, 25 Feb 2012 18:43:23 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: Message-ID: Seems very nice and has a direct integration with Github +1 On Sat, Feb 25, 2012 at 17:41, Raoul Bonnal wrote: > Found a candidate https://gemnasium.com/ > > > On 25/02/12 14.49, "Raoul Bonnal" wrote: > > > Something we need and I need to figure out how to do is, check the > > plugins? interdependencies/dependencies and notify to the author, ml or > the > > web site the need to update them; maybe would be useful to test the > plugin > > with upgraded dependencies and let that know to the developers. This > would > > be useful because gems are updated frequently and if the developer > maintains > > a lot of plugins it?s a mess follow everything ( at least for me). > > > > PS: If you need to mirror the test bots I can see if there are machines > > available here, do they require a lot of resources ? > > > > > > On 25/02/12 10.35, "Peter Cock" wrote: > > > >> > >> > >> On Saturday, February 25, 2012, Raoul Bonnal wrote: > >>> +1 > >>> > >>> > >>> On 25/02/12 09.42, "Pjotr Prins" > > >>> wrote: > >>> > >>>>> ## Vision statement: BioRuby is agile > >>>>> > >>>>> The Ruby community is always working on agile processes. BioRuby can > >>>>> benefit from behaviour driven development (BDD), specifications, > >>>>> doctests and integration and unit testing. > >>>>> > >>>>> Realisation: > >>>>> > >>>>> In addition to unit testing we should concentrate on introducing > >>>>> Rspec, Cucumber, rubydoctests across the board. Also we should use > the > >>>>> continuous integration testing by services such as travis-ci (I have > a > >>>>> writeup on the latter soon) and perhaps use the OBF test services for > >>>>> stable plugins. > >> > >> Without an extensive testing process like this, I struggle to see > >> how a dynamic range of plugins from different authors can keep > >> interoperability - so this sounds good. As we've discussed, the > >> buildbot system as we're using it on the OBF testing service is > >> more suited to testing one code base under a single repository. > >> > >> So another +1 for looking at automated testing of all the biogem > >> packages. It will be a lot of work though... But should pay off :) > >> > >> Peter > >> > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From pjotr.public14 at thebird.nl Sat Feb 25 13:00:07 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 25 Feb 2012 19:00:07 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: Message-ID: <20120225180006.GA29616@thebird.nl> Lots of new projects listed by some fstrozzi ;j On Sat, Feb 25, 2012 at 06:43:23PM +0100, Francesco Strozzi wrote: > Seems very nice and has a direct integration with Github > > +1 > > On Sat, Feb 25, 2012 at 17:41, Raoul Bonnal wrote: > > > Found a candidate https://gemnasium.com/ > > > > > > On 25/02/12 14.49, "Raoul Bonnal" wrote: > > > > > Something we need and I need to figure out how to do is, check the > > > plugins? interdependencies/dependencies and notify to the author, ml or > > the > > > web site the need to update them; maybe would be useful to test the > > plugin > > > with upgraded dependencies and let that know to the developers. This > > would > > > be useful because gems are updated frequently and if the developer > > maintains > > > a lot of plugins it?s a mess follow everything ( at least for me). > > > > > > PS: If you need to mirror the test bots I can see if there are machines > > > available here, do they require a lot of resources ? > > > > > > > > > On 25/02/12 10.35, "Peter Cock" wrote: > > > > > >> > > >> > > >> On Saturday, February 25, 2012, Raoul Bonnal wrote: > > >>> +1 > > >>> > > >>> > > >>> On 25/02/12 09.42, "Pjotr Prins" > > > >>> wrote: > > >>> > > >>>>> ## Vision statement: BioRuby is agile > > >>>>> > > >>>>> The Ruby community is always working on agile processes. BioRuby can > > >>>>> benefit from behaviour driven development (BDD), specifications, > > >>>>> doctests and integration and unit testing. > > >>>>> > > >>>>> Realisation: > > >>>>> > > >>>>> In addition to unit testing we should concentrate on introducing > > >>>>> Rspec, Cucumber, rubydoctests across the board. Also we should use > > the > > >>>>> continuous integration testing by services such as travis-ci (I have > > a > > >>>>> writeup on the latter soon) and perhaps use the OBF test services for > > >>>>> stable plugins. > > >> > > >> Without an extensive testing process like this, I struggle to see > > >> how a dynamic range of plugins from different authors can keep > > >> interoperability - so this sounds good. As we've discussed, the > > >> buildbot system as we're using it on the OBF testing service is > > >> more suited to testing one code base under a single repository. > > >> > > >> So another +1 for looking at automated testing of all the biogem > > >> packages. It will be a lot of work though... But should pay off :) > > >> > > >> Peter > > >> > > > > > > > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > > Francesco > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Sat Feb 25 17:45:23 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 25 Feb 2012 22:45:23 +0000 Subject: [BioRuby] Developing a VISION In-Reply-To: References: Message-ID: On Sat, Feb 25, 2012 at 1:49 PM, Raoul Bonnal wrote: > > PS: If you need to mirror the test bots I can see if there are machines > available here, do they require a lot of resources ? > Yes, more buildslave machines would be good, and the load isn't very high. We should probably move this to a new thread (or resume one of the old ones). Peter From francesco.strozzi at gmail.com Mon Feb 27 04:38:58 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 27 Feb 2012 10:38:58 +0100 Subject: [BioRuby] Ruby VideoCasts Message-ID: Hi all, I've just discovered this nice index of some of the best videocasts talking about Ruby and Rails, all available in the same place and tagged by arguments. http://showmedo.com/videotutorials/ruby Cheers -- Francesco From pjotr.public14 at thebird.nl Mon Feb 27 04:55:25 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 10:55:25 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120225084200.GA28069@thebird.nl> Message-ID: <20120227095525.GA12126@thebird.nl> Continuous integration testing is very useful for biogems/plugins. The Ruby community has come up with travis-ci, which is integrated into github! Any time code is submitted to github, the automated testing on different platforms kicks in. Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 gem for integrated testing. See https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > +1 > > > On 25/02/12 09.42, "Pjotr Prins" wrote: > > > ## Vision statement: BioRuby is agile > > > > The Ruby community is always working on agile processes. BioRuby can > > benefit from behaviour driven development (BDD), specifications, > > doctests and integration and unit testing. > > > > Realisation: > > > > In addition to unit testing we should concentrate on introducing > > Rspec, Cucumber, rubydoctests across the board. Also we should use the > > continuous integration testing by services such as travis-ci (I have a > > writeup on the latter soon) and perhaps use the OBF test services for > > stable plugins. > > From bonnal at ingm.org Mon Feb 27 05:19:26 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 27 Feb 2012 11:19:26 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120227095525.GA12126@thebird.nl> Message-ID: Cool Pjotr, I could add this feature/tempalte to biogem I'll open an issue/request On 27/02/12 10.55, "Pjotr Prins" wrote: > Continuous integration testing is very useful for biogems/plugins. The > Ruby community has come up with travis-ci, which is integrated into > github! Any time code is submitted to github, the automated testing on > different platforms kicks in. > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > gem for integrated testing. See > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: >> +1 >> >> >> On 25/02/12 09.42, "Pjotr Prins" wrote: >> >>> ## Vision statement: BioRuby is agile >>> >>> The Ruby community is always working on agile processes. BioRuby can >>> benefit from behaviour driven development (BDD), specifications, >>> doctests and integration and unit testing. >>> >>> Realisation: >>> >>> In addition to unit testing we should concentrate on introducing >>> Rspec, Cucumber, rubydoctests across the board. Also we should use the >>> continuous integration testing by services such as travis-ci (I have a >>> writeup on the latter soon) and perhaps use the OBF test services for >>> stable plugins. >> >> From pjotr.public14 at thebird.nl Mon Feb 27 05:33:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 11:33:27 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120227095525.GA12126@thebird.nl> Message-ID: <20120227103327.GB12848@thebird.nl> Excellent idea. On Mon, Feb 27, 2012 at 11:19:26AM +0100, Raoul Bonnal wrote: > Cool Pjotr, I could add this feature/tempalte to biogem I'll open an > issue/request > > > On 27/02/12 10.55, "Pjotr Prins" wrote: > > > Continuous integration testing is very useful for biogems/plugins. The > > Ruby community has come up with travis-ci, which is integrated into > > github! Any time code is submitted to github, the automated testing on > > different platforms kicks in. > > > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > > gem for integrated testing. See > > > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > >> +1 > >> > >> > >> On 25/02/12 09.42, "Pjotr Prins" wrote: > >> > >>> ## Vision statement: BioRuby is agile > >>> > >>> The Ruby community is always working on agile processes. BioRuby can > >>> benefit from behaviour driven development (BDD), specifications, > >>> doctests and integration and unit testing. > >>> > >>> Realisation: > >>> > >>> In addition to unit testing we should concentrate on introducing > >>> Rspec, Cucumber, rubydoctests across the board. Also we should use the > >>> continuous integration testing by services such as travis-ci (I have a > >>> writeup on the latter soon) and perhaps use the OBF test services for > >>> stable plugins. > >> > >> > > From rob.syme at gmail.com Mon Feb 27 05:44:26 2012 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 27 Feb 2012 18:44:26 +0800 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120227103327.GB12848@thebird.nl> References: <20120227095525.GA12126@thebird.nl> <20120227103327.GB12848@thebird.nl> Message-ID: Very nice. Does this make the open-bio testing apparatus redundant (for our purposes)? -r On Feb 27, 2012 6:33 PM, "Pjotr Prins" wrote: > Excellent idea. > > On Mon, Feb 27, 2012 at 11:19:26AM +0100, Raoul Bonnal wrote: > > Cool Pjotr, I could add this feature/tempalte to biogem I'll open an > > issue/request > > > > > > On 27/02/12 10.55, "Pjotr Prins" wrote: > > > > > Continuous integration testing is very useful for biogems/plugins. The > > > Ruby community has come up with travis-ci, which is integrated into > > > github! Any time code is submitted to github, the automated testing on > > > different platforms kicks in. > > > > > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > > > gem for integrated testing. See > > > > > > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > > > > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > > >> +1 > > >> > > >> > > >> On 25/02/12 09.42, "Pjotr Prins" wrote: > > >> > > >>> ## Vision statement: BioRuby is agile > > >>> > > >>> The Ruby community is always working on agile processes. BioRuby can > > >>> benefit from behaviour driven development (BDD), specifications, > > >>> doctests and integration and unit testing. > > >>> > > >>> Realisation: > > >>> > > >>> In addition to unit testing we should concentrate on introducing > > >>> Rspec, Cucumber, rubydoctests across the board. Also we should use > the > > >>> continuous integration testing by services such as travis-ci (I have > a > > >>> writeup on the latter soon) and perhaps use the OBF test services for > > >>> stable plugins. > > >> > > >> > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Mon Feb 27 05:58:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 11:58:27 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120227095525.GA12126@thebird.nl> <20120227103327.GB12848@thebird.nl> Message-ID: <20120227105827.GA13537@thebird.nl> On Mon, Feb 27, 2012 at 06:44:26PM +0800, Rob Syme wrote: > Very nice. > Does this make the open-bio testing apparatus redundant (for our > purposes)? > -r For the biogems: yes, I think so. For the large BioRuby library, and perhaps a few meta-biogems (bio-core) the open-bio setup is very useful. Pj. From pjotr.public14 at thebird.nl Mon Feb 27 06:14:13 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 12:14:13 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120227095525.GA12126@thebird.nl> References: <20120225084200.GA28069@thebird.nl> <20120227095525.GA12126@thebird.nl> Message-ID: <20120227111413.GA13769@thebird.nl> bioruby-gff3-plugin now runs on ruby 1.8.7 ruby 1.9.2 jruby 1.9 mode rubinius 1.9 mode http://travis-ci.org/#!/pjotrp/bioruby-gff3-plugin the changes were in the tests only :). Tested without even installing Rubinius. This is almost miraculous stuff. You can see the power of the Travis Ruby stack - including webserver, rvm, vagrant etc. etc. I hope that Travis-ci will stay. Pj. On Mon, Feb 27, 2012 at 10:55:25AM +0100, Pjotr Prins wrote: > Continuous integration testing is very useful for biogems/plugins. The > Ruby community has come up with travis-ci, which is integrated into > github! Any time code is submitted to github, the automated testing on > different platforms kicks in. > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > gem for integrated testing. See > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > > +1 > > > > > > On 25/02/12 09.42, "Pjotr Prins" wrote: > > > > > ## Vision statement: BioRuby is agile > > > > > > The Ruby community is always working on agile processes. BioRuby can > > > benefit from behaviour driven development (BDD), specifications, > > > doctests and integration and unit testing. > > > > > > Realisation: > > > > > > In addition to unit testing we should concentrate on introducing > > > Rspec, Cucumber, rubydoctests across the board. Also we should use the > > > continuous integration testing by services such as travis-ci (I have a > > > writeup on the latter soon) and perhaps use the OBF test services for > > > stable plugins. > > > > > From pjotr.public14 at thebird.nl Mon Feb 27 06:55:44 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 12:55:44 +0100 Subject: [BioRuby] Travis-ci on biogems.info Message-ID: <20120227115544.GA14668@thebird.nl> Will pick up the Travis-ci build status: fail|passing|unknown. http://www.biogems.info/ (master branch of each repo only). Pj. From p.j.a.cock at googlemail.com Mon Feb 27 07:41:15 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 27 Feb 2012 12:41:15 +0000 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: > Hello all, > > There seems to have been a new test failure or regression in Linux 64 Ruby 1.9, > > Revision 48bd150a6180d59879872bd85dd95c7ddf1a19c0 passed, > http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/22/steps/test/logs/stdio > commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0 > Author: Naohisa Goto > Date: ? Tue Nov 22 17:32:23 2011 +0900 > Test bug fix: fixed incomplete Windows platform detection. > https://github.com/bioruby/bioruby/commit/48bd150a6180d59879872bd85dd95c7ddf1a19c0 > > Revision 688779e71a27e861fb01e07f816384561b8cfe45 failed, > http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/23/steps/test/logs/stdio > commit 688779e71a27e861fb01e07f816384561b8cfe45 > Author: Naohisa Goto > Date: ? Thu Nov 24 11:49:30 2011 +0900 > Rakefile: new tasks: test-all to run all tests, etc. > https://github.com/bioruby/bioruby/commit/688779e71a27e861fb01e07f816384561b8cfe45 > > ?1) Failure: > test_output_fasta(Bio::FuncTestSequenceOutputEMBL) > [/home/buildslave/BuildBot_BioRuby/lin1964/build/test/functional/bio/sequence/test_output_embl.rb:47]: > Exception raised: > <#>. > > I hope that helps and that someone can reproduce the failure locally. > If need be I can try to bisect the failure here. This issue doesn't happen on two other Ruby 1.9.3 machines (under Windows XP 32 bit, and a 32 bit Linux Machine). Can anyone else reproduce this, or might it be a problem specific to my 64 bit Linux machine? Peter From pjotr.public14 at thebird.nl Mon Feb 27 15:22:05 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 21:22:05 +0100 Subject: [BioRuby] GSoC 2012 Message-ID: <20120227202205.GA17212@thebird.nl> We have listed the following GSoC projects at http://www.open-bio.org/wiki/Google_Summer_of_Code - Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI - Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser (FFI?) - Adding social networking functionality to BioRuby.org - Update bio-images a plugin to represent bio-object with cool images - Update to the Ruby Ensembl API Feel free to comment. The BioRuby panel. From yannick.wurm at unil.ch Tue Feb 28 06:28:32 2012 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Tue, 28 Feb 2012 11:28:32 +0000 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: References: Message-ID: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> On 24 Feb 2012, at 07:59, Raoul Bonnal wrote: > ++1 > > On 23/02/12 19.37, "Yannick Wurm" wrote: >> * making it idiot-proof > This is a key point, user experience is everything. Thanks Raoul. Yes, I think there is still a lot of potential for idiot-proofing (or should one say biologist-proofing??) at all levels between biological stuff and machines (most interfaces of PCR machines, robots, online bio* forms suck *really* *bad*!). Getting ruby/apple/google minimalist philosophies into things can only make the world a better place :) Thats the kind of idea driving our approach with our blast server/wrapper http://www.sequenceserver.com (still a work in progress - e.g. hoping to elminate the necessity of choosing blast algorithms soon - http://goo.gl/nP8u8 ) Have you watched some noobs code? I was surprised to see that some biopython users new to programming don't actually ever execute whole scripts. Instead, they use the python shell... and copy-paste individual lines or blocks of code from their MS Word document. Similarly to the manner in which most run analyses in R. Going line by line & seeing where things screw up definitely reduces the initial hurdle. I wish I had known about 'Bioruby in the shell' when I started... >> * people should be able to test it without having to install >> anything. (I recently tried running the BioRubyOnRails & failed). > *It was developed a long time ago and Ror is great but life time cycle of > each release is very short. Sure I understand. Noob's don't. Thus if it doenst work out of the box as advertised one should make it work or get rid of it. Making it work everywhere is likely quite intense. The best compromise might be to remove the biorubyonrails from the documentation in its current form, and instead set up an online server that people can simply use (without local install). Cheers yannick ps: don't forget to show you use ruby in Mike Barton's http://bioinfsurvey.org/ Yannick Wurm Ants, Genomes & Evolution ? y.wurm at qmul.ac.uk ? skype:yannickwurm ? +44 207 882 3049 5.03A Fogg ? School of Biological & Chemical Sciences ? Queen Mary, University of London ? Mile End Road ? E1 4NX London ? UK From pjotr.public14 at thebird.nl Tue Feb 28 11:43:56 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 28 Feb 2012 17:43:56 +0100 Subject: [BioRuby] BioRuby.org website Message-ID: <20120228164356.GB22204@thebird.nl> In preparation of changing the BioRuby.org website, we are adding feature requests, in the form of cucumber features. See https://github.com/pjotrp/NA-BioRuby.org Feel free to add your own! Example from https://github.com/pjotrp/NA-BioRuby.org/blob/master/features/main-page.feature Feature: BioRuby.org main page The BioRuby project main page is the entry page for new comers to the project. This page should be informative, without information overload. It should invite people to 'jump right in'. Rob Syme made one nice example: http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling In this feature we describe scenarios for a visiting biologist, bioinformatician, and (non-bio) Ruby coder. Scenario: Visiting biologist Given I visit the main BioRuby.org page When I view the area for Biology Then I should see that Ruby is easy to learn And I should see that BioRuby gives me much functionality When I click the topic Then I should be taken to an area suitable for biologists Scenario: Visiting bioinformatician Given I visit the main BioRuby.org page When I view the area for Bioinformatics Then I should see that Ruby is easy to learn And I should see that BioRuby gives me much functionality And I should see that Ruby offers modularity and agility When I click the topic Then I should be taken to an area suitable for bioinformaticians Scenario: Visiting Ruby coder Given I visit the main BioRuby.org page When I view the area for coders Then I should see that Bioinformatics is exciting And I should see that BioRuby gives me much functionality When I click the topic Then I should be taken to an area suitable for Ruby coders From russell.whitaker at gmail.com Tue Feb 28 11:59:51 2012 From: russell.whitaker at gmail.com (Russell Whitaker) Date: Tue, 28 Feb 2012 08:59:51 -0800 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> References: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> Message-ID: On Tue, Feb 28, 2012 at 3:28 AM, Yannick Wurm wrote: > > Have you watched some noobs code? I was surprised to see that some biopython users > new to programming don't actually ever execute whole scripts. Instead, they use the python shell... > and copy-paste individual lines or blocks of code from their MS Word document. Similarly to the > manner in which most run analyses in R. > Going line by line & seeing where things screw up definitely reduces the initial hurdle. > I wish I had known about 'Bioruby in the shell' when I started... > This isn't only a practice of novices: I've been doing software construction for a couple of decades, and I explore code this way all the time, e.g. inspecting the state of objects in the interactive interpreter shell, determining the specific types of exceptions thrown in corner cases while writing TDD/BDD test cases in parallel, etc. These novices are intuitively using their code exploration tools to understand the mechanics of what they're doing. By the way, I prefer the term "novice" to "noob" or even "newbie": the tone of "noob" - intentionally or not - seems to imply a bit of condescension toward those early in their personal learning curves, and could be considered exclusionary. -- Russell Whitaker http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ http://www.linkedin.com/pub/russell-whitaker/0/b86/329 From yannick.wurm at unil.ch Tue Feb 28 17:43:16 2012 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Tue, 28 Feb 2012 22:43:16 +0000 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: References: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> Message-ID: On 28 Feb 2012, at 16:59, Russell Whitaker wrote: > By the way, I prefer the term "novice" to "noob" or even "newbie": the > tone of "noob" - intentionally or not - seems to imply a bit of condescension toward > those early in their personal learning curves, and could be considered exclusionary. Sorry, you're right. I was just trying to be young by forgetting that nobody said "noob" back when I was one :p From pjotr.public14 at thebird.nl Wed Feb 29 03:30:39 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 09:30:39 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120228164356.GB22204@thebird.nl> References: <20120228164356.GB22204@thebird.nl> Message-ID: <20120229083039.GA26459@thebird.nl> Feature: BioRuby.org main page beautiful code BioRuby is about beautiful code. The BioRuby main page should show rotating examples of beautiful code. Initially this will be static, eventually people can run it in a sand box. The example should come with a short description, which can be expanded on in separate pages. Scenario: Each page visit shows a new example of beautiful code Given I visit the main BioRuby.org page When I view the area which shows beautiful code Then I should see that Ruby is for beauty And I should see that BioRuby gives me much functionality Scenario: Under the example we display an explanation Given I see the beautiful code box Then I should see an explanation Scenario: Display a More info link Given I see the beautiful code box When I view the area which shows beautiful code Then I should see a 'More info' link And it takes me to the relevant page Scenario: Display a RUN button Given I see the beautiful code box When I view the area which shows beautiful code Then I should see a RUN button And it should execute the code Scenario: Display an EDIT button Given I see the beautiful code box When I view the area which shows beautiful code Then I should see an EDIT button And it should allow editing the code https://github.com/pjotrp/NA-BioRuby.org/blob/master/features/main-page-beautiful-code.feature From pjotr.public14 at thebird.nl Wed Feb 29 04:02:33 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 10:02:33 +0100 Subject: [BioRuby] BioRuby.org website Message-ID: <20120229090233.GB27695@thebird.nl> Feature: BioRuby.org main page direct answer section The BioRuby project main page is the entry page for new comers to the project. Visitors who are not (yet) on IRC or the mailing list, should be encouraged to post questions and receive immediate answers. One way to achieve this would be a Jabber connection to a 'room' where BioRuby members connect. Similar to IRC, but available directly from the main page. This chat will not be logged, so spammers will have no benefit. Scenario: BioRuby.org newbie visitor with a question Given I visit the main BioRuby.org page and someone is online When I click the button for contacting BioRuby And someone is online Then I should be able to post a question And get an answer Scenario: BioRuby.org newbie visitor with a question (2) Given I visit the main BioRuby.org page and no one is online When I click the button for contacting BioRuby And no one is online Then I should be able to post a question with an E-mail address And get an answer over E-mail https://github.com/pjotrp/NA-BioRuby.org/blob/master/features/main-page-direct-answers.feature From p.j.a.cock at googlemail.com Wed Feb 29 05:12:51 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 29 Feb 2012 10:12:51 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120229090233.GB27695@thebird.nl> References: <20120229090233.GB27695@thebird.nl> Message-ID: On Wed, Feb 29, 2012 at 9:02 AM, Pjotr Prins wrote: > Feature: BioRuby.org main page direct answer section > > ?The BioRuby project main page is the entry page for new comers to > ?the project. Visitors who are not (yet) on IRC or the mailing list, > ?should be encouraged to post questions and receive immediate > ?answers. One way to achieve this would be a Jabber connection to a > ?'room' where BioRuby members connect. Similar to IRC, but available > ?directly from the main page. This chat will not be logged, so > ?spammers will have no benefit. > > ?Scenario: BioRuby.org newbie visitor with a question > ? ?Given I visit the main BioRuby.org page and someone is online > ? ?When I click the button for contacting BioRuby > ? ?And someone is online > ? ?Then I should be able to post a question > ? ?And get an answer Could you embed an IRC client into the browser page? > ?Scenario: BioRuby.org newbie visitor with a question (2) > ? ?Given I visit the main BioRuby.org page and no one is online > ? ?When I click the button for contacting BioRuby > ? ?And no one is online > ? ?Then I should be able to post a question with an E-mail address > ? ?And get an answer over E-mail You don't think giving them instructions on how to join the mailing list is good enough? How would you implement that email form idea - keeping in mind the newcomer would reasonably expect their query to be 'private' and not be sent to the public mailing list on their behalf? Peter From pjotr.public14 at thebird.nl Wed Feb 29 09:54:43 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 15:54:43 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: References: <20120229090233.GB27695@thebird.nl> Message-ID: <20120229145443.GA28775@thebird.nl> On Wed, Feb 29, 2012 at 10:12:51AM +0000, Peter Cock wrote: > On Wed, Feb 29, 2012 at 9:02 AM, Pjotr Prins wrote: > > Feature: BioRuby.org main page direct answer section > > > > ?The BioRuby project main page is the entry page for new comers to > > ?the project. Visitors who are not (yet) on IRC or the mailing list, > > ?should be encouraged to post questions and receive immediate > > ?answers. One way to achieve this would be a Jabber connection to a > > ?'room' where BioRuby members connect. Similar to IRC, but available > > ?directly from the main page. This chat will not be logged, so > > ?spammers will have no benefit. > > > > ?Scenario: BioRuby.org newbie visitor with a question > > ? ?Given I visit the main BioRuby.org page and someone is online > > ? ?When I click the button for contacting BioRuby > > ? ?And someone is online > > ? ?Then I should be able to post a question > > ? ?And get an answer > > Could you embed an IRC client into the browser page? I suppose so. One problem is that our IRC gets logged. > > ?Scenario: BioRuby.org newbie visitor with a question (2) > > ? ?Given I visit the main BioRuby.org page and no one is online > > ? ?When I click the button for contacting BioRuby > > ? ?And no one is online > > ? ?Then I should be able to post a question with an E-mail address > > ? ?And get an answer over E-mail > > You don't think giving them instructions on how to join the mailing > list is good enough? How would you implement that email form > idea - keeping in mind the newcomer would reasonably expect > their query to be 'private' and not be sent to the public mailing > list on their behalf? Exactly. We will have a limited number of people who receive these. Privacy is key (I did not mention that), so people feel free to ask any question, and a low threshold. Glad someone is reading my stuff ;) Pj. From p.j.a.cock at googlemail.com Wed Feb 29 10:29:14 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 29 Feb 2012 15:29:14 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120229145443.GA28775@thebird.nl> References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> Message-ID: Pjotr wrote: >Peter wrote: >> Pjotr wrote: >> > ?Scenario: BioRuby.org newbie visitor with a question (2) >> > ? ?Given I visit the main BioRuby.org page and no one is online >> > ? ?When I click the button for contacting BioRuby >> > ? ?And no one is online >> > ? ?Then I should be able to post a question with an E-mail address >> > ? ?And get an answer over E-mail >> >> You don't think giving them instructions on how to join the mailing >> list is good enough? How would you implement that email form >> idea - keeping in mind the newcomer would reasonably expect >> their query to be 'private' and not be sent to the public mailing >> list on their behalf? > > Exactly. We will have a limited number of people who receive these. > > Privacy is key (I did not mention that), so people feel free to ask > any question, and a low threshold. > > Glad someone is reading my stuff ;) > > Pj. I can see why being able to ask questions "in private" might lower the barrier to entry, but you will need a dedicated (in the sense of committed) and patient team to handle those queries. Personally my preference is to encourage people to ask their questions on the mailing list in public (they can use a semi- anonymous email address if they like, assuming it doesn't get flagged as spam - I used to myself once). This means the entire development team and all the other users would see the question and might help, but also the fact that it is open means the question will be searchable by Google etc, and can spark useful discussions. Sites like http://biostar.stackexchange.com/ work in a similar open way but are more question & answer focused. Based on the tag usage this isn't yet very popular with BioRuby folk: http://biostar.stackexchange.com/questions/tagged/bioruby Do you feel that for many people the potential embarrassment of asking a 'silly question' puts people off asking 'in public'? Peter From pjotr.public14 at thebird.nl Wed Feb 29 10:33:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 16:33:54 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> Message-ID: <20120229153354.GA29186@thebird.nl> On Wed, Feb 29, 2012 at 03:29:14PM +0000, Peter Cock wrote: > I can see why being able to ask questions "in private" might > lower the barrier to entry, but you will need a dedicated (in the > sense of committed) and patient team to handle those queries. Yes. That is one of the intended tasks for the BioRuby panel. We already are more present on IRC. > Personally my preference is to encourage people to ask their > questions on the mailing list in public (they can use a semi- > anonymous email address if they like, assuming it doesn't > get flagged as spam - I used to myself once). This means > the entire development team and all the other users would > see the question and might help, but also the fact that it is > open means the question will be searchable by Google etc, > and can spark useful discussions. > > Sites like http://biostar.stackexchange.com/ work in a similar > open way but are more question & answer focused. Based > on the tag usage this isn't yet very popular with BioRuby folk: > http://biostar.stackexchange.com/questions/tagged/bioruby > > Do you feel that for many people the potential embarrassment > of asking a 'silly question' puts people off asking 'in public'? All these channels are very useful. And used by many. I simply want new comers to come in, and ask 'Why is Ruby preferred over, say, Perl?' - rather than have them dig around, so we can offer them an opiniated reply ;). Question from my end: Why not try? I am very much in favour of experiments. It is my nature. Pj. From cjfields at illinois.edu Wed Feb 29 11:13:55 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 29 Feb 2012 16:13:55 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> Message-ID: <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> On Feb 29, 2012, at 9:29 AM, Peter Cock wrote: > Pjotr wrote: >> Peter wrote: >>> Pjotr wrote: >>>> Scenario: BioRuby.org newbie visitor with a question (2) >>>> Given I visit the main BioRuby.org page and no one is online >>>> When I click the button for contacting BioRuby >>>> And no one is online >>>> Then I should be able to post a question with an E-mail address >>>> And get an answer over E-mail >>> >>> You don't think giving them instructions on how to join the mailing >>> list is good enough? How would you implement that email form >>> idea - keeping in mind the newcomer would reasonably expect >>> their query to be 'private' and not be sent to the public mailing >>> list on their behalf? >> >> Exactly. We will have a limited number of people who receive these. >> >> Privacy is key (I did not mention that), so people feel free to ask >> any question, and a low threshold. >> >> Glad someone is reading my stuff ;) >> >> Pj. > > I can see why being able to ask questions "in private" might > lower the barrier to entry, but you will need a dedicated (in the > sense of committed) and patient team to handle those queries. > > Personally my preference is to encourage people to ask their > questions on the mailing list in public (they can use a semi- > anonymous email address if they like, assuming it doesn't > get flagged as spam - I used to myself once). This means > the entire development team and all the other users would > see the question and might help, but also the fact that it is > open means the question will be searchable by Google etc, > and can spark useful discussions. > > Sites like http://biostar.stackexchange.com/ work in a similar > open way but are more question & answer focused. Based > on the tag usage this isn't yet very popular with BioRuby folk: > http://biostar.stackexchange.com/questions/tagged/bioruby The BioPerl folks don't monitor it much either. We should be promoting it more. > Do you feel that for many people the potential embarrassment > of asking a 'silly question' puts people off asking 'in public'? > > Peter Peter, I think you hit the nail on the head; allowing people to contact you (or other devs) privately means there is no cross-benefit to others. It makes more sense to promote the avenues already present (biostar, mail list, web site, IRC, etc) and encourage users to both search for answers and submit questions there. As an example, even though I currently oversee bioperl I certainly didn't write all the code (and I certainly don't want that distinction :). I always redirect users to the mail list, to the point I may actually cc the list in my response. The community benefits. All bioperl code specifically mentions who wrote and maintains the code, where to send questions, etc, and it's very possible the actual author (very likely not me) will respond if the question is asked where it is promoted to be asked. Asking me directly will not benefit anyone beyond having me redirect the question to an actual useful forum. Re: 'experimenting with this': that's a possibility, but then you run the risk of opening avenues for users that might be shut down later. chris From pjotr.public14 at thebird.nl Wed Feb 29 12:20:26 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 18:20:26 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> Message-ID: <20120229172026.GA29664@thebird.nl> On Wed, Feb 29, 2012 at 04:13:55PM +0000, Fields, Christopher J wrote: > Re: 'experimenting with this': that's a possibility, but then you > run the risk of opening avenues for users that might be shut down > later. I don't see why everyone is overreacting. I am not proposing this as an alternative channel to the others you mention. It is just to provide direct access to the BioRuby authors. Very much like providing a phone or Skype number. Our normal response to a regular question would be to point users to IRC, the ML, stackexchange, whatever. Lowering all barriers to entry, without it costing too much, is our goal. If it turns out we get hammered with bad questions, or get irritated, or it does not work, we just shut it down. If it works and we get more people on IRC and our ML, everyone gains. Note btw that I am proposing this functionality, and others, will be made available to other Bio* projects. Pj. From cjfields at illinois.edu Wed Feb 29 13:02:09 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 29 Feb 2012 18:02:09 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120229172026.GA29664@thebird.nl> References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> <20120229172026.GA29664@thebird.nl> Message-ID: <5ECDDDAF-98B7-453D-8928-F5C0E1A49377@illinois.edu> On Feb 29, 2012, at 11:20 AM, Pjotr Prins wrote: > On Wed, Feb 29, 2012 at 04:13:55PM +0000, Fields, Christopher J wrote: >> Re: 'experimenting with this': that's a possibility, but then you >> run the risk of opening avenues for users that might be shut down >> later. > > I don't see why everyone is overreacting. I am not proposing this as > an alternative channel to the others you mention. It is just to > provide direct access to the BioRuby authors. Very much like providing > a phone or Skype number. Our normal response to a regular question > would be to point users to IRC, the ML, stackexchange, whatever. > > Lowering all barriers to entry, without it costing too much, is our > goal. If it turns out we get hammered with bad questions, or get > irritated, or it does not work, we just shut it down. If it works and > we get more people on IRC and our ML, everyone gains. > > Note btw that I am proposing this functionality, and others, will be > made available to other Bio* projects. > > Pj. That's fine, I'm not saying "don't do it", just that (based on experience) users can feel a little burned when something they expect to work no longer does, and that spending time on this vs. coding is a tricky balance. If enough devs in the community can chip in and keep it up, more power to you. chris From pjotr.public14 at thebird.nl Sun Feb 5 21:37:31 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 5 Feb 2012 22:37:31 +0100 Subject: [BioRuby] JRuby going to be way faster than MRI Message-ID: <20120205213731.GB20253@thebird.nl> Today I attended an interesting talk by Charles Nutter of JRuby fame at FOSDEM 2012. The short of it is that much of the work on JRuby is on performance and low level access to C libraries (through FFI)... http://blog.thebird.nl/ Pj. From pjotr.public14 at thebird.nl Wed Feb 8 18:48:17 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 8 Feb 2012 19:48:17 +0100 Subject: [BioRuby] A question for BioRuby newbies Message-ID: <20120208184817.GA31948@thebird.nl> Hi All, This mailing list counts 180 subscribed readers. Which is impressive. Also since the introduction of http://biogems.info/ the number of BioRuby downloads has increased rapidly. You may also have noticed Ruby, in general, is making its mark in bioinformatics. More and more people are programming in Ruby, which I think rather delightful. And Biogems.info is proving to be cutting edge, and accelerating development. So here is a question to people who read the mailing list, but do not necessarily participate. What is needed to pull you in? At this point I have two ideas to increase participation. (1) First a race. I would like all readers to vote a few times a year on the most beautiful Biogem source code. We'll put up a few projects to choose from, and the winner will be highlighted on http://biogems.info/. Ruby is about beauty, and we are seeing some of that in the biogems. The other idea I got at FOSDEM this year from a convincing talk by Brian Ostergard, titled 'You are doing it all wrong' http://fosdem.org/2012/schedule/event/really_grow_community where he made a strong case to address inexperienced developers. And you know what, I believe he is right. So (2) We will look for ways to get inexperienced developers involved. One way is to define uncomplicated and moderately complicated tasks, feature requests and bug fixes. We are going to list these 'jobs' on http://biogems.info/. If anyone picks up a task he/she will get very *strong* support from the plugin owner, as well as the Biogem maintainers. You, the programmer, will get all the credit for the work. How does this sound? Does this appeal to you? Anyone of the less experienced, or even experienced, wants to voice his or her opinion? We may even turn some work into a Google Summer of Code project proposal. Pj. From mail at michaelbarton.me.uk Wed Feb 8 20:52:57 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Wed, 8 Feb 2012 15:52:57 -0500 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208184817.GA31948@thebird.nl> References: <20120208184817.GA31948@thebird.nl> Message-ID: <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> I think this is a very good idea. More public engagement would be a boon to the BioRuby project. I would be happy to help new developers work on my Scaffolder gem. Here are two additional suggestions from me for increasing BioRuby participation. First suggestion: I think the bioruby home page could be made simpler. A very rough estimate shows 80 links on the front page: curl http://bioruby.open-bio.org/ | tidy -i -q | grep href | wc -> 80 links Compare this with the Rails and Sinatra homepages: curl http://rubyonrails.org/ | tidy -i -q | grep href | wc -> 47 links curl http://www.sinatrarb.com/ | tidy -i -q | grep href | wc -> 20 links I think making the homepage simpler would be very beneficial. For instance I think the two most important links (Tutorial and Sample codes) pages should be given much greater prominence. These are the two pages which most beginners will want to get started with. Compare with the Sinatra page which has only six links on the front page pointing to the most significant parts of the project. I think the Tutorial and Sample codes pages could do with some love also. These pages do not match the visual layout of the bioruby home page, one is in a separate domain while the other is a wiki page. I think these pages deserve attention to make them simpler and more accessible. A common CSS theme also provides a unified front to the BioRuby project. Compare with the Sinatra intro and documentation pages: * http://www.sinatrarb.com/intro * http://www.sinatrarb.com/documentation My opinion is that the BioRuby website should head in this direction. I am not a web designer but I am happy to contribute effort to writing web copy and BioRuby recipes. I also think that bioruby should also have its own web address too. Second Suggestion: I think as BioRuby becomes more and more popular the code base will continue to increase in size. I think this will become a disadvantage as a larger code base is harder to navigate, harder to maintain, and more intimidating to make contributions to. Pjotr has addressed this with the BioGems project but I think we should follow the natural progression and consider splitting the Bio gem into smaller self-contained gems. I think this is already starting to happen with the replacement gff3 and 'faster' fasta gems. I think smaller gems would be easier to maintain and allow different development cycles. I think it also easier to create a gem for a new idea rather than find a place for it in a large pre-existing code base. Finally this would follow the smaller 'does just one thing' gem development philosophy in Ruby. Michael Barton On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: > Hi All, > > This mailing list counts 180 subscribed readers. > Which is impressive. Also since the introduction of > http://biogems.info/ the number of BioRuby downloads has > increased rapidly. > > You may also have noticed Ruby, in general, is making > its mark in bioinformatics. More and more people are > programming in Ruby, which I think rather delightful. > And Biogems.info is proving to be cutting edge, and > accelerating development. > > So here is a question to people who read the mailing list, > but do not necessarily participate. What is needed to pull > you in? > > At this point I have two ideas to increase participation. > > (1) First a race. I would like all readers to vote a few > times a year on the most beautiful Biogem source code. > We'll put up a few projects to choose from, and the winner > will be highlighted on http://biogems.info/. Ruby is about > beauty, and we are seeing some of that in the biogems. > > The other idea I got at FOSDEM this year from a convincing > talk by Brian Ostergard, titled 'You are doing it all > wrong' > > http://fosdem.org/2012/schedule/event/really_grow_commun > ity > > where he made a strong case to address inexperienced > developers. And you know what, I believe he is right. So > > (2) We will look for ways to get inexperienced developers > involved. One way is to define uncomplicated and > moderately complicated tasks, feature requests and bug > fixes. > > We are going to list these 'jobs' on http://biogems.info/. > If anyone picks up a task he/she will get very *strong* > support from the plugin owner, as well as the Biogem > maintainers. You, the programmer, will get all the credit > for the work. > > How does this sound? Does this appeal to you? Anyone of > the less experienced, or even experienced, wants to voice > his or her opinion? We may even turn some work into a > Google Summer of Code project proposal. > > Pj. _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mictadlo at gmail.com Wed Feb 8 22:38:08 2012 From: mictadlo at gmail.com (Mic) Date: Thu, 9 Feb 2012 08:38:08 +1000 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> Message-ID: Hi all, It would be great if BioRuby/Ruby would have: * a good BAM/tabix/vcf support * a gff3 support which doesn't read the whole file in the memory see http://biopython.org/wiki/GFF_Parsing#Limiting_to_features_of_interest * http://www.scipy.org/ * a powerful chart library like http://matplotlib.sourceforge.net/ * http://networkx.lanl.gov/ Maybe Google Summer of Code 2012 could help. On Thu, Feb 9, 2012 at 6:52 AM, Michael Barton wrote: > I think this is a very good idea. More public engagement > would be a boon to the BioRuby project. I would be happy to > help new developers work on my Scaffolder gem. Here are two > additional suggestions from me for increasing BioRuby > participation. > > First suggestion: > > I think the bioruby home page could be made simpler. A very > rough estimate shows 80 links on the front page: > > curl http://bioruby.open-bio.org/ | tidy -i -q | grep href | wc > -> 80 links > > Compare this with the Rails and Sinatra homepages: > > curl http://rubyonrails.org/ | tidy -i -q | grep href | wc > -> 47 links > > curl http://www.sinatrarb.com/ | tidy -i -q | grep href | wc > -> 20 links > > I think making the homepage simpler would be very > beneficial. For instance I think the two most important > links (Tutorial and Sample codes) pages should be given much > greater prominence. These are the two pages which most > beginners will want to get started with. Compare with the > Sinatra page which has only six links on the front page > pointing to the most significant parts of the project. > > I think the Tutorial and Sample codes pages could do with > some love also. These pages do not match the visual layout > of the bioruby home page, one is in a separate domain while > the other is a wiki page. I think these pages deserve > attention to make them simpler and more accessible. A common > CSS theme also provides a unified front to the BioRuby > project. > > Compare with the Sinatra intro and documentation pages: > * http://www.sinatrarb.com/intro > * http://www.sinatrarb.com/documentation > > My opinion is that the BioRuby website should head in this > direction. I am not a web designer but I am happy to > contribute effort to writing web copy and BioRuby recipes. I > also think that bioruby should also have its own web address > too. > > Second Suggestion: > > I think as BioRuby becomes more and more popular the code > base will continue to increase in size. I think this will > become a disadvantage as a larger code base is harder to > navigate, harder to maintain, and more intimidating to make > contributions to. > > Pjotr has addressed this with the BioGems project but I > think we should follow the natural progression and consider > splitting the Bio gem into smaller self-contained gems. I > think this is already starting to happen with the > replacement gff3 and 'faster' fasta gems. > > I think smaller gems would be easier to maintain and allow > different development cycles. I think it also easier to > create a gem for a new idea rather than find a place for it > in a large pre-existing code base. Finally this would follow > the smaller 'does just one thing' gem development philosophy > in Ruby. > > Michael Barton > > On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: > > > Hi All, > > > > This mailing list counts 180 subscribed readers. > > Which is impressive. Also since the introduction of > > http://biogems.info/ the number of BioRuby downloads has > > increased rapidly. > > > > You may also have noticed Ruby, in general, is making > > its mark in bioinformatics. More and more people are > > programming in Ruby, which I think rather delightful. > > And Biogems.info is proving to be cutting edge, and > > accelerating development. > > > > So here is a question to people who read the mailing list, > > but do not necessarily participate. What is needed to pull > > you in? > > > > At this point I have two ideas to increase participation. > > > > (1) First a race. I would like all readers to vote a few > > times a year on the most beautiful Biogem source code. > > We'll put up a few projects to choose from, and the winner > > will be highlighted on http://biogems.info/. Ruby is about > > beauty, and we are seeing some of that in the biogems. > > > > The other idea I got at FOSDEM this year from a convincing > > talk by Brian Ostergard, titled 'You are doing it all > > wrong' > > > > http://fosdem.org/2012/schedule/event/really_grow_commun > > ity > > > > where he made a strong case to address inexperienced > > developers. And you know what, I believe he is right. So > > > > (2) We will look for ways to get inexperienced developers > > involved. One way is to define uncomplicated and > > moderately complicated tasks, feature requests and bug > > fixes. > > > > We are going to list these 'jobs' on http://biogems.info/. > > If anyone picks up a task he/she will get very *strong* > > support from the plugin owner, as well as the Biogem > > maintainers. You, the programmer, will get all the credit > > for the work. > > > > How does this sound? Does this appeal to you? Anyone of > > the less experienced, or even experienced, wants to voice > > his or her opinion? We may even turn some work into a > > Google Summer of Code project proposal. > > > > Pj. _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > From mictadlo at gmail.com Wed Feb 8 23:01:21 2012 From: mictadlo at gmail.com (Mic) Date: Thu, 9 Feb 2012 09:01:21 +1000 Subject: [BioRuby] EU-codefest in July In-Reply-To: <20120126103423.GA10234@thebird.nl> References: <20120126103423.GA10234@thebird.nl> Message-ID: HI Pjotr, Will be any videos of the talks available or are there any videos from year before available? Cheers, On Thu, Jan 26, 2012 at 8:34 PM, Pjotr Prins wrote: > EU-codefest 2012 will be 19 and 20 July in Lodi Italy > > In coordination with the BOSC committee we are organising the first > EU-Codefest, a low-key event the week after BOSC 2012. > > http://www.open-bio.org/wiki/EU_Codefest_2012 > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Thu Feb 9 09:04:22 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 09 Feb 2012 10:04:22 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: Message-ID: Hi Mic, On 08/02/12 23.38, "Mic" wrote: > Hi all, > It would be great if BioRuby/Ruby would have: > * a good BAM/tabix/vcf support About BAM: https://rubygems.org/gems/bio-samtools but any suggestion contribute or idea is more than welcome > * http://www.scipy.org/ > * a powerful chart library like http://matplotlib.sourceforge.net/ https://github.com/SciRuby/sciruby The developers are very active and some of them are working in bioinformatics, but they want to keep it separated from BioRuby because SciRuby can be useful for other purposes other than bioinformatics. There was a graphic library http://rubyvis.rubyforge.org/ (there was a GSoC project bio-images) now called http://mbostock.github.com/d3/ and another library which uses SVG is http://raphaeljs.com/ > * http://networkx.lanl.gov/ About network I don't know. > > Maybe Google Summer of Code 2012 could help. > > On Thu, Feb 9, 2012 at 6:52 AM, Michael Barton > wrote: > >> I think this is a very good idea. More public engagement >> would be a boon to the BioRuby project. I would be happy to >> help new developers work on my Scaffolder gem. Here are two >> additional suggestions from me for increasing BioRuby >> participation. >> >> First suggestion: >> >> I think the bioruby home page could be made simpler. A very >> rough estimate shows 80 links on the front page: >> >> curl http://bioruby.open-bio.org/ | tidy -i -q | grep href | wc >> -> 80 links >> >> Compare this with the Rails and Sinatra homepages: >> >> curl http://rubyonrails.org/ | tidy -i -q | grep href | wc >> -> 47 links >> >> curl http://www.sinatrarb.com/ | tidy -i -q | grep href | wc >> -> 20 links >> >> I think making the homepage simpler would be very >> beneficial. For instance I think the two most important >> links (Tutorial and Sample codes) pages should be given much >> greater prominence. These are the two pages which most >> beginners will want to get started with. Compare with the >> Sinatra page which has only six links on the front page >> pointing to the most significant parts of the project. >> >> I think the Tutorial and Sample codes pages could do with >> some love also. These pages do not match the visual layout >> of the bioruby home page, one is in a separate domain while >> the other is a wiki page. I think these pages deserve >> attention to make them simpler and more accessible. A common >> CSS theme also provides a unified front to the BioRuby >> project. >> >> Compare with the Sinatra intro and documentation pages: >> * http://www.sinatrarb.com/intro >> * http://www.sinatrarb.com/documentation >> >> My opinion is that the BioRuby website should head in this >> direction. I am not a web designer but I am happy to >> contribute effort to writing web copy and BioRuby recipes. I >> also think that bioruby should also have its own web address >> too. >> >> Second Suggestion: >> >> I think as BioRuby becomes more and more popular the code >> base will continue to increase in size. I think this will >> become a disadvantage as a larger code base is harder to >> navigate, harder to maintain, and more intimidating to make >> contributions to. >> >> Pjotr has addressed this with the BioGems project but I >> think we should follow the natural progression and consider >> splitting the Bio gem into smaller self-contained gems. I >> think this is already starting to happen with the >> replacement gff3 and 'faster' fasta gems. >> >> I think smaller gems would be easier to maintain and allow >> different development cycles. I think it also easier to >> create a gem for a new idea rather than find a place for it >> in a large pre-existing code base. Finally this would follow >> the smaller 'does just one thing' gem development philosophy >> in Ruby. >> >> Michael Barton >> >> On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: >> >>> Hi All, >>> >>> This mailing list counts 180 subscribed readers. >>> Which is impressive. Also since the introduction of >>> http://biogems.info/ the number of BioRuby downloads has >>> increased rapidly. >>> >>> You may also have noticed Ruby, in general, is making >>> its mark in bioinformatics. More and more people are >>> programming in Ruby, which I think rather delightful. >>> And Biogems.info is proving to be cutting edge, and >>> accelerating development. >>> >>> So here is a question to people who read the mailing list, >>> but do not necessarily participate. What is needed to pull >>> you in? >>> >>> At this point I have two ideas to increase participation. >>> >>> (1) First a race. I would like all readers to vote a few >>> times a year on the most beautiful Biogem source code. >>> We'll put up a few projects to choose from, and the winner >>> will be highlighted on http://biogems.info/. Ruby is about >>> beauty, and we are seeing some of that in the biogems. >>> >>> The other idea I got at FOSDEM this year from a convincing >>> talk by Brian Ostergard, titled 'You are doing it all >>> wrong' >>> >>> http://fosdem.org/2012/schedule/event/really_grow_commun >>> ity >>> >>> where he made a strong case to address inexperienced >>> developers. And you know what, I believe he is right. So >>> >>> (2) We will look for ways to get inexperienced developers >>> involved. One way is to define uncomplicated and >>> moderately complicated tasks, feature requests and bug >>> fixes. >>> >>> We are going to list these 'jobs' on http://biogems.info/. >>> If anyone picks up a task he/she will get very *strong* >>> support from the plugin owner, as well as the Biogem >>> maintainers. You, the programmer, will get all the credit >>> for the work. >>> >>> How does this sound? Does this appeal to you? Anyone of >>> the less experienced, or even experienced, wants to voice >>> his or her opinion? We may even turn some work into a >>> Google Summer of Code project proposal. >>> >>> Pj. _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Thu Feb 9 09:22:28 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 9 Feb 2012 10:22:28 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> Message-ID: <20120209092228.GB7020@thebird.nl> Hi Mic, On Thu, Feb 09, 2012 at 08:38:08AM +1000, Mic wrote: > * a gff3 support which doesn't read the whole file in the memory > see [1]http://biopython.org/wiki/GFF_Parsing#Limiting_to_features_of_interest The current bio-gff3 biogem only loads an index into memory, which is not too costly, and caches records. The problem with the GFF3 standard is (potentially) deep references, which is not so relevant for 99% of real GFF3 data. I agree we can do better. Still, for most practical purposes, the bio-gff3-plugin gem delivers. You may want to use the lru,line,lazy 75m 75m 0m17 (0.8.6) 50K 730M version. See the explanation on https://github.com/pjotrp/bioruby-gff3-plugin It is a tad slow. About six times slower than the full memory version. Speed is the first improvement I would work on. Pj. From p.j.a.cock at googlemail.com Thu Feb 9 09:25:38 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 9 Feb 2012 09:25:38 +0000 Subject: [BioRuby] EU-codefest in July In-Reply-To: References: <20120126103423.GA10234@thebird.nl> Message-ID: On Wed, Feb 8, 2012 at 11:01 PM, Mic wrote: > HI Pjotr, > Will be any videos of the talks available or are there any > videos from year before available? > > Cheers, Hi Mic, The BOSC committee are looking into this possibility for 2012, and volunteers with technical expertise would be most helpful. We're not promising anything yet though ;) For BOSC 2011 some of the talks were recorded, but this was not pre-planned, and I don't have contact details for the participant who filmed this. If we can track him down, and he still has the files, and the speakers are OK with it, then perhaps we can share some BOSC videos from last year. Regards, Peter (One of the BOSC committee) From pjotr.public14 at thebird.nl Thu Feb 9 10:03:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 9 Feb 2012 11:03:54 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics Message-ID: <20120209100353.GA8686@thebird.nl> We would like to highlight a project which sets a shining example for using Ruby for bioinformatics. We will vote on that on this list. Hereby I invite everyone to have a look at the projects on http://biogems.info/ and pick out a code snippet you really like. Send it to the mailing list, and explain why you think you like it. You can put forward one of your own projects :) ~~~ As an example, I am going to propose an implementation feature in the biogem tool, which represents a bit of Ruby meta-programming. It is called opening classes, and can be useful in overriding BioRuby itself, something I'll show below. Biogem does not implement everything from scratch. It uses a library from the Jeweler project, which was never designed to be shared(!). I.e. Jeweler was subverted for our purposes. Raoul put this together. The code I refer to lives, for example, in my forked project: https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb what you see here is that Biogem reopens the Jeweler::Generator class with class Jeweler class Generator (...) next, it overrides methods in that class. Because the file (jeweler.rb) gets included *later* than the original class, the overridden methods get called. The original methods can be renamed, e.g. alias original_render_template render_template and can be called from the overriding method. This technique of reopening classes and overriding behaviour is used in Ruby on Rails (indeed), but also in bio-logger and the bio-alignment gems. In bio-alignment it is used to make the BioRuby Bio::Sequence object enumerable, see https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bioruby.rb Having Bio::Sequence enumerable allows you to use enumerable functional methods, such as 'map'. For example I can now write @seq.map { |codon| codon.to_s }.join(' ') There is a case to be made to have standard BioRuby use Enumerable. However BioRuby has to support Ruby 1.8, which differs in this area. By reopening the class I can make it look like it is part of BioRuby anyway. I think it is a very powerful feature, and Raoul did the right thing in making Jeweler work for Biogem. I think it is an impressive example of beautiful code. Pj From cjfields at illinois.edu Fri Feb 10 18:04:31 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 10 Feb 2012 18:04:31 +0000 Subject: [BioRuby] Google Summer of Code project ideas References: <4F355910.4060203@gmail.com> Message-ID: Hi all, I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due in a couple of weeks, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. So, for each of the OBF projects that wants to do GSoC again this year, please: a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. c.) Let me know via email that you have done so and it's ready for Google to peruse. Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) Rob ---- Robert Buels (prospective) 2012 OBF GSoC Organization Admin From pjotr.public14 at thebird.nl Fri Feb 10 19:03:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 10 Feb 2012 20:03:35 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <4F355910.4060203@gmail.com> Message-ID: <20120210190335.GA20909@thebird.nl> Building out on the idea of involving newbies in easy projects, I would like to invite all plugin authors to come up with ideas on this list. Even the smallest idea will help. So think beyond SoC. Michael came up with gemifying, or componentizing BioRuby. And also upgrading our web presentation. Good ideas, any others? Francesco, what about bio-ngs? Pj. On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > Hi all, > > I'm going to be OBF project admin again this year for Google Summer of code. OBF's application is due in a couple of weeks, and we need to update our project ideas on the OBF wiki page and on each project's individual wiki pages. > > So, for each of the OBF projects that wants to do GSoC again this year, please: > > a.) Update the list of project ideas on your project's GSoC page (BioPython, BioPerl, BioRuby, etc). Add new ones, remove ones that have already been done or no longer relevant, etc. > > b.) Update the list of project ideas on the main OBF GSoC page (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > > c.) Let me know via email that you have done so and it's ready for Google to peruse. > > Please have the updates done, if possible, by this Friday (March 11). The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organization again this year, so let's come up with some good ones. :-) > > Rob > > ---- > Robert Buels > (prospective) 2012 OBF GSoC Organization Admin > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Sat Feb 11 07:47:51 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 11 Feb 2012 08:47:51 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> Message-ID: <20120211074751.GA23063@thebird.nl> Dear Toshiaki and Naohisa, I believe Michael has a very valid point. How about defining a project (potentially SoC), where we lay out the functionality we want from such a web presence? Pj. On Wed, Feb 08, 2012 at 03:52:57PM -0500, Michael Barton wrote: > I think making the homepage simpler would be very > beneficial. For instance I think the two most important > links (Tutorial and Sample codes) pages should be given much > greater prominence. These are the two pages which most > beginners will want to get started with. Compare with the > Sinatra page which has only six links on the front page > pointing to the most significant parts of the project. > > I think the Tutorial and Sample codes pages could do with > some love also. These pages do not match the visual layout > of the bioruby home page, one is in a separate domain while > the other is a wiki page. I think these pages deserve > attention to make them simpler and more accessible. A common > CSS theme also provides a unified front to the BioRuby > project. > > Compare with the Sinatra intro and documentation pages: > * http://www.sinatrarb.com/intro > * http://www.sinatrarb.com/documentation > > My opinion is that the BioRuby website should head in this > direction. I am not a web designer but I am happy to > contribute effort to writing web copy and BioRuby recipes. I > also think that bioruby should also have its own web address > too. From pjotr.public14 at thebird.nl Sat Feb 11 17:46:16 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 11 Feb 2012 18:46:16 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120209100353.GA8686@thebird.nl> References: <20120209100353.GA8686@thebird.nl> Message-ID: <20120211174616.GA24074@thebird.nl> Correct me if I am wrong, but has everyone moved across to BioPython now? Or even to the dark side? Pj. On Thu, Feb 09, 2012 at 11:03:54AM +0100, Pjotr Prins wrote: > We would like to highlight a project which sets a shining example for > using Ruby for bioinformatics. We will vote on that on this list. > > Hereby I invite everyone to have a look at the projects on > http://biogems.info/ and pick out a code snippet you really like. > Send it to the mailing list, and explain why you think you like it. > > You can put forward one of your own projects :) > > ~~~ > > As an example, I am going to propose an implementation feature in the > biogem tool, which represents a bit of Ruby meta-programming. It is > called opening classes, and can be useful in overriding BioRuby > itself, something I'll show below. > > Biogem does not implement everything from scratch. It uses a library > from the Jeweler project, which was never designed to be shared(!). > I.e. Jeweler was subverted for our purposes. > > Raoul put this together. The code I refer to lives, for example, in my > forked project: > > https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb > > what you see here is that Biogem reopens the Jeweler::Generator class with > > class Jeweler > class Generator > > (...) > > next, it overrides methods in that class. Because the file > (jeweler.rb) gets included *later* than the original class, the > overridden methods get called. The original methods can be renamed, > e.g. > > alias original_render_template render_template > > and can be called from the overriding method. > > This technique of reopening classes and overriding behaviour is used > in Ruby on Rails (indeed), but also in bio-logger and the > bio-alignment gems. In bio-alignment it is used to make the BioRuby > Bio::Sequence object enumerable, see > > https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bioruby.rb > > Having Bio::Sequence enumerable allows you to use enumerable > functional methods, such as 'map'. For example I can now write > > @seq.map { |codon| codon.to_s }.join(' ') > > There is a case to be made to have standard BioRuby use Enumerable. > However BioRuby has to support Ruby 1.8, which differs in this area. > By reopening the class I can make it look like it is part of BioRuby > anyway. I think it is a very powerful feature, and Raoul did the > right thing in making Jeweler work for Biogem. I think it is an > impressive example of beautiful code. > > Pj > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Sat Feb 11 19:08:37 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 11 Feb 2012 19:08:37 +0000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? > > Pj. I haven't noticed any BioRuby developers posting on the Biopython mailing lists recently - but you'd be welcome ;) On a related topic, my first BioRuby pull request was merged, so there is a little direct cross project contribution going on :) https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d Peter From hlapp at drycafe.net Sat Feb 11 20:16:30 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sat, 11 Feb 2012 15:16:30 -0500 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> On Feb 11, 2012, at 12:46 PM, Pjotr Prins wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? The dark side is already here. You, too, can haz perl. All your gem are belong to us. -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From bonnal at ingm.org Sat Feb 11 20:15:02 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 11 Feb 2012 21:15:02 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> Message-ID: LOL On 11/02/12 18.46, "Pjotr Prins" wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? > > Pj. > > On Thu, Feb 09, 2012 at 11:03:54AM +0100, Pjotr Prins wrote: >> We would like to highlight a project which sets a shining example for >> using Ruby for bioinformatics. We will vote on that on this list. >> >> Hereby I invite everyone to have a look at the projects on >> http://biogems.info/ and pick out a code snippet you really like. >> Send it to the mailing list, and explain why you think you like it. >> >> You can put forward one of your own projects :) >> >> ~~~ >> >> As an example, I am going to propose an implementation feature in the >> biogem tool, which represents a bit of Ruby meta-programming. It is >> called opening classes, and can be useful in overriding BioRuby >> itself, something I'll show below. >> >> Biogem does not implement everything from scratch. It uses a library >> from the Jeweler project, which was never designed to be shared(!). >> I.e. Jeweler was subverted for our purposes. >> >> Raoul put this together. The code I refer to lives, for example, in my >> forked project: >> >> >> https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb >> >> what you see here is that Biogem reopens the Jeweler::Generator class with >> >> class Jeweler >> class Generator >> >> (...) >> >> next, it overrides methods in that class. Because the file >> (jeweler.rb) gets included *later* than the original class, the >> overridden methods get called. The original methods can be renamed, >> e.g. >> >> alias original_render_template render_template >> >> and can be called from the overriding method. >> >> This technique of reopening classes and overriding behaviour is used >> in Ruby on Rails (indeed), but also in bio-logger and the >> bio-alignment gems. In bio-alignment it is used to make the BioRuby >> Bio::Sequence object enumerable, see >> >> >> https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bio >> ruby.rb >> >> Having Bio::Sequence enumerable allows you to use enumerable >> functional methods, such as 'map'. For example I can now write >> >> @seq.map { |codon| codon.to_s }.join(' ') >> >> There is a case to be made to have standard BioRuby use Enumerable. >> However BioRuby has to support Ruby 1.8, which differs in this area. >> By reopening the class I can make it look like it is part of BioRuby >> anyway. I think it is a very powerful feature, and Raoul did the >> right thing in making Jeweler work for Biogem. I think it is an >> impressive example of beautiful code. >> >> Pj >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From georgkam at gmail.com Sat Feb 11 20:27:44 2012 From: georgkam at gmail.com (George Githinji) Date: Sat, 11 Feb 2012 23:27:44 +0300 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: Hi All Beauty is in the eyes of the beholder! The Bio-Alignment plugin can read and interconvert a nucleotide alignment to an amino acid alignment. I liked the simplicity of how PJ has implemented the codon to amino acid conversion helper method while taking care of the gaps or undefined aa translations. # lazily convert to Amino acid (once only) def to_aa aa = translate if not aa if gap? return '-' elsif undefined? return 'X' else raise 'What?' end end aa end This method does not have any ruby 'magic' and is self documenting. The gap? and undefined? methods are implemented as simple one line standalone methods. Again I like this simple 'trick' of getting an array of codons from a sequence in the codonsequence class. seq.scan(/\S\S\S/) #gets an array of codons The longer alternative would be to create a bio::sequence::NA object and iterate seq = Bio::Sequence::NA.new("blahahahha") seq.window_search(3, 3) do |subseq| puts subseq end It seems more intuitive to represent a sequence as an array of codon objects. In this way the codons have some state and can carry 'luggage'. getting the string representation of the sequence is as simple as def to_s @seq.map { |codon| codon.to_s }.join(' ') end To be more DRY, the to_nt method in the same class could be aliased from the to_s method It seems the bio-plugins are a rich source of tricks and great learning.... ! On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock wrote: > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins wrote: >> Correct me if I am wrong, but has everyone moved across to BioPython >> now? Or even to the dark side? >> >> Pj. > > I haven't noticed any BioRuby developers posting on the Biopython > mailing lists recently - but you'd be welcome ;) > > On a related topic, my first BioRuby pull request was merged, so > there is a little direct cross project contribution going on :) > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From cjfields at illinois.edu Sat Feb 11 22:00:23 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sat, 11 Feb 2012 22:00:23 +0000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> Message-ID: <2927BD64-ACC7-4F9E-9B25-2FF82C329421@illinois.edu> On Feb 11, 2012, at 2:16 PM, Hilmar Lapp wrote: > On Feb 11, 2012, at 12:46 PM, Pjotr Prins wrote: > >> Correct me if I am wrong, but has everyone moved across to BioPython >> now? Or even to the dark side? > > The dark side is already here. You, too, can haz perl. All your gem are belong to us. :) chris From pjotr.public14 at thebird.nl Sun Feb 12 08:43:13 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 12 Feb 2012 09:43:13 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <386EC4DB-A68E-4FFD-8695-B990D539270C@drycafe.net> Message-ID: <20120212084313.GB25607@thebird.nl> On Sat, Feb 11, 2012 at 03:16:30PM -0500, Hilmar Lapp wrote: > > On Feb 11, 2012, at 12:46 PM, Pjotr Prins wrote: > > > Correct me if I am wrong, but has everyone moved across to BioPython > > now? Or even to the dark side? > > The dark side is already here. You, too, can haz perl. All your gem are belong to us. We have HAL! Oh wait... something odd is happening, I don't feel right Pj. From bonnal at ingm.org Sun Feb 12 23:17:30 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 00:17:30 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120210190335.GA20909@thebird.nl> Message-ID: I agree with Pjotr, So please post your ideas here and update the wiki. It's time to re-start IRC meetings, what about Feb 16 around: 9:00 GMT 10:00 Italy 18:00 Japan 4:00 NewYork ( too early ? :-) About BioNGS, I think it's too complicated by itself, but I could have 2 students working on this project. On 10/02/12 20.03, "Pjotr Prins" wrote: > Building out on the idea of involving newbies in easy projects, I > would like to invite all plugin authors to come up with ideas on this > list. Even the smallest idea will help. So think beyond SoC. > > Michael came up with gemifying, or componentizing BioRuby. And also > upgrading our web presentation. Good ideas, any others? > > Francesco, what about bio-ngs? > > Pj. > > On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: >> Hi all, >> >> I'm going to be OBF project admin again this year for Google Summer of code. >> OBF's application is due in a couple of weeks, and we need to update our >> project ideas on the OBF wiki page and on each project's individual wiki >> pages. >> >> So, for each of the OBF projects that wants to do GSoC again this year, >> please: >> >> a.) Update the list of project ideas on your project's GSoC page (BioPython, >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been >> done or no longer relevant, etc. >> >> b.) Update the list of project ideas on the main OBF GSoC page >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. >> >> c.) Let me know via email that you have done so and it's ready for Google to >> peruse. >> >> Please have the updates done, if possible, by this Friday (March 11). The >> number and quality of the project ideas are part of the evaluation process >> for whether OBF is accepted as a Summer of Code organization again this year, >> so let's come up with some good ones. :-) >> >> Rob >> >> ---- >> Robert Buels >> (prospective) 2012 OBF GSoC Organization Admin >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnal at ingm.org Sun Feb 12 23:35:05 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 00:35:05 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120211174616.GA24074@thebird.nl> Message-ID: I like this idea and commenting or posting snipped code is the chance to discuss about Ruby and design patterns or obscure techniques. Pjotr commented the way I reopened a class -thanks!- and that is called Monkey Patch technique http://en.wikipedia.org/wiki/Monkey_patch ; Metaprogramming Ruby by Paolo Perrotta it's something every Ruby developer should read. So +1 to use this ml for basic/advanced ruby questions not only for bio stuffs and the talented/skilled coders will provide support for sure. PS: I'm studing D :-) On 11/02/12 18.46, "Pjotr Prins" wrote: > Correct me if I am wrong, but has everyone moved across to BioPython > now? Or even to the dark side? > > Pj. > > On Thu, Feb 09, 2012 at 11:03:54AM +0100, Pjotr Prins wrote: >> We would like to highlight a project which sets a shining example for >> using Ruby for bioinformatics. We will vote on that on this list. >> >> Hereby I invite everyone to have a look at the projects on >> http://biogems.info/ and pick out a code snippet you really like. >> Send it to the mailing list, and explain why you think you like it. >> >> You can put forward one of your own projects :) >> >> ~~~ >> >> As an example, I am going to propose an implementation feature in the >> biogem tool, which represents a bit of Ruby meta-programming. It is >> called opening classes, and can be useful in overriding BioRuby >> itself, something I'll show below. >> >> Biogem does not implement everything from scratch. It uses a library >> from the Jeweler project, which was never designed to be shared(!). >> I.e. Jeweler was subverted for our purposes. >> >> Raoul put this together. The code I refer to lives, for example, in my >> forked project: >> >> >> https://github.com/pjotrp/bioruby-gem/blob/master/lib/bio-gem/mod/jeweler.rb >> >> what you see here is that Biogem reopens the Jeweler::Generator class with >> >> class Jeweler >> class Generator >> >> (...) >> >> next, it overrides methods in that class. Because the file >> (jeweler.rb) gets included *later* than the original class, the >> overridden methods get called. The original methods can be renamed, >> e.g. >> >> alias original_render_template render_template >> >> and can be called from the overriding method. >> >> This technique of reopening classes and overriding behaviour is used >> in Ruby on Rails (indeed), but also in bio-logger and the >> bio-alignment gems. In bio-alignment it is used to make the BioRuby >> Bio::Sequence object enumerable, see >> >> >> https://github.com/pjotrp/bioruby-alignment/blob/master/lib/bio-alignment/bio >> ruby.rb >> >> Having Bio::Sequence enumerable allows you to use enumerable >> functional methods, such as 'map'. For example I can now write >> >> @seq.map { |codon| codon.to_s }.join(' ') >> >> There is a case to be made to have standard BioRuby use Enumerable. >> However BioRuby has to support Ruby 1.8, which differs in this area. >> By reopening the class I can make it look like it is part of BioRuby >> anyway. I think it is a very powerful feature, and Raoul did the >> right thing in making Jeweler work for Biogem. I think it is an >> impressive example of beautiful code. >> >> Pj >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From russell.whitaker at gmail.com Mon Feb 13 00:02:26 2012 From: russell.whitaker at gmail.com (Russell Whitaker) Date: Sun, 12 Feb 2012 16:02:26 -0800 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120211174616.GA24074@thebird.nl> Message-ID: On Sun, Feb 12, 2012 at 3:35 PM, Raoul Bonnal wrote: >[SNIP] > PS: I'm studing D :-) > Do tell: what do you like about D? For that matter, have you evaluated Scala? I've been curious about both... -- Russell Whitaker http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ http://www.linkedin.com/pub/russell-whitaker/0/b86/329 From pjotr.public14 at thebird.nl Mon Feb 13 07:09:31 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 08:09:31 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120211174616.GA24074@thebird.nl> Message-ID: <20120213070931.GA31051@thebird.nl> I have written about D and Scala in 'Ruby is a pony, Scala is a thoroughbred, D is a dragon'. http://blog.thebird.nl/?p=93 There is more on Scala examples on that site too. I may add D stuff in the future. We all need to write more about software and programming. Over the last year I prefer to program in Ruby and D - they are at both ends at the convenience vs. performance spectrum ;). D natively links against C libraries, something I like a lot (saves a lot of data copying). There will be biogem examples of bindings soon. Also the LLVM version of D2 is doing well, D will become part of Fedora and Debian based systems. If the JVM complex 'ecosystem' is no big issue, JRuby and Scala are also a brilliant match. You can check out my BioScala code and documents on github. JRuby is a great performer, so that may come naturally to you. Ruby gems work really well on the JVM, even when written in C. The JRuby developers have done a remarkable job. Personally, I think it boils down to background and experience. C/C++ programmers I see taking to D like a fish to water. People with a Java background may well prefer the JVM. Even after the balanced choice for D, I really miss some of the niceties of Scala. I guess, if I were programming Scala, I would do less in Ruby. I would strongly suggest to buy and read both Andrei's D book and Martin's Scala book. They are both classics in their own right - and see what appeals to you most. D and Scala are both next generation (strongly typed) languages designed by geniuses. They both work well with Ruby. Pj. On Sun, Feb 12, 2012 at 04:02:26PM -0800, Russell Whitaker wrote: > On Sun, Feb 12, 2012 at 3:35 PM, Raoul Bonnal wrote: > >[SNIP] > > PS: I'm studing D :-) > > > > Do tell: what do you like about D? For that matter, have you evaluated Scala? > I've been curious about both... > > -- > Russell Whitaker > http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ > http://www.linkedin.com/pub/russell-whitaker/0/b86/329 > From bonnal at ingm.org Mon Feb 13 07:16:31 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 08:16:31 +0100 Subject: [BioRuby] Article Published Message-ID: Dear all, We are happy to announce another paper! This time on 'Biogem: an effective tool based approach for scaling up open source software development in bioinformatics'. This was a community paper where all early biogem authors contributed to the paper in its final form. http://bioinformatics.oxfordjournals.org/content/early/2012/02/12/bioinforma tics.bts080.short?rss=1 Enjoy, Ra & Pj. From bonnal at ingm.org Mon Feb 13 07:44:21 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 08:44:21 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213070931.GA31051@thebird.nl> Message-ID: I'm studing D because of Pjotr :-), next will be Scala. Actually I tried Scala 2 year ago but my feeling was not so good with that language, maybe it's me. I feel comfortable reading D book, and I find the language a bit natural to me. Pjotr is right, we as bioinformaticians should know both and try others. What now is impossible with Ruby and Python is writing parallel applications. I'm looking for the best way to write parallel code and use the resources efficiently without forgetting easiness. Obviously there are other techniques like Hadoop for processing "big data", so ... Nothing is decided and we should discuss more. I'm here and I want to hear about your experience/opinion/approach. PS: Scala and D, both have binding to OpenCL On 13/02/12 08.09, "Pjotr Prins" wrote: > I have written about D and Scala in 'Ruby is a pony, Scala is a > thoroughbred, D is a dragon'. > > http://blog.thebird.nl/?p=93 > > There is more on Scala examples on that site too. I may add D stuff in > the future. We all need to write more about software and programming. > > Over the last year I prefer to program in Ruby and D - they are at > both ends at the convenience vs. performance spectrum ;). D natively > links against C libraries, something I like a lot (saves a lot of data > copying). There will be biogem examples of bindings soon. Also the > LLVM version of D2 is doing well, D will become part of Fedora and > Debian based systems. > > If the JVM complex 'ecosystem' is no big issue, JRuby and Scala are > also a brilliant match. You can check out my BioScala code and > documents on github. JRuby is a great performer, so that may come > naturally to you. Ruby gems work really well on the JVM, even when > written in C. The JRuby developers have done a remarkable job. > > Personally, I think it boils down to background and experience. C/C++ > programmers I see taking to D like a fish to water. People with a Java > background may well prefer the JVM. Even after the balanced choice for > D, I really miss some of the niceties of Scala. I guess, if I were > programming Scala, I would do less in Ruby. > > I would strongly suggest to buy and read both Andrei's D book and > Martin's Scala book. They are both classics in their own right - and > see what appeals to you most. > > D and Scala are both next generation (strongly typed) languages > designed by geniuses. They both work well with Ruby. > > Pj. > > On Sun, Feb 12, 2012 at 04:02:26PM -0800, Russell Whitaker wrote: >> On Sun, Feb 12, 2012 at 3:35 PM, Raoul Bonnal wrote: >>> [SNIP] >>> PS: I'm studing D :-) >>> >> >> Do tell: what do you like about D? For that matter, have you evaluated Scala? >> I've been curious about both... >> >> -- >> Russell Whitaker >> http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ >> http://www.linkedin.com/pub/russell-whitaker/0/b86/329 >> From pjotr.public14 at thebird.nl Mon Feb 13 07:54:30 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 08:54:30 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> Message-ID: <20120213075430.GA1086@thebird.nl> OK, here another candidate for the price of beautiful code: https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb Trevor has implemented some hairy logic into the RE code. I mean hairy, that if it were done by someone else it would become spaghetti code (plenty of examples there in the real world!). You can see, that even when choosing sensible names, and explaining the code with good comments, it may still be hard to understand! But I think def add_cuts_from_cut_ranges(cut_ranges) pretty much sums it up :). Still, it is beautiful, because it is hard to think of doing it better. The Ruby code is short and self explanatory and RE library has almost become a DSL for cutting sequences using restriction enzymes. That is beautiful. Pj. On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > Hi All > Beauty is in the eyes of the beholder! > The Bio-Alignment plugin can read and interconvert a nucleotide > alignment to an amino acid alignment. I liked the simplicity of how > PJ has implemented the codon to amino acid conversion helper method > while taking care of the gaps or undefined aa translations. > > # lazily convert to Amino acid (once only) > def to_aa > aa = translate > if not aa > if gap? > return '-' > elsif undefined? > return 'X' > else > raise 'What?' > end > end > aa > end > > This method does not have any ruby 'magic' and is self documenting. > The gap? and undefined? methods are implemented as simple one line > standalone methods. > > Again I like this simple 'trick' of getting an array of codons from a > sequence in the codonsequence class. > > seq.scan(/\S\S\S/) #gets an array of codons > > The longer alternative would be to create a bio::sequence::NA object > and iterate > seq = Bio::Sequence::NA.new("blahahahha") > seq.window_search(3, 3) do |subseq| > puts subseq > end > > It seems more intuitive to represent a sequence as an array of codon > objects. In this way the codons have some state and can carry > 'luggage'. getting the string representation of the sequence is as > simple as > def to_s > @seq.map { |codon| codon.to_s }.join(' ') > end > > To be more DRY, the to_nt method in the same class could be aliased > from the to_s method > > It seems the bio-plugins are a rich source of tricks and great learning.... ! > > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock wrote: > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins wrote: > >> Correct me if I am wrong, but has everyone moved across to BioPython > >> now? Or even to the dark side? > >> > >> Pj. > > > > I haven't noticed any BioRuby developers posting on the Biopython > > mailing lists recently - but you'd be welcome ;) > > > > On a related topic, my first BioRuby pull request was merged, so > > there is a little direct cross project contribution going on :) > > > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > > > Peter > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://biorelated.wordpress.com/ > Twitter: http://twitter.com/#!/george_l > From francesco.strozzi at gmail.com Mon Feb 13 10:06:03 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 13 Feb 2012 11:06:03 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213075430.GA1086@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <20120213075430.GA1086@thebird.nl> Message-ID: Some code I particularly liked comes from the BioNGS Wrapper library (by Raoul). The gem is in development and I'm contributing to it so I could look at the code from a very close perspective! https://gist.github.com/1815501 What is interesting is the use of an internal DSL which makes the code particularly expressive and readable, and writing a wrapper becomes only a matter of defining the options that the command line binary expects. The library is quite large and includes also methods to define aliases for the options. This module makes use also of the powerful Thor gem (used in Rails) to create and define tasks that can be used to launch the binaries and to include them in larger workflows and pipelines. Now let's say you want to turn your freshly new wrapped binary into a mighty Thor taks, all you need to do is: https://gist.github.com/1815523 The amazing part is that the parameters passed to the block works like arguments definition for the Thor task itself. The code that makes this possible behind the scenes is here: https://gist.github.com/1815481 It checks also if the number of arguments passed are equal to the arguments of the block. If not, it raises an error to the user as he/she is calling the task with the wrong number of arguments. To understand every part you need to know a bit the way the Thor library defines tasks (more here: https://github.com/wycats/thor) but the code here in BioNGS definitely worth a look! P.S. I'm diving into Scala too :-). I took the Odersky book few months ago and now I'm about to start looking in details at this new programming language. Easy and powerful parallelism is the new goal we need to achieve to keep up with the big data era. Cheers On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: > OK, here another candidate for the price of beautiful code: > > > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb > > Trevor has implemented some hairy logic into the RE code. I mean > hairy, that if it were done by someone else it would become spaghetti > code (plenty of examples there in the real world!). You can see, that > even when choosing sensible names, and explaining the code with good > comments, it may still be hard to understand! But I think > > def add_cuts_from_cut_ranges(cut_ranges) > > pretty much sums it up :). Still, it is beautiful, because it is hard > to think of doing it better. The Ruby code is short and self > explanatory and RE library has almost become a DSL for cutting > sequences using restriction enzymes. That is beautiful. > > Pj. > > On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > > Hi All > > Beauty is in the eyes of the beholder! > > The Bio-Alignment plugin can read and interconvert a nucleotide > > alignment to an amino acid alignment. I liked the simplicity of how > > PJ has implemented the codon to amino acid conversion helper method > > while taking care of the gaps or undefined aa translations. > > > > # lazily convert to Amino acid (once only) > > def to_aa > > aa = translate > > if not aa > > if gap? > > return '-' > > elsif undefined? > > return 'X' > > else > > raise 'What?' > > end > > end > > aa > > end > > > > This method does not have any ruby 'magic' and is self documenting. > > The gap? and undefined? methods are implemented as simple one line > > standalone methods. > > > > Again I like this simple 'trick' of getting an array of codons from a > > sequence in the codonsequence class. > > > > seq.scan(/\S\S\S/) #gets an array of codons > > > > The longer alternative would be to create a bio::sequence::NA object > > and iterate > > seq = Bio::Sequence::NA.new("blahahahha") > > seq.window_search(3, 3) do |subseq| > > puts subseq > > end > > > > It seems more intuitive to represent a sequence as an array of codon > > objects. In this way the codons have some state and can carry > > 'luggage'. getting the string representation of the sequence is as > > simple as > > def to_s > > @seq.map { |codon| codon.to_s }.join(' ') > > end > > > > To be more DRY, the to_nt method in the same class could be aliased > > from the to_s method > > > > It seems the bio-plugins are a rich source of tricks and great > learning.... ! > > > > > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock > wrote: > > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > pjotr.public14 at thebird.nl> wrote: > > >> Correct me if I am wrong, but has everyone moved across to BioPython > > >> now? Or even to the dark side? > > >> > > >> Pj. > > > > > > I haven't noticed any BioRuby developers posting on the Biopython > > > mailing lists recently - but you'd be welcome ;) > > > > > > On a related topic, my first BioRuby pull request was merged, so > > > there is a little direct cross project contribution going on :) > > > > > > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > > > > > Peter > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > -- > > --------------- > > Sincerely > > George > > Skype: george_g2 > > Blog: http://biorelated.wordpress.com/ > > Twitter: http://twitter.com/#!/george_l > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From pjotr.public14 at thebird.nl Mon Feb 13 10:34:08 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 11:34:08 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <20120213075430.GA1086@thebird.nl> Message-ID: <20120213103408.GA4358@thebird.nl> Excellent. May I propose that at least the other half of the authors of the Biogem paper send in an example of beautiful code? We can compile these snippets on a special page on one of the websites (or both). That will help courses, 'newbies' and even 'die hard' Perl users, such as Yoda, to see what this Ruby thing is about. Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh herh herh. Pj. On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: > Some code I particularly liked comes from the BioNGS Wrapper library (by > Raoul). The gem is in development and I'm contributing to it so I could > look at the code from a very close perspective! > > https://gist.github.com/1815501 > > What is interesting is the use of an internal DSL which makes the code > particularly expressive and readable, and writing a wrapper becomes only a > matter of defining the options that the command line binary expects. The > library is quite large and includes also methods to define aliases for the > options. > This module makes use also of the powerful Thor gem (used in Rails) to > create and define tasks that can be used to launch the binaries and to > include them in larger workflows and pipelines. > Now let's say you want to turn your freshly new wrapped binary into a > mighty Thor taks, all you need to do is: > > https://gist.github.com/1815523 > > The amazing part is that the parameters passed to the block works like > arguments definition for the Thor task itself. The code that makes this > possible behind the scenes is here: > > https://gist.github.com/1815481 > > It checks also if the number of arguments passed are equal to the arguments > of the block. If not, it raises an error to the user as he/she is calling > the task with the wrong number of arguments. To understand every part you > need to know a bit the way the Thor library defines tasks (more here: > https://github.com/wycats/thor) but the code here in BioNGS definitely > worth a look! > > P.S. I'm diving into Scala too :-). I took the Odersky book few months ago > and now I'm about to start looking in details at this new programming > language. Easy and powerful parallelism is the new goal we need to achieve > to keep up with the big data era. > > Cheers > > On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: > > > OK, here another candidate for the price of beautiful code: > > > > > > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb > > > > Trevor has implemented some hairy logic into the RE code. I mean > > hairy, that if it were done by someone else it would become spaghetti > > code (plenty of examples there in the real world!). You can see, that > > even when choosing sensible names, and explaining the code with good > > comments, it may still be hard to understand! But I think > > > > def add_cuts_from_cut_ranges(cut_ranges) > > > > pretty much sums it up :). Still, it is beautiful, because it is hard > > to think of doing it better. The Ruby code is short and self > > explanatory and RE library has almost become a DSL for cutting > > sequences using restriction enzymes. That is beautiful. > > > > Pj. > > > > On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > > > Hi All > > > Beauty is in the eyes of the beholder! > > > The Bio-Alignment plugin can read and interconvert a nucleotide > > > alignment to an amino acid alignment. I liked the simplicity of how > > > PJ has implemented the codon to amino acid conversion helper method > > > while taking care of the gaps or undefined aa translations. > > > > > > # lazily convert to Amino acid (once only) > > > def to_aa > > > aa = translate > > > if not aa > > > if gap? > > > return '-' > > > elsif undefined? > > > return 'X' > > > else > > > raise 'What?' > > > end > > > end > > > aa > > > end > > > > > > This method does not have any ruby 'magic' and is self documenting. > > > The gap? and undefined? methods are implemented as simple one line > > > standalone methods. > > > > > > Again I like this simple 'trick' of getting an array of codons from a > > > sequence in the codonsequence class. > > > > > > seq.scan(/\S\S\S/) #gets an array of codons > > > > > > The longer alternative would be to create a bio::sequence::NA object > > > and iterate > > > seq = Bio::Sequence::NA.new("blahahahha") > > > seq.window_search(3, 3) do |subseq| > > > puts subseq > > > end > > > > > > It seems more intuitive to represent a sequence as an array of codon > > > objects. In this way the codons have some state and can carry > > > 'luggage'. getting the string representation of the sequence is as > > > simple as > > > def to_s > > > @seq.map { |codon| codon.to_s }.join(' ') > > > end > > > > > > To be more DRY, the to_nt method in the same class could be aliased > > > from the to_s method > > > > > > It seems the bio-plugins are a rich source of tricks and great > > learning.... ! > > > > > > > > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock > > wrote: > > > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > > pjotr.public14 at thebird.nl> wrote: > > > >> Correct me if I am wrong, but has everyone moved across to BioPython > > > >> now? Or even to the dark side? > > > >> > > > >> Pj. > > > > > > > > I haven't noticed any BioRuby developers posting on the Biopython > > > > mailing lists recently - but you'd be welcome ;) > > > > > > > > On a related topic, my first BioRuby pull request was merged, so > > > > there is a little direct cross project contribution going on :) > > > > > > > > > > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d > > > > > > > > Peter > > > > _______________________________________________ > > > > BioRuby Project - http://www.bioruby.org/ > > > > BioRuby mailing list > > > > BioRuby at lists.open-bio.org > > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > > > > > -- > > > --------------- > > > Sincerely > > > George > > > Skype: george_g2 > > > Blog: http://biorelated.wordpress.com/ > > > Twitter: http://twitter.com/#!/george_l > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From georgkam at gmail.com Mon Feb 13 10:36:25 2012 From: georgkam at gmail.com (George Githinji) Date: Mon, 13 Feb 2012 13:36:25 +0300 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213103408.GA4358@thebird.nl> References: <20120209100353.GA8686@thebird.nl> <20120211174616.GA24074@thebird.nl> <20120213075430.GA1086@thebird.nl> <20120213103408.GA4358@thebird.nl> Message-ID: Good idea PJ! On Mon, Feb 13, 2012 at 1:34 PM, Pjotr Prins wrote: > Excellent. > > May I propose that at least the other half of the authors of the > Biogem paper send in an example of beautiful code? We can compile > these snippets on a special page on one of the websites (or both). > That will help courses, 'newbies' and even 'die hard' Perl users, such > as Yoda, to see what this Ruby thing is about. > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > herh herh. > > Pj. > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: >> Some code I particularly liked comes from the BioNGS Wrapper library (by >> Raoul). The gem is in development and I'm contributing to it so I could >> look at the code from a very close perspective! >> >> https://gist.github.com/1815501 >> >> What is interesting is the use of an internal DSL which makes the code >> particularly expressive and readable, and writing a wrapper becomes only a >> matter of defining the options that the command line binary expects. The >> library is quite large and includes also methods to define aliases for the >> options. >> This module makes use also of the powerful Thor gem (used in Rails) to >> create and define tasks that can be used to launch the binaries and to >> include them in larger workflows and pipelines. >> Now let's say you want to turn your freshly new wrapped binary into a >> mighty Thor taks, all you need to do is: >> >> https://gist.github.com/1815523 >> >> The amazing part is that the parameters passed to the block works like >> arguments definition for the Thor task itself. The code that makes this >> possible behind the scenes is here: >> >> https://gist.github.com/1815481 >> >> It checks also if the number of arguments passed are equal to the arguments >> of the block. If not, it raises an error to the user as he/she is calling >> the task with the wrong number of arguments. To understand every part you >> need to know a bit the way the Thor library defines tasks (more here: >> https://github.com/wycats/thor) but the code here in BioNGS definitely >> worth a look! >> >> P.S. I'm diving into Scala too :-). I took the Odersky book few months ago >> and now I'm about to start looking in details at this new programming >> language. Easy and powerful parallelism is the new goal we need to achieve >> to keep up with the big data era. >> >> Cheers >> >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: >> >> > OK, here another candidate for the price of beautiful code: >> > >> > >> > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb >> > >> > Trevor has implemented some hairy logic into the RE code. I mean >> > hairy, that if it were done by someone else it would become spaghetti >> > code (plenty of examples there in the real world!). You can see, that >> > even when choosing sensible names, and explaining the code with good >> > comments, it may still be hard to understand! But I think >> > >> > ?def add_cuts_from_cut_ranges(cut_ranges) >> > >> > pretty much sums it up :). Still, it is beautiful, because it is hard >> > to think of doing it better. The Ruby code is short and self >> > explanatory and RE library has almost become a DSL for cutting >> > sequences using restriction enzymes. That is beautiful. >> > >> > Pj. >> > >> > On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: >> > > Hi All >> > > Beauty is in the eyes of the beholder! >> > > The Bio-Alignment plugin can ?read and interconvert a nucleotide >> > > alignment to an amino acid alignment. ?I liked the simplicity of how >> > > PJ has implemented the codon to amino acid conversion helper method >> > > while taking care of the gaps or undefined aa translations. >> > > >> > > ? ? ? # lazily convert to Amino acid (once only) >> > > ? ? ? def to_aa >> > > ? ? ? ? aa = translate >> > > ? ? ? ? if not aa >> > > ? ? ? ? ? if gap? >> > > ? ? ? ? ? ? return '-' >> > > ? ? ? ? ? elsif undefined? >> > > ? ? ? ? ? ? return 'X' >> > > ? ? ? ? ? else >> > > ? ? ? ? ? ? raise 'What?' >> > > ? ? ? ? ? end >> > > ? ? ? ? end >> > > ? ? ? ? aa >> > > ? ? ? end >> > > >> > > This method does not have any ruby 'magic' and is self documenting. >> > > The gap? and undefined? methods are implemented as simple one line >> > > standalone methods. >> > > >> > > Again I like this simple 'trick' of getting an array of codons from a >> > > sequence in the codonsequence class. >> > > >> > > seq.scan(/\S\S\S/) #gets an array of codons >> > > >> > > The longer alternative would be to create a bio::sequence::NA object >> > > and iterate >> > > seq = Bio::Sequence::NA.new("blahahahha") >> > > seq.window_search(3, 3) do |subseq| >> > > ? puts subseq >> > > end >> > > >> > > It seems more intuitive to represent a sequence as an array of codon >> > > objects. In this way the codons have some state and can carry >> > > 'luggage'. getting the string representation of the sequence is as >> > > simple as >> > > def to_s >> > > ?@seq.map { |codon| codon.to_s }.join(' ') >> > > end >> > > >> > > To be more DRY, the to_nt method in the same class could be aliased >> > > from the to_s method >> > > >> > > It seems the bio-plugins are a rich source of tricks and great >> > learning.... ! >> > > >> > > >> > > On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock >> > wrote: >> > > > On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < >> > pjotr.public14 at thebird.nl> wrote: >> > > >> Correct me if I am wrong, but has everyone moved across to BioPython >> > > >> now? Or even to the dark side? >> > > >> >> > > >> Pj. >> > > > >> > > > I haven't noticed any BioRuby developers posting on the Biopython >> > > > mailing lists recently - but you'd be welcome ;) >> > > > >> > > > On a related topic, my first BioRuby pull request was merged, so >> > > > there is a little direct cross project contribution going on :) >> > > > >> > > > >> > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d >> > > > >> > > > Peter >> > > > _______________________________________________ >> > > > BioRuby Project - http://www.bioruby.org/ >> > > > BioRuby mailing list >> > > > BioRuby at lists.open-bio.org >> > > > http://lists.open-bio.org/mailman/listinfo/bioruby >> > > >> > > >> > > >> > > -- >> > > --------------- >> > > Sincerely >> > > George >> > > Skype: george_g2 >> > > Blog: http://biorelated.wordpress.com/ >> > > Twitter: http://twitter.com/#!/george_l >> > > >> > _______________________________________________ >> > BioRuby Project - http://www.bioruby.org/ >> > BioRuby mailing list >> > BioRuby at lists.open-bio.org >> > http://lists.open-bio.org/mailman/listinfo/bioruby >> > >> >> >> >> -- >> >> Francesco >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From bonnal at ingm.org Mon Feb 13 10:37:20 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 11:37:20 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: Message-ID: Thanks Francesco, You have cute code in BioNGS as well. I like the piece of code which saves in an history file the commands executed by the user: https://github.com/helios/bioruby-ngs/blob/master/lib/bio/ngs/task.rb Every time the user runs biongs the command line is cached, the original idea was to save the commands to create a workflow on the fly. It is another example of Monkey Patching with injection of new code. On 13/02/12 11.06, "Francesco Strozzi" wrote: > Some code I particularly liked comes from the BioNGS Wrapper library (by > Raoul). The gem is in development and I'm contributing to it so I could > look at the code from a very close perspective! > > https://gist.github.com/1815501 > > What is interesting is the use of an internal DSL which makes the code > particularly expressive and readable, and writing a wrapper becomes only a > matter of defining the options that the command line binary expects. The > library is quite large and includes also methods to define aliases for the > options. > This module makes use also of the powerful Thor gem (used in Rails) to > create and define tasks that can be used to launch the binaries and to > include them in larger workflows and pipelines. > Now let's say you want to turn your freshly new wrapped binary into a > mighty Thor taks, all you need to do is: > > https://gist.github.com/1815523 > > The amazing part is that the parameters passed to the block works like > arguments definition for the Thor task itself. The code that makes this > possible behind the scenes is here: > > https://gist.github.com/1815481 > > It checks also if the number of arguments passed are equal to the arguments > of the block. If not, it raises an error to the user as he/she is calling > the task with the wrong number of arguments. To understand every part you > need to know a bit the way the Thor library defines tasks (more here: > https://github.com/wycats/thor) but the code here in BioNGS definitely > worth a look! > > P.S. I'm diving into Scala too :-). I took the Odersky book few months ago > and now I'm about to start looking in details at this new programming > language. Easy and powerful parallelism is the new goal we need to achieve > to keep up with the big data era. > > Cheers > > On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: > >> OK, here another candidate for the price of beautiful code: >> >> >> https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/util >> /restriction_enzyme/range/sequence_range/calculated_cuts.rb >> >> Trevor has implemented some hairy logic into the RE code. I mean >> hairy, that if it were done by someone else it would become spaghetti >> code (plenty of examples there in the real world!). You can see, that >> even when choosing sensible names, and explaining the code with good >> comments, it may still be hard to understand! But I think >> >> def add_cuts_from_cut_ranges(cut_ranges) >> >> pretty much sums it up :). Still, it is beautiful, because it is hard >> to think of doing it better. The Ruby code is short and self >> explanatory and RE library has almost become a DSL for cutting >> sequences using restriction enzymes. That is beautiful. >> >> Pj. >> >> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: >>> Hi All >>> Beauty is in the eyes of the beholder! >>> The Bio-Alignment plugin can read and interconvert a nucleotide >>> alignment to an amino acid alignment. I liked the simplicity of how >>> PJ has implemented the codon to amino acid conversion helper method >>> while taking care of the gaps or undefined aa translations. >>> >>> # lazily convert to Amino acid (once only) >>> def to_aa >>> aa = translate >>> if not aa >>> if gap? >>> return '-' >>> elsif undefined? >>> return 'X' >>> else >>> raise 'What?' >>> end >>> end >>> aa >>> end >>> >>> This method does not have any ruby 'magic' and is self documenting. >>> The gap? and undefined? methods are implemented as simple one line >>> standalone methods. >>> >>> Again I like this simple 'trick' of getting an array of codons from a >>> sequence in the codonsequence class. >>> >>> seq.scan(/\S\S\S/) #gets an array of codons >>> >>> The longer alternative would be to create a bio::sequence::NA object >>> and iterate >>> seq = Bio::Sequence::NA.new("blahahahha") >>> seq.window_search(3, 3) do |subseq| >>> puts subseq >>> end >>> >>> It seems more intuitive to represent a sequence as an array of codon >>> objects. In this way the codons have some state and can carry >>> 'luggage'. getting the string representation of the sequence is as >>> simple as >>> def to_s >>> @seq.map { |codon| codon.to_s }.join(' ') >>> end >>> >>> To be more DRY, the to_nt method in the same class could be aliased >>> from the to_s method >>> >>> It seems the bio-plugins are a rich source of tricks and great >> learning.... ! >>> >>> >>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock >> wrote: >>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < >> pjotr.public14 at thebird.nl> wrote: >>>>> Correct me if I am wrong, but has everyone moved across to BioPython >>>>> now? Or even to the dark side? >>>>> >>>>> Pj. >>>> >>>> I haven't noticed any BioRuby developers posting on the Biopython >>>> mailing lists recently - but you'd be welcome ;) >>>> >>>> On a related topic, my first BioRuby pull request was merged, so >>>> there is a little direct cross project contribution going on :) >>>> >>>> >> https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd0 >> 94c5d >>>> >>>> Peter >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >>> >>> >>> -- >>> --------------- >>> Sincerely >>> George >>> Skype: george_g2 >>> Blog: http://biorelated.wordpress.com/ >>> Twitter: http://twitter.com/#!/george_l >>> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > > From bonnal at ingm.org Mon Feb 13 10:46:26 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 11:46:26 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120213103408.GA4358@thebird.nl> Message-ID: Yeah, I was thinking the exact same thing. This kind of documentation will be of great help!!! I'm thinking about teaching Ruby @ Uni. What I missed from the previous email is: Beautiful code come from coders but that is not enough, working with people in this ML I found that the quality of code and its beauty increase only if you chat/talk with people and you are available to accept critics and contributes. Another tab ? ;-) On 13/02/12 11.34, "Pjotr Prins" wrote: > Excellent. > > May I propose that at least the other half of the authors of the > Biogem paper send in an example of beautiful code? We can compile > these snippets on a special page on one of the websites (or both). > That will help courses, 'newbies' and even 'die hard' Perl users, such > as Yoda, to see what this Ruby thing is about. > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > herh herh. > > Pj. > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: >> Some code I particularly liked comes from the BioNGS Wrapper library (by >> Raoul). The gem is in development and I'm contributing to it so I could >> look at the code from a very close perspective! >> >> https://gist.github.com/1815501 >> >> What is interesting is the use of an internal DSL which makes the code >> particularly expressive and readable, and writing a wrapper becomes only a >> matter of defining the options that the command line binary expects. The >> library is quite large and includes also methods to define aliases for the >> options. >> This module makes use also of the powerful Thor gem (used in Rails) to >> create and define tasks that can be used to launch the binaries and to >> include them in larger workflows and pipelines. >> Now let's say you want to turn your freshly new wrapped binary into a >> mighty Thor taks, all you need to do is: >> >> https://gist.github.com/1815523 >> >> The amazing part is that the parameters passed to the block works like >> arguments definition for the Thor task itself. The code that makes this >> possible behind the scenes is here: >> >> https://gist.github.com/1815481 >> >> It checks also if the number of arguments passed are equal to the arguments >> of the block. If not, it raises an error to the user as he/she is calling >> the task with the wrong number of arguments. To understand every part you >> need to know a bit the way the Thor library defines tasks (more here: >> https://github.com/wycats/thor) but the code here in BioNGS definitely >> worth a look! >> >> P.S. I'm diving into Scala too :-). I took the Odersky book few months ago >> and now I'm about to start looking in details at this new programming >> language. Easy and powerful parallelism is the new goal we need to achieve >> to keep up with the big data era. >> >> Cheers >> >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins wrote: >> >>> OK, here another candidate for the price of beautiful code: >>> >>> >>> https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti >>> l/restriction_enzyme/range/sequence_range/calculated_cuts.rb >>> >>> Trevor has implemented some hairy logic into the RE code. I mean >>> hairy, that if it were done by someone else it would become spaghetti >>> code (plenty of examples there in the real world!). You can see, that >>> even when choosing sensible names, and explaining the code with good >>> comments, it may still be hard to understand! But I think >>> >>> def add_cuts_from_cut_ranges(cut_ranges) >>> >>> pretty much sums it up :). Still, it is beautiful, because it is hard >>> to think of doing it better. The Ruby code is short and self >>> explanatory and RE library has almost become a DSL for cutting >>> sequences using restriction enzymes. That is beautiful. >>> >>> Pj. >>> >>> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: >>>> Hi All >>>> Beauty is in the eyes of the beholder! >>>> The Bio-Alignment plugin can read and interconvert a nucleotide >>>> alignment to an amino acid alignment. I liked the simplicity of how >>>> PJ has implemented the codon to amino acid conversion helper method >>>> while taking care of the gaps or undefined aa translations. >>>> >>>> # lazily convert to Amino acid (once only) >>>> def to_aa >>>> aa = translate >>>> if not aa >>>> if gap? >>>> return '-' >>>> elsif undefined? >>>> return 'X' >>>> else >>>> raise 'What?' >>>> end >>>> end >>>> aa >>>> end >>>> >>>> This method does not have any ruby 'magic' and is self documenting. >>>> The gap? and undefined? methods are implemented as simple one line >>>> standalone methods. >>>> >>>> Again I like this simple 'trick' of getting an array of codons from a >>>> sequence in the codonsequence class. >>>> >>>> seq.scan(/\S\S\S/) #gets an array of codons >>>> >>>> The longer alternative would be to create a bio::sequence::NA object >>>> and iterate >>>> seq = Bio::Sequence::NA.new("blahahahha") >>>> seq.window_search(3, 3) do |subseq| >>>> puts subseq >>>> end >>>> >>>> It seems more intuitive to represent a sequence as an array of codon >>>> objects. In this way the codons have some state and can carry >>>> 'luggage'. getting the string representation of the sequence is as >>>> simple as >>>> def to_s >>>> @seq.map { |codon| codon.to_s }.join(' ') >>>> end >>>> >>>> To be more DRY, the to_nt method in the same class could be aliased >>>> from the to_s method >>>> >>>> It seems the bio-plugins are a rich source of tricks and great >>> learning.... ! >>>> >>>> >>>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock >>> wrote: >>>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < >>> pjotr.public14 at thebird.nl> wrote: >>>>>> Correct me if I am wrong, but has everyone moved across to BioPython >>>>>> now? Or even to the dark side? >>>>>> >>>>>> Pj. >>>>> >>>>> I haven't noticed any BioRuby developers posting on the Biopython >>>>> mailing lists recently - but you'd be welcome ;) >>>>> >>>>> On a related topic, my first BioRuby pull request was merged, so >>>>> there is a little direct cross project contribution going on :) >>>>> >>>>> >>> https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd >>> 094c5d >>>>> >>>>> Peter >>>>> _______________________________________________ >>>>> BioRuby Project - http://www.bioruby.org/ >>>>> BioRuby mailing list >>>>> BioRuby at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >>>> >>>> >>>> -- >>>> --------------- >>>> Sincerely >>>> George >>>> Skype: george_g2 >>>> Blog: http://biorelated.wordpress.com/ >>>> Twitter: http://twitter.com/#!/george_l >>>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >>> >> >> >> >> -- >> >> Francesco >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Mon Feb 13 10:50:28 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 13 Feb 2012 11:50:28 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120210190335.GA20909@thebird.nl> Message-ID: <20120213105028.GA5237@thebird.nl> I am pretty hopeless with IRC. But I guess we should discuss possibilities for GSoC. Also, if anyone is interested, I could talk about Scala and D using Google Hangout. On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: > I agree with Pjotr, > So please post your ideas here and update the wiki. > It's time to re-start IRC meetings, what about Feb 16 around: > 9:00 GMT > 10:00 Italy > 18:00 Japan > 4:00 NewYork ( too early ? :-) > > About BioNGS, I think it's too complicated by itself, but I could have 2 > students working on this project. > > On 10/02/12 20.03, "Pjotr Prins" wrote: > > > Building out on the idea of involving newbies in easy projects, I > > would like to invite all plugin authors to come up with ideas on this > > list. Even the smallest idea will help. So think beyond SoC. > > > > Michael came up with gemifying, or componentizing BioRuby. And also > > upgrading our web presentation. Good ideas, any others? > > > > Francesco, what about bio-ngs? > > > > Pj. > > > > On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > >> Hi all, > >> > >> I'm going to be OBF project admin again this year for Google Summer of code. > >> OBF's application is due in a couple of weeks, and we need to update our > >> project ideas on the OBF wiki page and on each project's individual wiki > >> pages. > >> > >> So, for each of the OBF projects that wants to do GSoC again this year, > >> please: > >> > >> a.) Update the list of project ideas on your project's GSoC page (BioPython, > >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been > >> done or no longer relevant, etc. > >> > >> b.) Update the list of project ideas on the main OBF GSoC page > >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > >> > >> c.) Let me know via email that you have done so and it's ready for Google to > >> peruse. > >> > >> Please have the updates done, if possible, by this Friday (March 11). The > >> number and quality of the project ideas are part of the evaluation process > >> for whether OBF is accepted as a Summer of Code organization again this year, > >> so let's come up with some good ones. :-) > >> > >> Rob > >> > >> ---- > >> Robert Buels > >> (prospective) 2012 OBF GSoC Organization Admin > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From bonnal at ingm.org Mon Feb 13 10:58:13 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 13 Feb 2012 11:58:13 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120213105028.GA5237@thebird.nl> Message-ID: I know that :-) so, please post ideas in this ML. +1 for Scala/D over Google Hangout On 13/02/12 11.50, "Pjotr Prins" wrote: > I am pretty hopeless with IRC. But I guess we should discuss > possibilities for GSoC. Also, if anyone is interested, I could talk > about Scala and D using Google Hangout. > > On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: >> I agree with Pjotr, >> So please post your ideas here and update the wiki. >> It's time to re-start IRC meetings, what about Feb 16 around: >> 9:00 GMT >> 10:00 Italy >> 18:00 Japan >> 4:00 NewYork ( too early ? :-) >> >> About BioNGS, I think it's too complicated by itself, but I could have 2 >> students working on this project. >> >> On 10/02/12 20.03, "Pjotr Prins" wrote: >> >>> Building out on the idea of involving newbies in easy projects, I >>> would like to invite all plugin authors to come up with ideas on this >>> list. Even the smallest idea will help. So think beyond SoC. >>> >>> Michael came up with gemifying, or componentizing BioRuby. And also >>> upgrading our web presentation. Good ideas, any others? >>> >>> Francesco, what about bio-ngs? >>> >>> Pj. >>> >>> On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: >>>> Hi all, >>>> >>>> I'm going to be OBF project admin again this year for Google Summer of >>>> code. >>>> OBF's application is due in a couple of weeks, and we need to update our >>>> project ideas on the OBF wiki page and on each project's individual wiki >>>> pages. >>>> >>>> So, for each of the OBF projects that wants to do GSoC again this year, >>>> please: >>>> >>>> a.) Update the list of project ideas on your project's GSoC page >>>> (BioPython, >>>> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been >>>> done or no longer relevant, etc. >>>> >>>> b.) Update the list of project ideas on the main OBF GSoC page >>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. >>>> >>>> c.) Let me know via email that you have done so and it's ready for Google >>>> to >>>> peruse. >>>> >>>> Please have the updates done, if possible, by this Friday (March 11). The >>>> number and quality of the project ideas are part of the evaluation process >>>> for whether OBF is accepted as a Summer of Code organization again this >>>> year, >>>> so let's come up with some good ones. :-) >>>> >>>> Rob >>>> >>>> ---- >>>> Robert Buels >>>> (prospective) 2012 OBF GSoC Organization Admin >>>> >>>> >>>> _______________________________________________ >>>> BioRuby Project - http://www.bioruby.org/ >>>> BioRuby mailing list >>>> BioRuby at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >>> _______________________________________________ >>> BioRuby Project - http://www.bioruby.org/ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> From cjfields at illinois.edu Mon Feb 13 14:17:06 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 13 Feb 2012 14:17:06 +0000 Subject: [BioRuby] Article Published In-Reply-To: References: Message-ID: <5D185D71-962B-4C4E-A1B5-D1AC1D7D190B@illinois.edu> congrats to everyone involved! chris On Feb 13, 2012, at 1:16 AM, Raoul Bonnal wrote: > Dear all, > > We are happy to announce another paper! This time on 'Biogem: an > effective tool based approach for scaling up open source software > development in bioinformatics'. This was a community paper where all > early biogem authors contributed to the paper in its final form. > > http://bioinformatics.oxfordjournals.org/content/early/2012/02/12/bioinforma > tics.bts080.short?rss=1 > > Enjoy, > > Ra & Pj. > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From francesco.strozzi at gmail.com Mon Feb 13 14:42:28 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 13 Feb 2012 15:42:28 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120213105028.GA5237@thebird.nl> Message-ID: Ok for me too about IRC meetings. And also about Google Hangouts with Scala / D. Cheers On Mon, Feb 13, 2012 at 11:58, Raoul Bonnal wrote: > > I know that :-) so, please post ideas in this ML. > > +1 for Scala/D over Google Hangout > > On 13/02/12 11.50, "Pjotr Prins" wrote: > > > I am pretty hopeless with IRC. But I guess we should discuss > > possibilities for GSoC. Also, if anyone is interested, I could talk > > about Scala and D using Google Hangout. > > > > On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: > >> I agree with Pjotr, > >> So please post your ideas here and update the wiki. > >> It's time to re-start IRC meetings, what about Feb 16 around: > >> 9:00 GMT > >> 10:00 Italy > >> 18:00 Japan > >> 4:00 NewYork ( too early ? :-) > >> > >> About BioNGS, I think it's too complicated by itself, but I could have 2 > >> students working on this project. > >> > >> On 10/02/12 20.03, "Pjotr Prins" wrote: > >> > >>> Building out on the idea of involving newbies in easy projects, I > >>> would like to invite all plugin authors to come up with ideas on this > >>> list. Even the smallest idea will help. So think beyond SoC. > >>> > >>> Michael came up with gemifying, or componentizing BioRuby. And also > >>> upgrading our web presentation. Good ideas, any others? > >>> > >>> Francesco, what about bio-ngs? > >>> > >>> Pj. > >>> > >>> On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > >>>> Hi all, > >>>> > >>>> I'm going to be OBF project admin again this year for Google Summer of > >>>> code. > >>>> OBF's application is due in a couple of weeks, and we need to update > our > >>>> project ideas on the OBF wiki page and on each project's individual > wiki > >>>> pages. > >>>> > >>>> So, for each of the OBF projects that wants to do GSoC again this > year, > >>>> please: > >>>> > >>>> a.) Update the list of project ideas on your project's GSoC page > >>>> (BioPython, > >>>> BioPerl, BioRuby, etc). Add new ones, remove ones that have already > been > >>>> done or no longer relevant, etc. > >>>> > >>>> b.) Update the list of project ideas on the main OBF GSoC page > >>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > >>>> > >>>> c.) Let me know via email that you have done so and it's ready for > Google > >>>> to > >>>> peruse. > >>>> > >>>> Please have the updates done, if possible, by this Friday (March 11). > The > >>>> number and quality of the project ideas are part of the evaluation > process > >>>> for whether OBF is accepted as a Summer of Code organization again > this > >>>> year, > >>>> so let's come up with some good ones. :-) > >>>> > >>>> Rob > >>>> > >>>> ---- > >>>> Robert Buels > >>>> (prospective) 2012 OBF GSoC Organization Admin > >>>> > >>>> > >>>> _______________________________________________ > >>>> BioRuby Project - http://www.bioruby.org/ > >>>> BioRuby mailing list > >>>> BioRuby at lists.open-bio.org > >>>> http://lists.open-bio.org/mailman/listinfo/bioruby > >>>> > >>> _______________________________________________ > >>> BioRuby Project - http://www.bioruby.org/ > >>> BioRuby mailing list > >>> BioRuby at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From mictadlo at gmail.com Tue Feb 14 04:33:04 2012 From: mictadlo at gmail.com (Mic) Date: Tue, 14 Feb 2012 14:33:04 +1000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> Message-ID: Hi, Did anyone try out * GO: http://en.wikipedia.org/wiki/Go_(programming_language) * Rust: http://en.wikipedia.org/wiki/Rust_(programming_language) * Vala: http://en.wikipedia.org/wiki/Vala_(programming_language) On Mon, Feb 13, 2012 at 8:46 PM, Raoul Bonnal wrote: > Yeah, I was thinking the exact same thing. > > This kind of documentation will be of great help!!! I'm thinking about > teaching Ruby @ Uni. > > What I missed from the previous email is: > Beautiful code come from coders but that is not enough, working with people > in this ML I found that the quality of code and its beauty increase only if > you chat/talk with people and you are available to accept critics and > contributes. > > Another tab ? ;-) > > > On 13/02/12 11.34, "Pjotr Prins" wrote: > > > Excellent. > > > > May I propose that at least the other half of the authors of the > > Biogem paper send in an example of beautiful code? We can compile > > these snippets on a special page on one of the websites (or both). > > That will help courses, 'newbies' and even 'die hard' Perl users, such > > as Yoda, to see what this Ruby thing is about. > > > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > > herh herh. > > > > Pj. > > > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: > >> Some code I particularly liked comes from the BioNGS Wrapper library (by > >> Raoul). The gem is in development and I'm contributing to it so I could > >> look at the code from a very close perspective! > >> > >> https://gist.github.com/1815501 > >> > >> What is interesting is the use of an internal DSL which makes the code > >> particularly expressive and readable, and writing a wrapper becomes > only a > >> matter of defining the options that the command line binary expects. The > >> library is quite large and includes also methods to define aliases for > the > >> options. > >> This module makes use also of the powerful Thor gem (used in Rails) to > >> create and define tasks that can be used to launch the binaries and to > >> include them in larger workflows and pipelines. > >> Now let's say you want to turn your freshly new wrapped binary into a > >> mighty Thor taks, all you need to do is: > >> > >> https://gist.github.com/1815523 > >> > >> The amazing part is that the parameters passed to the block works like > >> arguments definition for the Thor task itself. The code that makes this > >> possible behind the scenes is here: > >> > >> https://gist.github.com/1815481 > >> > >> It checks also if the number of arguments passed are equal to the > arguments > >> of the block. If not, it raises an error to the user as he/she is > calling > >> the task with the wrong number of arguments. To understand every part > you > >> need to know a bit the way the Thor library defines tasks (more here: > >> https://github.com/wycats/thor) but the code here in BioNGS definitely > >> worth a look! > >> > >> P.S. I'm diving into Scala too :-). I took the Odersky book few months > ago > >> and now I'm about to start looking in details at this new programming > >> language. Easy and powerful parallelism is the new goal we need to > achieve > >> to keep up with the big data era. > >> > >> Cheers > >> > >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins >wrote: > >> > >>> OK, here another candidate for the price of beautiful code: > >>> > >>> > >>> > https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti > >>> l/restriction_enzyme/range/sequence_range/calculated_cuts.rb > >>> > >>> Trevor has implemented some hairy logic into the RE code. I mean > >>> hairy, that if it were done by someone else it would become spaghetti > >>> code (plenty of examples there in the real world!). You can see, that > >>> even when choosing sensible names, and explaining the code with good > >>> comments, it may still be hard to understand! But I think > >>> > >>> def add_cuts_from_cut_ranges(cut_ranges) > >>> > >>> pretty much sums it up :). Still, it is beautiful, because it is hard > >>> to think of doing it better. The Ruby code is short and self > >>> explanatory and RE library has almost become a DSL for cutting > >>> sequences using restriction enzymes. That is beautiful. > >>> > >>> Pj. > >>> > >>> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > >>>> Hi All > >>>> Beauty is in the eyes of the beholder! > >>>> The Bio-Alignment plugin can read and interconvert a nucleotide > >>>> alignment to an amino acid alignment. I liked the simplicity of how > >>>> PJ has implemented the codon to amino acid conversion helper method > >>>> while taking care of the gaps or undefined aa translations. > >>>> > >>>> # lazily convert to Amino acid (once only) > >>>> def to_aa > >>>> aa = translate > >>>> if not aa > >>>> if gap? > >>>> return '-' > >>>> elsif undefined? > >>>> return 'X' > >>>> else > >>>> raise 'What?' > >>>> end > >>>> end > >>>> aa > >>>> end > >>>> > >>>> This method does not have any ruby 'magic' and is self documenting. > >>>> The gap? and undefined? methods are implemented as simple one line > >>>> standalone methods. > >>>> > >>>> Again I like this simple 'trick' of getting an array of codons from a > >>>> sequence in the codonsequence class. > >>>> > >>>> seq.scan(/\S\S\S/) #gets an array of codons > >>>> > >>>> The longer alternative would be to create a bio::sequence::NA object > >>>> and iterate > >>>> seq = Bio::Sequence::NA.new("blahahahha") > >>>> seq.window_search(3, 3) do |subseq| > >>>> puts subseq > >>>> end > >>>> > >>>> It seems more intuitive to represent a sequence as an array of codon > >>>> objects. In this way the codons have some state and can carry > >>>> 'luggage'. getting the string representation of the sequence is as > >>>> simple as > >>>> def to_s > >>>> @seq.map { |codon| codon.to_s }.join(' ') > >>>> end > >>>> > >>>> To be more DRY, the to_nt method in the same class could be aliased > >>>> from the to_s method > >>>> > >>>> It seems the bio-plugins are a rich source of tricks and great > >>> learning.... ! > >>>> > >>>> > >>>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock < > p.j.a.cock at googlemail.com> > >>> wrote: > >>>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > >>> pjotr.public14 at thebird.nl> wrote: > >>>>>> Correct me if I am wrong, but has everyone moved across to BioPython > >>>>>> now? Or even to the dark side? > >>>>>> > >>>>>> Pj. > >>>>> > >>>>> I haven't noticed any BioRuby developers posting on the Biopython > >>>>> mailing lists recently - but you'd be welcome ;) > >>>>> > >>>>> On a related topic, my first BioRuby pull request was merged, so > >>>>> there is a little direct cross project contribution going on :) > >>>>> > >>>>> > >>> > https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd > >>> 094c5d > >>>>> > >>>>> Peter > >>>>> _______________________________________________ > >>>>> BioRuby Project - http://www.bioruby.org/ > >>>>> BioRuby mailing list > >>>>> BioRuby at lists.open-bio.org > >>>>> http://lists.open-bio.org/mailman/listinfo/bioruby > >>>> > >>>> > >>>> > >>>> -- > >>>> --------------- > >>>> Sincerely > >>>> George > >>>> Skype: george_g2 > >>>> Blog: http://biorelated.wordpress.com/ > >>>> Twitter: http://twitter.com/#!/george_l > >>>> > >>> _______________________________________________ > >>> BioRuby Project - http://www.bioruby.org/ > >>> BioRuby mailing list > >>> BioRuby at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioruby > >>> > >> > >> > >> > >> -- > >> > >> Francesco > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Feb 14 07:19:50 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 08:19:50 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> Message-ID: <20120214071950.GA11317@thebird.nl> New programming languages are great. It is a form of evolution :). You should try to learn a language every year. The Clojure fan-boys have been quiet here - that is another one. Personally I looked a Go, and did not like it that much (apart from Go-routines). It is a bit over its hype now, so we can see what happens. Programming languages, nevertheless, do not solve the problem of programming. Never believe the person who tells you that all problems will be solved by programming language X. I know people who stick with C++ and are extremely productive, mostly because they have very rich libraries. I think they could do better with D, in the really long term. But who am I to suggest that? And I know people who are extremely productive with Ruby. Go figure. Pj. On Tue, Feb 14, 2012 at 02:33:04PM +1000, Mic wrote: > Hi, > Did anyone try out > * GO: [1]http://en.wikipedia.org/wiki/Go_(programming_language) > * Rust: [2]http://en.wikipedia.org/wiki/Rust_(programming_language) > * Vala: [3]http://en.wikipedia.org/wiki/Vala_(programming_language) > > On Mon, Feb 13, 2012 at 8:46 PM, Raoul Bonnal <[4]bonnal at ingm.org> wrote: > > Yeah, I was thinking the exact same thing. > > This kind of documentation will be of great help!!! I'm thinking about > teaching Ruby @ Uni. > > What I missed from the previous email is: > Beautiful code come from coders but that is not enough, working with > people > in this ML I found that the quality of code and its beauty increase only > if > you chat/talk with people and you are available to accept critics and > contributes. > > Another tab ? ;-) > > On 13/02/12 11.34, "Pjotr Prins" <[5]pjotr.public14 at thebird.nl> wrote: > > > Excellent. > > > > May I propose that at least the other half of the authors of the > > Biogem paper send in an example of beautiful code? We can compile > > these snippets on a special page on one of the websites (or both). > > That will help courses, 'newbies' and even 'die hard' Perl users, such > > as Yoda, to see what this Ruby thing is about. > > > > Maybe it is time for a 'Bioinformatics Ruby Academy'. Ruby rules. Herh > > herh herh. > > > > Pj. > > > > On Mon, Feb 13, 2012 at 11:06:03AM +0100, Francesco Strozzi wrote: > >> Some code I particularly liked comes from the BioNGS Wrapper library > (by > >> Raoul). The gem is in development and I'm contributing to it so I > could > >> look at the code from a very close perspective! > >> > >> [6]https://gist.github.com/1815501 > >> > >> What is interesting is the use of an internal DSL which makes the > code > >> particularly expressive and readable, and writing a wrapper becomes > only a > >> matter of defining the options that the command line binary expects. > The > >> library is quite large and includes also methods to define aliases > for the > >> options. > >> This module makes use also of the powerful Thor gem (used in Rails) > to > >> create and define tasks that can be used to launch the binaries and > to > >> include them in larger workflows and pipelines. > >> Now let's say you want to turn your freshly new wrapped binary into a > >> mighty Thor taks, all you need to do is: > >> > >> [7]https://gist.github.com/1815523 > >> > >> The amazing part is that the parameters passed to the block works > like > >> arguments definition for the Thor task itself. The code that makes > this > >> possible behind the scenes is here: > >> > >> [8]https://gist.github.com/1815481 > >> > >> It checks also if the number of arguments passed are equal to the > arguments > >> of the block. If not, it raises an error to the user as he/she is > calling > >> the task with the wrong number of arguments. To understand every part > you > >> need to know a bit the way the Thor library defines tasks (more here: > >> [9]https://github.com/wycats/thor) but the code here in BioNGS > definitely > >> worth a look! > >> > >> P.S. I'm diving into Scala too :-). I took the Odersky book few > months ago > >> and now I'm about to start looking in details at this new programming > >> language. Easy and powerful parallelism is the new goal we need to > achieve > >> to keep up with the big data era. > >> > >> Cheers > >> > >> On Mon, Feb 13, 2012 at 08:54, Pjotr Prins > <[10]pjotr.public14 at thebird.nl>wrote: > >> > >>> OK, here another candidate for the price of beautiful code: > >>> > >>> > >>> > [11]https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti > >>> l/restriction_enzyme/range/sequence_range/calculated_cuts.rb > >>> > >>> Trevor has implemented some hairy logic into the RE code. I mean > >>> hairy, that if it were done by someone else it would become > spaghetti > >>> code (plenty of examples there in the real world!). You can see, > that > >>> even when choosing sensible names, and explaining the code with good > >>> comments, it may still be hard to understand! But I think > >>> > >>> def add_cuts_from_cut_ranges(cut_ranges) > >>> > >>> pretty much sums it up :). Still, it is beautiful, because it is > hard > >>> to think of doing it better. The Ruby code is short and self > >>> explanatory and RE library has almost become a DSL for cutting > >>> sequences using restriction enzymes. That is beautiful. > >>> > >>> Pj. > >>> > >>> On Sat, Feb 11, 2012 at 11:27:44PM +0300, George Githinji wrote: > >>>> Hi All > >>>> Beauty is in the eyes of the beholder! > >>>> The Bio-Alignment plugin can read and interconvert a nucleotide > >>>> alignment to an amino acid alignment. I liked the simplicity of > how > >>>> PJ has implemented the codon to amino acid conversion helper method > >>>> while taking care of the gaps or undefined aa translations. > >>>> > >>>> # lazily convert to Amino acid (once only) > >>>> def to_aa > >>>> aa = translate > >>>> if not aa > >>>> if gap? > >>>> return '-' > >>>> elsif undefined? > >>>> return 'X' > >>>> else > >>>> raise 'What?' > >>>> end > >>>> end > >>>> aa > >>>> end > >>>> > >>>> This method does not have any ruby 'magic' and is self documenting. > >>>> The gap? and undefined? methods are implemented as simple one line > >>>> standalone methods. > >>>> > >>>> Again I like this simple 'trick' of getting an array of codons from > a > >>>> sequence in the codonsequence class. > >>>> > >>>> seq.scan(/\S\S\S/) #gets an array of codons > >>>> > >>>> The longer alternative would be to create a bio::sequence::NA > object > >>>> and iterate > >>>> seq = Bio::Sequence::NA.new("blahahahha") > >>>> seq.window_search(3, 3) do |subseq| > >>>> puts subseq > >>>> end > >>>> > >>>> It seems more intuitive to represent a sequence as an array of > codon > >>>> objects. In this way the codons have some state and can carry > >>>> 'luggage'. getting the string representation of the sequence is as > >>>> simple as > >>>> def to_s > >>>> @seq.map { |codon| codon.to_s }.join(' ') > >>>> end > >>>> > >>>> To be more DRY, the to_nt method in the same class could be aliased > >>>> from the to_s method > >>>> > >>>> It seems the bio-plugins are a rich source of tricks and great > >>> learning.... ! > >>>> > >>>> > >>>> On Sat, Feb 11, 2012 at 10:08 PM, Peter Cock > <[12]p.j.a.cock at googlemail.com> > >>> wrote: > >>>>> On Sat, Feb 11, 2012 at 5:46 PM, Pjotr Prins < > >>> [13]pjotr.public14 at thebird.nl> wrote: > >>>>>> Correct me if I am wrong, but has everyone moved across to > BioPython > >>>>>> now? Or even to the dark side? > >>>>>> > >>>>>> Pj. > >>>>> > >>>>> I haven't noticed any BioRuby developers posting on the Biopython > >>>>> mailing lists recently - but you'd be welcome ;) > >>>>> > >>>>> On a related topic, my first BioRuby pull request was merged, so > >>>>> there is a little direct cross project contribution going on :) > >>>>> > >>>>> > >>> > [14]https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd > >>> 094c5d > >>>>> > >>>>> Peter > >>>>> _______________________________________________ > >>>>> BioRuby Project - [15]http://www.bioruby.org/ > >>>>> BioRuby mailing list > >>>>> [16]BioRuby at lists.open-bio.org > >>>>> [17]http://lists.open-bio.org/mailman/listinfo/bioruby > >>>> > >>>> > >>>> > >>>> -- > >>>> --------------- > >>>> Sincerely > >>>> George > >>>> Skype: george_g2 > >>>> Blog: [18]http://biorelated.wordpress.com/ > >>>> Twitter: [19]http://twitter.com/#!/george_l > >>>> > >>> _______________________________________________ > >>> BioRuby Project - [20]http://www.bioruby.org/ > >>> BioRuby mailing list > >>> [21]BioRuby at lists.open-bio.org > >>> [22]http://lists.open-bio.org/mailman/listinfo/bioruby > >>> > >> > >> > >> > >> -- > >> > >> Francesco > >> _______________________________________________ > >> BioRuby Project - [23]http://www.bioruby.org/ > >> BioRuby mailing list > >> [24]BioRuby at lists.open-bio.org > >> [25]http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - [26]http://www.bioruby.org/ > > BioRuby mailing list > > [27]BioRuby at lists.open-bio.org > > [28]http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby Project - [29]http://www.bioruby.org/ > BioRuby mailing list > [30]BioRuby at lists.open-bio.org > [31]http://lists.open-bio.org/mailman/listinfo/bioruby > > References > > Visible links > 1. http://en.wikipedia.org/wiki/Go_(programming_language) > 2. http://en.wikipedia.org/wiki/Rust_(programming_language) > 3. http://en.wikipedia.org/wiki/Vala_(programming_language) > 4. mailto:bonnal at ingm.org > 5. mailto:pjotr.public14 at thebird.nl > 6. https://gist.github.com/1815501 > 7. https://gist.github.com/1815523 > 8. https://gist.github.com/1815481 > 9. https://github.com/wycats/thor > 10. mailto:pjotr.public14 at thebird.nl > 11. https://github.com/trevor/bioruby-restriction_enzyme/blob/master/lib/bio/uti > 12. mailto:p.j.a.cock at googlemail.com > 13. mailto:pjotr.public14 at thebird.nl > 14. https://github.com/bioruby/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd > 15. http://www.bioruby.org/ > 16. mailto:BioRuby at lists.open-bio.org > 17. http://lists.open-bio.org/mailman/listinfo/bioruby > 18. http://biorelated.wordpress.com/ > 19. http://twitter.com/#!/george_l > 20. http://www.bioruby.org/ > 21. mailto:BioRuby at lists.open-bio.org > 22. http://lists.open-bio.org/mailman/listinfo/bioruby > 23. http://www.bioruby.org/ > 24. mailto:BioRuby at lists.open-bio.org > 25. http://lists.open-bio.org/mailman/listinfo/bioruby > 26. http://www.bioruby.org/ > 27. mailto:BioRuby at lists.open-bio.org > 28. http://lists.open-bio.org/mailman/listinfo/bioruby > 29. http://www.bioruby.org/ > 30. mailto:BioRuby at lists.open-bio.org > 31. http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Tue Feb 14 08:24:32 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 09:24:32 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> Message-ID: <20120214082432.GA12201@thebird.nl> On Mon, Feb 13, 2012 at 11:46:26AM +0100, Raoul Bonnal wrote: > in this ML I found that the quality of code and its beauty increase > only if you chat/talk with people and you are available to accept > critics and contributes. I feel we can keep the momentum going if we use this list as a more general outlet of our personal development. It may be a metamorphosis of the old style of ML. Bio* is no longer about specialized libraries, it is mainly about the problem of software development in biology. I feel Ruby attracts the right type of people - that is why we have 'beautiful code' in the subject ;). The ML is the first place to share information. This is what new potential recruits may find interesting. Have them find us. In that vein I am presenting another piece of beautiful code, the omnipresent FlatFile handler of BioRuby. See https://github.com/bioruby/bioruby/blob/master/sample/any2fasta.rb e.g. ARGV.each do | fn | ff = Bio::FlatFile.auto(fn) ff.each_entry do |entry| if regex != nil next if eval("entry.seq !~ #{regex}") end print entry.seq.to_fasta(entry.definition,70) end end which does a lot of work in a few lines, with remarkable flexibility! Including automatic data format checking and a runtime defined regex search. Nowadays we would probably do it a little different. The eval can be taken out of the loop and the regex compiled (in a Pythonesque way). Also both each_entry and the Sequence objects should be lazy (it is not underneath) and properly iterate to avoid loading everything in RAM and parsing too much. But hey, it is still a great example what what we can do with Ruby anyway! I wrote this simple example any2fasta.rb 6 years ago, but the FlatFile and Sequence code is not mine. It is mostly by Toshiaka and Naohisa going all the way back to 2002. So the beautiful code is really by those two geniuses who are at the heart of the BioRuby project. Pj. From ngoto at gen-info.osaka-u.ac.jp Tue Feb 14 08:49:21 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 14 Feb 2012 17:49:21 +0900 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120211074751.GA23063@thebird.nl> References: <20120208184817.GA31948@thebird.nl> <20120208205257.GA10435@bartonh-mbp-01.uanet.edu> <20120211074751.GA23063@thebird.nl> Message-ID: <20120214084921.C3C971CBC528@idnmail.gen-info.osaka-u.ac.jp> Hi Michael, Pjotr and all, I've put current website contents of http://bioruby.org to GitHub. (excluding archives directory) https://github.com/ngoto/bioruby.org-webpage Please send new web contents with your idea. Due to the server-side restrictions and mirroring to http://bioruby.open-bio.org/, only static files are allowed. (CGI and server-side dynamic contents cannot be used.) Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Sat, 11 Feb 2012 08:47:51 +0100 Pjotr Prins wrote: > Dear Toshiaki and Naohisa, > > I believe Michael has a very valid point. How about defining a > project (potentially SoC), where we lay out the functionality we want > from such a web presence? > > Pj. > > On Wed, Feb 08, 2012 at 03:52:57PM -0500, Michael Barton wrote: > > I think making the homepage simpler would be very > > beneficial. For instance I think the two most important > > links (Tutorial and Sample codes) pages should be given much > > greater prominence. These are the two pages which most > > beginners will want to get started with. Compare with the > > Sinatra page which has only six links on the front page > > pointing to the most significant parts of the project. > > > > I think the Tutorial and Sample codes pages could do with > > some love also. These pages do not match the visual layout > > of the bioruby home page, one is in a separate domain while > > the other is a wiki page. I think these pages deserve > > attention to make them simpler and more accessible. A common > > CSS theme also provides a unified front to the BioRuby > > project. > > > > Compare with the Sinatra intro and documentation pages: > > * http://www.sinatrarb.com/intro > > * http://www.sinatrarb.com/documentation > > > > My opinion is that the BioRuby website should head in this > > direction. I am not a web designer but I am happy to > > contribute effort to writing web copy and BioRuby recipes. I > > also think that bioruby should also have its own web address > > too. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From bonnal at ingm.org Tue Feb 14 09:50:43 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 14 Feb 2012 10:50:43 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: Message-ID: Hi all, I updated http://bioruby.open-bio.org/wiki/Google_Summer_of_Code starting from this thread, fell free to modify (title?) fill, add text and other projects as well. By Feb 24 we must have our proposals ready to go. On 13/02/12 15.42, "Francesco Strozzi" wrote: > Ok for me too about IRC meetings. And also about Google Hangouts with Scala / > D. > > Cheers > > On Mon, Feb 13, 2012 at 11:58, Raoul Bonnal wrote: >> >> I know that :-) so, please post ideas in this ML. >> >> +1 for Scala/D over Google Hangout >> >> On 13/02/12 11.50, "Pjotr Prins" wrote: >> >>> > I am pretty hopeless with IRC. But I guess we should discuss >>> > possibilities for GSoC. Also, if anyone is interested, I could talk >>> > about Scala and D using Google Hangout. >>> > >>> > On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: >>>> >> I agree with Pjotr, >>>> >> So please post your ideas here and update the wiki. >>>> >> It's time to re-start IRC meetings, what about Feb 16 around: >>>> >> 9:00 GMT >>>> >> 10:00 Italy >>>> >> 18:00 Japan >>>> >> 4:00 ?NewYork ( too early ? :-) >>>> >> >>>> >> About BioNGS, I think it's too complicated by itself, but I could have 2 >>>> >> students working on this project. >>>> >> >>>> >> On 10/02/12 20.03, "Pjotr Prins" wrote: >>>> >> >>>>> >>> Building out on the idea of involving newbies in easy projects, I >>>>> >>> would like to invite all plugin authors to come up with ideas on this >>>>> >>> list. Even the smallest idea will help. So think beyond SoC. >>>>> >>> >>>>> >>> Michael came up with gemifying, or componentizing BioRuby. And also >>>>> >>> upgrading our web presentation. Good ideas, any others? >>>>> >>> >>>>> >>> Francesco, what about bio-ngs? >>>>> >>> >>>>> >>> Pj. >>>>> >>> >>>>> >>> On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: >>>>>> >>>> Hi all, >>>>>> >>>> >>>>>> >>>> I'm going to be OBF project admin again this year for Google Summer of >>>>>> >>>> code. >>>>>> >>>> OBF's application is due in a couple of weeks, and we need to update our >>>>>> >>>> project ideas on the OBF wiki page and on each project's individual wiki >>>>>> >>>> pages. >>>>>> >>>> >>>>>> >>>> So, for each of the OBF projects that wants to do GSoC again this >>>>>> year, >>>>>> >>>> please: >>>>>> >>>> >>>>>> >>>> a.) Update the list of project ideas on your project's GSoC page >>>>>> >>>> (BioPython, >>>>>> >>>> BioPerl, BioRuby, etc). ?Add new ones, remove ones that have already been >>>>>> >>>> done or no longer relevant, etc. >>>>>> >>>> >>>>>> >>>> b.) Update the list of project ideas on the main OBF GSoC page >>>>>> >>>> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. >>>>>> >>>> >>>>>> >>>> c.) Let me know via email that you have done so and it's ready for >>>>>> Google >>>>>> >>>> to >>>>>> >>>> peruse. >>>>>> >>>> >>>>>> >>>> Please have the updates done, if possible, by this Friday (March >>>>>> 11). The >>>>>> >>>> number and quality of the project ideas are part of the evaluation >>>>>> process >>>>>> >>>> for whether OBF is accepted as a Summer of Code organization again this >>>>>> >>>> year, >>>>>> >>>> so let's come up with some good ones. ?:-) >>>>>> >>>> >>>>>> >>>> Rob >>>>>> >>>> >>>>>> >>>> ---- >>>>>> >>>> Robert Buels >>>>>> >>>> (prospective) 2012 OBF GSoC Organization Admin >>>>>> >>>> >>>>>> >>>> >>>>>> >>>> _______________________________________________ >>>>>> >>>> BioRuby Project - http://www.bioruby.org/ >>>>>> >>>> BioRuby mailing list >>>>>> >>>> BioRuby at lists.open-bio.org >>>>>> >>>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>>>> >>>> >>>>> >>> _______________________________________________ >>>>> >>> BioRuby Project - http://www.bioruby.org/ >>>>> >>> BioRuby mailing list >>>>> >>> BioRuby at lists.open-bio.org >>>>> >>> http://lists.open-bio.org/mailman/listinfo/bioruby >>>> >> >>>> >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > From ngoto at gen-info.osaka-u.ac.jp Tue Feb 14 11:22:59 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Tue, 14 Feb 2012 20:22:59 +0900 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: Message-ID: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> Hi Raoul, I think "Restyling BioRuby.org" is very difficult for Google Summer of Code 2012 because the FAQ says that documentation-only work cannot be accepted. http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/faqs#documentation >> 12. Are proposals for documentation work eligible for Google Summer of Code? >> >> While we greatly appreciate the value of documentation, this program is an exercise in developing code; we can't accept proposals for documentation-only work at this time. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Tue, 14 Feb 2012 10:50:43 +0100 Raoul Bonnal wrote: > Hi all, > I updated http://bioruby.open-bio.org/wiki/Google_Summer_of_Code starting > from this thread, fell free to modify (title?) fill, add text and other > projects as well. > By Feb 24 we must have our proposals ready to go. > > > From bonnal at ingm.org Tue Feb 14 11:25:28 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 14 Feb 2012 12:25:28 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On 14/02/12 12.22, "Naohisa GOTO" wrote: > Hi Raoul, > > I think "Restyling BioRuby.org" is very difficult for > Google Summer of Code 2012 because the FAQ says that > documentation-only work cannot be accepted. Ok good to know. > > http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/ > faqs#documentation >>> 12. Are proposals for documentation work eligible for Google Summer of Code? >>> >>> While we greatly appreciate the value of documentation, this program is an >>> exercise in developing code; we can't accept proposals for >>> documentation-only work at this time. > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > On Tue, 14 Feb 2012 10:50:43 +0100 > Raoul Bonnal wrote: > >> Hi all, >> I updated http://bioruby.open-bio.org/wiki/Google_Summer_of_Code starting >> from this thread, fell free to modify (title?) fill, add text and other >> projects as well. >> By Feb 24 we must have our proposals ready to go. >> >> >> From pjotr.public14 at thebird.nl Tue Feb 14 11:35:23 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 12:35:23 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> References: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120214113523.GB17407@thebird.nl> On Tue, Feb 14, 2012 at 08:22:59PM +0900, Naohisa GOTO wrote: > I think "Restyling BioRuby.org" is very difficult for > Google Summer of Code 2012 because the FAQ says that > documentation-only work cannot be accepted. > > http://www.google-melange.com/gsoc/document/show/gsoc_program/google/gsoc2012/faqs#documentation > >> 12. Are proposals for documentation work eligible for Google Summer of Code? > >> > >> While we greatly appreciate the value of documentation, this program is an exercise in developing code; we can't accept proposals for documentation-only work at this time. Depends on the programming component. If we use staticmatic and HAML to generate the site, with coffeescript to interact with github and others, I think it becomes a very interesting programming job. Also the 'documentation' could consist of real example scripts, which execute. Possibly showing results online. I don't think students should be documenting, but they can put software together to make creating tutorials easier. I realize bioruby.org needs to be static, but it does not mean we can not host other services elsewhere, and even use Ruby on Rails. GSoC students are supposed to learn to program and to contribute to the main project. That is the key. If a project aims to achieve that, it can be part of GSoC. Restyling the Bioruby.org goes much deeper than documentation, in my opinion. Pj. From marian.povolny at gmail.com Tue Feb 14 12:53:13 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Tue, 14 Feb 2012 13:53:13 +0100 Subject: [BioRuby] GSoC participation without biology knowledge? Message-ID: Hello everybody, I'm a prospective GSoC student and would like to ask a short question before properly introducing myself on the mailing list. I have no knowledge about biology whatsoever. Would I be able to contribute to the bioruby project anyway? From the project list, the following project seems to be a fit: "Support Next Generation Sequencing (NGS) in BioRuby". I do have experience with Bash, Linux and Rails, but like I said, I don't have any experience related to biology beyond primary school. However, I'm looking into ways to enter the field and this would be a great starting point, if possible, of course. Thx, Marjan From pjotr.public14 at thebird.nl Tue Feb 14 14:57:40 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 14 Feb 2012 15:57:40 +0100 Subject: [BioRuby] GSoC participation without biology knowledge? In-Reply-To: References: Message-ID: <20120214145740.GB18873@thebird.nl> Hi Marjan, The idea is programming first. The biology we can help with, if needed :) Pj. On Tue, Feb 14, 2012 at 01:53:13PM +0100, Marjan Povolni wrote: > Hello everybody, > > I'm a prospective GSoC student and would like to ask a short question > before properly introducing myself on the mailing list. > > I have no knowledge about biology whatsoever. Would I be able to contribute > to the bioruby project anyway? From the project list, the following project > seems to be a fit: "Support Next Generation Sequencing (NGS) in BioRuby". I > do have experience with Bash, Linux and Rails, but like I said, I don't > have any experience related to biology beyond primary school. > > However, I'm looking into ways to enter the field and this would be a great > starting point, if possible, of course. > > Thx, > Marjan > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Tue Feb 14 16:50:56 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 14 Feb 2012 17:50:56 +0100 Subject: [BioRuby] MAF UCSC and intervals Message-ID: Dear all, Can we parse a .MAF file and extract a spliced alignment like http://biopython.org/wiki/Multiple_Alignment_Format#Retrieving_a_pre-spliced _alignment_over_a_given_set_of_exons ? Why this ? I?m looking for new coding transcripts and I want to use https://github.com/mlin/PhyloCSF/wiki but I must recreate a specific alignment for every new transcript I identified with cufflinks. -- Ra From bonnal at ingm.org Thu Feb 16 09:13:24 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 16 Feb 2012 10:13:24 +0100 Subject: [BioRuby] GSoC participation without biology knowledge? In-Reply-To: <20120214145740.GB18873@thebird.nl> Message-ID: Hi Marjna, Pjotr is right but I think it also important to understand which are your motivations and interests in Bioinformatics, and from your email it seems you are intrigued by this field. The general ideas is to have people contributing to the Bio* projects also after the end of GSoC. So please, introduce yourself and let's discuss about GSoC projects. On 14/02/12 15.57, "Pjotr Prins" wrote: > Hi Marjan, > > The idea is programming first. The biology we can help with, if > needed :) > > Pj. > > On Tue, Feb 14, 2012 at 01:53:13PM +0100, Marjan Povolni wrote: >> Hello everybody, >> >> I'm a prospective GSoC student and would like to ask a short question >> before properly introducing myself on the mailing list. >> >> I have no knowledge about biology whatsoever. Would I be able to contribute >> to the bioruby project anyway? From the project list, the following project >> seems to be a fit: "Support Next Generation Sequencing (NGS) in BioRuby". I >> do have experience with Bash, Linux and Rails, but like I said, I don't >> have any experience related to biology beyond primary school. >> >> However, I'm looking into ways to enter the field and this would be a great >> starting point, if possible, of course. >> >> Thx, >> Marjan >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Thu Feb 16 09:43:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 10:43:35 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120210190335.GA20909@thebird.nl> Message-ID: <20120216094335.GA32160@thebird.nl> We are on IRC today: irc.freenode.net join #bioruby the channel logs are here (thanks to Toshiaki): http://irc.bioruby.org On Mon, Feb 13, 2012 at 12:17:30AM +0100, Raoul Bonnal wrote: > I agree with Pjotr, > So please post your ideas here and update the wiki. > It's time to re-start IRC meetings, what about Feb 16 around: > 9:00 GMT > 10:00 Italy > 18:00 Japan > 4:00 NewYork ( too early ? :-) > > About BioNGS, I think it's too complicated by itself, but I could have 2 > students working on this project. > > On 10/02/12 20.03, "Pjotr Prins" wrote: > > > Building out on the idea of involving newbies in easy projects, I > > would like to invite all plugin authors to come up with ideas on this > > list. Even the smallest idea will help. So think beyond SoC. > > > > Michael came up with gemifying, or componentizing BioRuby. And also > > upgrading our web presentation. Good ideas, any others? > > > > Francesco, what about bio-ngs? > > > > Pj. > > > > On Fri, Feb 10, 2012 at 06:04:31PM +0000, Fields, Christopher J wrote: > >> Hi all, > >> > >> I'm going to be OBF project admin again this year for Google Summer of code. > >> OBF's application is due in a couple of weeks, and we need to update our > >> project ideas on the OBF wiki page and on each project's individual wiki > >> pages. > >> > >> So, for each of the OBF projects that wants to do GSoC again this year, > >> please: > >> > >> a.) Update the list of project ideas on your project's GSoC page (BioPython, > >> BioPerl, BioRuby, etc). Add new ones, remove ones that have already been > >> done or no longer relevant, etc. > >> > >> b.) Update the list of project ideas on the main OBF GSoC page > >> (http://www.open-bio.org/wiki/Google_Summer_of_Code) to match. > >> > >> c.) Let me know via email that you have done so and it's ready for Google to > >> peruse. > >> > >> Please have the updates done, if possible, by this Friday (March 11). The > >> number and quality of the project ideas are part of the evaluation process > >> for whether OBF is accepted as a Summer of Code organization again this year, > >> so let's come up with some good ones. :-) > >> > >> Rob > >> > >> ---- > >> Robert Buels > >> (prospective) 2012 OBF GSoC Organization Admin > >> > >> > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From marian.povolny at gmail.com Thu Feb 16 10:28:03 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Thu, 16 Feb 2012 11:28:03 +0100 Subject: [BioRuby] My proper GSoC introduction Message-ID: Hello once again, My name is Marjan Povolni, I'm 27 years old and currently wrapping up my Masters in CS. My dissertation project will be done in a weeks time, but due to some bureaucracy requirements I won't be graduating until April. I saw that the requirement for GSoC is to be enrolled in an academic institution on April 23rd, so that fits me well. I also have some 5 years of professional experience working for a local outsourcing company, working with lots of technologies. If someone's interested in details, you can take a look at my LinkedIn page: http://rs.linkedin.com/in/mpovolni. I'm very curious, want to learn new stuff and get better at what I'm doing, and that seemed always to be to the contrary of what was required of me at that company, so... ...currently I'm switching to freelancing as a Rails developer and have an offer to be a TA and a Ph.D. student at the University of Novi Sad, at the systems lab, but that's starting in October. They're mainly doing research on operating systems, compilers and parallel programming, but as is the case for most labs in our country (Serbia), they have no funded projects, so I will be pretty much free to choose what I'm going to work on. Currently I'm looking into specializing in CUDA/OpenCL, and parallel algorithms and their use in bioinformatics. Those are my plans, a GSoC project would be of great help to me, but even if it doesn't work out, I'm still determined to continue with them ;) Best regards, Marjan From pjotr.public14 at thebird.nl Thu Feb 16 11:00:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 12:00:54 +0100 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: References: Message-ID: <20120216110054.GA32635@thebird.nl> Hi Marjan, Thanks for the intro. Looks to me we ought to set you a right challenge :). With you in mind we are going to propose to write the worlds fastest GFF3/GTF parser using parallel D actors, and provide bindings for Ruby (and later Python). The parser ought to iterate through the data files, possibly handling information back through a simple filter. How does that sound? Parsing GFF3/GTF in seconds, rather than hours. Would be a true open-bio Bio* project. Peter, you like this? Pj. On Thu, Feb 16, 2012 at 11:28:03AM +0100, Marjan Povolni wrote: > Hello once again, > > My name is Marjan Povolni, I'm 27 years old and currently wrapping up my > Masters in CS. My dissertation project will be done in a weeks time, but > due to some bureaucracy requirements I won't be graduating until April. I > saw that the requirement for GSoC is to be enrolled in an academic > institution on April 23rd, so that fits me well. > > I also have some 5 years of professional experience working for a local > outsourcing company, working with lots of technologies. If someone's > interested in details, you can take a look at my LinkedIn page: > http://rs.linkedin.com/in/mpovolni. I'm very curious, want to learn new > stuff and get better at what I'm doing, and that seemed always to be to the > contrary of what was required of me at that company, so... > > ...currently I'm switching to freelancing as a Rails developer and have an > offer to be a TA and a Ph.D. student at the University of Novi Sad, at the > systems lab, but that's starting in October. They're mainly doing research > on operating systems, compilers and parallel programming, but as is the > case for most labs in our country (Serbia), they have no funded projects, > so I will be pretty much free to choose what I'm going to work on. > Currently I'm looking into specializing in CUDA/OpenCL, and parallel > algorithms and their use in bioinformatics. > > Those are my plans, a GSoC project would be of great help to me, but even > if it doesn't work out, I'm still determined to continue with them ;) > > Best regards, > Marjan > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Thu Feb 16 11:33:49 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 16 Feb 2012 11:33:49 +0000 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: <20120216110054.GA32635@thebird.nl> References: <20120216110054.GA32635@thebird.nl> Message-ID: On Thu, Feb 16, 2012 at 11:00 AM, Pjotr Prins wrote: > Hi Marjan, > > Thanks for the intro. > > Looks to me we ought to set you a right challenge :). With you in mind > we are going to propose to write the worlds fastest GFF3/GTF parser > using parallel D actors, and provide bindings for Ruby (and later > Python). The parser ought to iterate through the data files, possibly > handling information back through a simple filter. > > How does that sound? Parsing GFF3/GTF in seconds, rather than hours. > > Would be a true open-bio Bio* project. Peter, you like this? > > Pj. We'd want Brad involved for Biopython + GFF, but it certainly sounds like an interesting project. The D dependency might make for some interesting build dependencies, but that is a different matter. Peter From pjotr.public14 at thebird.nl Thu Feb 16 11:42:56 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 12:42:56 +0100 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: References: <20120216110054.GA32635@thebird.nl> Message-ID: <20120216114256.GA914@thebird.nl> On Thu, Feb 16, 2012 at 11:33:49AM +0000, Peter Cock wrote: > We'd want Brad involved for Biopython + GFF Good point. > but it certainly sounds like an interesting project. The D > dependency might make for some interesting build dependencies, but > that is a different matter. D2 is getting to be part of standard distro's (Fedora, Debian). For Windows binary DLL's can be distributed. So, that covers much of the community. Only OSX loses out again, but then Apple still ships Ruby 1.8.7! So, for the FFI, one needs to build the interface using a pre-installed D compiler. Not too bad. If people want that speed... For the GSoC task I don't think the deployment problem is too much of a concern. But we do want a working library. I actually started on that parser, last year at BOSC. But somehow there is too much on my plate :/ Pj. From bonnal at ingm.org Thu Feb 16 11:42:54 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 16 Feb 2012 12:42:54 +0100 Subject: [BioRuby] My proper GSoC introduction In-Reply-To: Message-ID: We can create a gem/plugins which downloads and compiles the lib in a sandbox, biongs works in that way. In case the machine is a biolinux we can skip the sandbox. On 16/02/12 12.33, "Peter Cock" wrote: > On Thu, Feb 16, 2012 at 11:00 AM, Pjotr Prins > wrote: >> Hi Marjan, >> >> Thanks for the intro. >> >> Looks to me we ought to set you a right challenge :). With you in mind >> we are going to propose to write the worlds fastest GFF3/GTF parser >> using parallel D actors, and provide bindings for Ruby (and later >> Python). The parser ought to iterate through the data files, possibly >> handling information back through a simple filter. >> >> How does that sound? Parsing GFF3/GTF in seconds, rather than hours. >> >> Would be a true open-bio Bio* project. Peter, you like this? >> >> Pj. > > We'd want Brad involved for Biopython + GFF, but it certainly > sounds like an interesting project. The D dependency might > make for some interesting build dependencies, but that is a > different matter. > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Thu Feb 16 13:16:22 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 14:16:22 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120208184817.GA31948@thebird.nl> References: <20120208184817.GA31948@thebird.nl> Message-ID: <20120216131622.GA2318@thebird.nl> Following up on the E-mail on addressing newbies, I have the following suggestion using Github issues and Cucumber features: Any biogem hosted on github can create a feature request. The feature should be written out in cucumber, with accompanying test cases. For example I wrote the following feature: Feature: Alignment editing, the bridge rule Remove columns that contain too many gaps Drop all bridges in less than 'min_bridges_fraction' (default 1/3 or 33%). The dropped columns are tracked by the table columns. Scenario: Apply the bridge rule to an amino acid alignment Given I have an alignment """ ----SNSFSRPTIIFSGCSTACSGK--SELVCGFRSFMLSDV SSIISNSFSRPTIIFSGCSTACSGK--SEQVCGFR---LSDV SSIISNSFSRPTIIFSGCSTACSGKLTSEQVCGFR---LSDV ----PKLFSRPTIIFSGCSTACSGK--SEPVCGFRSFMLSDV ----------PTIIFSGCSKACSGKGLSELVCGFRSFMLSDV ----------PTIIFSGCSKACSGK-----FRSFRSFMLSAV ----------PTIIFSGCSKACSGK-----VCGIFHAVRSFM ----------PTIIFSGCSKACSGK--SELVCGFRSFMLSAV -------------IFHAVR-TC-HP----------------- """ When I apply rule 3 with max_gap_size 4 Then it should have removed 4 bridges """ SNSFSRPTIIFSGCSTACSGKSELVCGFRSFMLSDV SNSFSRPTIIFSGCSTACSGKSEQVCGFR---LSDV SNSFSRPTIIFSGCSTACSGKSEQVCGFR---LSDV PKLFSRPTIIFSGCSTACSGKSEPVCGFRSFMLSDV ------PTIIFSGCSKACSGKSELVCGFRSFMLSDV ------PTIIFSGCSKACSGK---FRSFRSFMLSAV ------PTIIFSGCSKACSGK---VCGIFHAVRSFM ------PTIIFSGCSKACSGKSELVCGFRSFMLSAV ---------IFHAVR-TC-HP--------------- """ Then I should be able to track removed columns This was the most important step. Now we need to announce the feature request. I propose to raise an issue through github, e.g. https://github.com/pjotrp/bioruby-alignment/issues/1 the issue should contain a link to the feature, i.e https://github.com/pjotrp/bioruby-alignment/blob/master/features/edit/del_bridges.feature and be marked with the 'Newbie' label. We can also introduce more labels, such as 'Experienced', 'Advanced' and targets, such as 'Rails' and 'FFI'. This is enough information to automatically create a consolidated list on the bioruby or biogems website(s). And this list can be used by people who want to try a contribution or bug fix. We should define a number of such tasks for newbies. Bug fixes are also possible, as long as it is written out as a feature (note that features are automatically tests!). What do you think? Pj. On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote: > Hi All, > > This mailing list counts 180 subscribed readers. Which is impressive. > Also since the introduction of http://biogems.info/ the number of > BioRuby downloads has increased rapidly. > > You may also have noticed Ruby, in general, is making its mark in > bioinformatics. More and more people are programming in Ruby, which I > think rather delightful. And Biogems.info is proving to be cutting > edge, and accelerating development. > > So here is a question to people who read the mailing list, but do not > necessarily participate. What is needed to pull you in? > > At this point I have two ideas to increase participation. > > (1) First a race. I would like all readers to vote a few times a year on > the most beautiful Biogem source code. We'll put up a few projects to > choose from, and the winner will be highlighted on > http://biogems.info/. Ruby is about beauty, and we are seeing > some of that in the biogems. > > The other idea I got at FOSDEM this year from a convincing talk by Brian > Ostergard, titled 'You are doing it all wrong' > > http://fosdem.org/2012/schedule/event/really_grow_community > > where he made a strong case to address inexperienced developers. And > you know what, I believe he is right. So > > (2) We will look for ways to get inexperienced developers involved. > One way is to define uncomplicated and moderately complicated tasks, > feature requests and bug fixes. > > We are going to list these 'jobs' on http://biogems.info/. If anyone > picks up a task he/she will get very *strong* support from the plugin > owner, as well as the Biogem maintainers. You, the programmer, > will get all the credit for the work. > > How does this sound? Does this appeal to you? Anyone of the less > experienced, or even experienced, wants to voice his or her opinion? > We may even turn some work into a Google Summer of Code project > proposal. > > Pj. > From pjotr.public14 at thebird.nl Thu Feb 16 14:31:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 15:31:35 +0100 Subject: [BioRuby] Feature request: Gblocks implementation in Ruby Message-ID: <20120216143135.GA3760@thebird.nl> Feature: GBlocks implementation in Ruby https://github.com/pjotrp/bioruby-alignment/issues/2 (another example of a newbie assignment). From pjotr.public14 at thebird.nl Thu Feb 16 14:35:02 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 15:35:02 +0100 Subject: [BioRuby] A question for BioRuby newbies In-Reply-To: <20120216131622.GA2318@thebird.nl> References: <20120208184817.GA31948@thebird.nl> <20120216131622.GA2318@thebird.nl> Message-ID: <20120216143502.GA3876@thebird.nl> On Thu, Feb 16, 2012 at 02:16:22PM +0100, Pjotr Prins wrote: > Following up on the E-mail on addressing newbies, I have the > following suggestion using Github issues and Cucumber features: Next to listing the features/tasks/assignment on biogems.info and bioruby.org would be to show who fixed it - giving credit to newcomers is important. Pj. From pjotr.public14 at thebird.nl Thu Feb 16 15:46:12 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 16 Feb 2012 16:46:12 +0100 Subject: [BioRuby] A question for teachers In-Reply-To: <20120216143502.GA3876@thebird.nl> References: <20120208184817.GA31948@thebird.nl> <20120216131622.GA2318@thebird.nl> <20120216143502.GA3876@thebird.nl> Message-ID: <20120216154612.GB5276@thebird.nl> Some of you must be teaching students bioinformatics. Does this idea of creating feature requests look useful to you? From bonnal at ingm.org Thu Feb 16 15:53:05 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 16 Feb 2012 16:53:05 +0100 Subject: [BioRuby] A question for teachers In-Reply-To: <20120216154612.GB5276@thebird.nl> Message-ID: I'm not teaching but it's a very interesting approach. On 16/02/12 16.46, "Pjotr Prins" wrote: > Some of you must be teaching students bioinformatics. Does this idea > of creating feature requests look useful to you? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mail at michaelbarton.me.uk Thu Feb 16 16:14:51 2012 From: mail at michaelbarton.me.uk (Michael Barton) Date: Thu, 16 Feb 2012 11:14:51 -0500 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120214113523.GB17407@thebird.nl> References: <20120214112259.EC6011CBC491@idnmail.gen-info.osaka-u.ac.jp> <20120214113523.GB17407@thebird.nl> Message-ID: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> Excuse my late reply to your emails Pjotr and Naohisa. I wanted to find the time to reply in detail. > > I think "Restyling BioRuby.org" is very difficult for > > Google Summer of Code 2012 because the FAQ says that > > documentation-only work cannot be accepted. I agree with this. I think if our aim is to attract new people to BioRuby then giving out tasks to update documentation is not very exciting. I would like to offer a suggestion that BiorUby GSOC projects could also push scientific problems with new ruby code. As we are scientists in addition to coders we could coach on the scientific investigative side as well as on coding. I also think encouraging GSOC students to publish their projects, such as a bioinformatics application note could be a good way demonstrate the success of BioRuby GSOC projects as a concrete outcome. I think this would demonstrate BioRuby is an exciting community where "open source work leads to publications" which I think is primary barrier to scientists committing time. I speak for myself in this case as I'm at the point in my career where publications are becoming critical to finding a new position when my current one ends. I've never been involved in a GSOC project however so please correct my ignorance if I am wrong. Perhaps somewhere on the redesigned site we could list publications that have directly come form BioRuby projects. Concretely, rather than "we used BioRuby in this project" it would be "I wrote this for BioRuby and published it." I think recent BioGems paper is a good example of this. > Depends on the programming component. If we use > staticmatic and HAML to generate the site, with > coffeescript to interact with github and others, I think > it becomes a very interesting programming job. I've used nanoc to generate the scaffolder documentation here: http://next.gs. The github repo for the site is here: https://github.com/scaffolder/scaffolder-website. The static site generator "stasis" also looks interesting and follows a rails centric theme: http://stasis.me. As Pjotr wrote these could generate the static HTML which is uploaded to BioRuby.org. > Also the 'documentation' could consist of real example > scripts, which execute. Possibly showing results online. I > don't think students should be documenting, but they can > put software together to make creating tutorials easier. I strongly agree with this. Documentation code should be executable to ensure that it works as expected. I've read somewhere in the past about gems that allow this. Mike From mictadlo at gmail.com Fri Feb 17 06:22:03 2012 From: mictadlo at gmail.com (Mic) Date: Fri, 17 Feb 2012 16:22:03 +1000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120214082432.GA12201@thebird.nl> References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> Message-ID: Hi all D currently has some problems, because many projects http://www.dsource.org/projects/ are no any more in active developed. The other problem is that Tango has also stooped. On other hand it sounds good, because you can access C, C++ and it is native language. Therefore it should uses less memory compare to Java eg. http://biostar.stackexchange.com/questions/10376/how-to-efficiently-parse-a-huge-fastq-file . The Qt people think that they have removed all pitfalls in C++. Whether is true or not and how efficient the code with Qt is I do not know. I worked with Scala for a while, but I have found the language quite difficult to learn and also other people complain about it too. The other problem with Scala is that it is not possible to copy a little Java code in to Scala. Then I discover Groovy a very similar language to Ruby and easier to learn compare to Scala. The advantage of Groovy is that it is possible to copy Java code without to modefing it to Groovy. I have not tried out Groovy++ which is as fast as Java. Unfortunately, I run few month back with Groovy in to problems see http://jira.codehaus.org/browse/GROOVY-4851. Other Ruby like static language which I discover is http://www.mirah.org/wiki/MirahFeatures . Cheers, On Tue, Feb 14, 2012 at 6:24 PM, Pjotr Prins wrote: > On Mon, Feb 13, 2012 at 11:46:26AM +0100, Raoul Bonnal wrote: > > in this ML I found that the quality of code and its beauty increase > > only if you chat/talk with people and you are available to accept > > critics and contributes. > > I feel we can keep the momentum going if we use this list as a more > general outlet of our personal development. It may be a metamorphosis > of the old style of ML. Bio* is no longer about specialized libraries, > it is mainly about the problem of software development in biology. I > feel Ruby attracts the right type of people - that is why we have > 'beautiful code' in the subject ;). > > The ML is the first place to share information. This is what new > potential recruits may find interesting. Have them find us. > > In that vein I am presenting another piece of beautiful code, the > omnipresent FlatFile handler of BioRuby. See > > https://github.com/bioruby/bioruby/blob/master/sample/any2fasta.rb > > e.g. > > ARGV.each do | fn | > ff = Bio::FlatFile.auto(fn) > ff.each_entry do |entry| > if regex != nil > next if eval("entry.seq !~ #{regex}") > end > print entry.seq.to_fasta(entry.definition,70) > end > end > > which does a lot of work in a few lines, with remarkable flexibility! > Including automatic data format checking and a runtime defined regex > search. > > Nowadays we would probably do it a little different. The eval can be > taken out of the loop and the regex compiled (in a Pythonesque way). > Also both each_entry and the Sequence objects should be lazy (it is > not underneath) and properly iterate to avoid loading everything in > RAM and parsing too much. But hey, it is still a great example what > what we can do with Ruby anyway! > > I wrote this simple example any2fasta.rb 6 years ago, but the FlatFile > and Sequence code is not mine. It is mostly by Toshiaka and Naohisa > going all the way back to 2002. So the beautiful code is really by > those two geniuses who are at the heart of the BioRuby project. > > Pj. > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From georgkam at gmail.com Fri Feb 17 07:32:38 2012 From: georgkam at gmail.com (George Githinji) Date: Fri, 17 Feb 2012 10:32:38 +0300 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> Message-ID: Hi Mic, > D currently has some problems, because many projects > http://www.dsource.org/projects/ are no any more in active developed. The > other problem is that Tango has also stooped. Phobos (http://dlang.org/phobos/index.html) is the standard runtime library that comes with the D language compiler thus Tango is more of an auxiliary library for those that want to do things different. Tango development might not have stopped and tango has now been ported to D2 see this announcement http://forum.dlang.org/thread/jgagrl$1ta5$1 at digitalmars.com I found this comparison table useful to evaluate the language features. http://dlang.org/comparison.html It seems most D community concerns are about syntax breaks and worry on stability. With the recent release they have fixed a lot of bugs(http://forum.dlang.org/thread/jhfdcu$iht$1 at digitalmars.com) . This reddit discussion highlights some of the community concerns (http://www.reddit.com/r/programming/comments/pqft5/d_reference_compiler_2058_is_out_15_new_features/) You might find it useful. Again these are personal opinions :) -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From pjotr.public14 at thebird.nl Fri Feb 17 08:38:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 17 Feb 2012 09:38:54 +0100 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> Message-ID: <20120217083854.GA11837@thebird.nl> On Fri, Feb 17, 2012 at 10:32:38AM +0300, George Githinji wrote: > Tango development might not have stopped and tango has now been ported > to D2 see this announcement > http://forum.dlang.org/thread/jgagrl$1ta5$1 at digitalmars.com Indeed. Even if Tango had been dropped, it would not be a good reason to say D has 'issues'. Saying that software libraries are not maintained is rubbish - how many Ruby modules do you think are not maintained? Much about the D1 schism is FUD. As I wrote in my blog ''Finally some things that keep cropping up when I bring up D. First, the licensing issues. D, for historical reasons was closed source. That is changing now, with D2 compilers getting part of Fedora and Debian to follow. Second the schism and negativism of D1 users caused by an the move to D2. That you'll find on the Internet. D2 is not compatible with D1, and that has caused grief. D2 was reinvented as the language designers progressed their ideas.'' http://blog.thebird.nl/?p=93 : I realise this is is not an appropriate mailing list to really vent opinions about programming languages. Clojure, Groovy, and many more, are fine languages. If anyone suggests that a language is superior over another, I would like to point out that there must be a lot of dumb people out there :). Every language has its pros and cons, and there is only one way to find out - that is by trying them yourself. So let us refrain from a flaming discussion on this ML. This list is about Ruby. We are using other languages to bind against Ruby, and the mechanisms for binding are universal. You can select pretty much any computer language, and try that with Ruby (or not). This means we can all gain, as long as the system can be deployed. With all languages mentioned here, that is possible. It is a good thing to experiment. I believe multi-language programming is necessary for big data analysis. The reason is parallel computing and efficient data structures. You may want to read our book chapter on language bindings in Sharing programming resources between Bio* projects through remote procedure call and native call stack strategies by Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter Willis, Christopher Fields and Toshiaki Katayama chapter 21 in Evolutionary Genomics: statistical and computational methods, ed. Anisimova M. within Meth. Mol. Biol. Series of Humana-Springer 2012 coming out in a month from now :). Notice the authors are from Perl, Python, Java and Ruby communities. Pj. From bonnal at ingm.org Fri Feb 17 12:07:11 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 17 Feb 2012 13:07:11 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> Message-ID: Quick update. I added some new project, MAF parser and BioImage * Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI * Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser (FFI?) * Testing framework for biogem plugins * Restyling BioRuby.org * Update bio-images a plugin to represent bio-object with cool images I'm thinking about biongs but I need to figure out and "easy" task for a student. As usual, please login and make contributes to all of them, do not hesitate to propose new projects. There is something you miss in BioRuby ? Propose a a project for a new Biogem (BioRuby plugin)! http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Proposal_2012 -- Ra From pjotr.public14 at thebird.nl Fri Feb 17 17:21:03 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 17 Feb 2012 18:21:03 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: References: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> Message-ID: <20120217172103.GA16813@thebird.nl> Thanks Raoul. I added: Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI Rationale GFF3/GTF parsers are used by genome browsers and next-gen sequencing tools. Current parsers are slow and use a lot of memory. A fast low-memory parser would be beneficial to many bio-medical projects Approach Based on existing implementation we can design a fast parser using the D programming language. D provides capabilities for hand-crafting high-performance parsers. If required, parallelization of records can be introduced by using Actors. D can compile libraries which can be bound to Ruby using a C-style interface. This means the GFF3/GTF parser can be used from Ruby. The design will focus on iterating records and feeding them back to the Ruby environment. The library will also be useful for Python, Perl and the JVM. Difficulty and needed skills This is a challenging project. Advanced programming concepts, concurrency, foreign language bindings. The project requires An interest in high performance computing. Some affinity with coding in C and one or more interpreted languages Mentors Pjotr Prins (author of bio-gff3), Raoul Bonnal Other interested parties Naohisa Goto (author BioRuby's GFF3 parser), Brad Chapman (author Biopython's GFF3 parser) and Peter Cock (Biopython), Chris Fields (BioPerl). On Fri, Feb 17, 2012 at 01:07:11PM +0100, Raoul Bonnal wrote: > Quick update. I added some new project, MAF parser and BioImage > * Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI > * Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser > (FFI?) > * Testing framework for biogem plugins > * Restyling BioRuby.org > * Update bio-images a plugin to represent bio-object with cool images > > I'm thinking about biongs but I need to figure out and "easy" task for a > student. > > As usual, please login and make contributes to all of them, do not hesitate > to propose new projects. There is something you miss in BioRuby ? Propose a > a project for a new Biogem (BioRuby plugin)! > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Proposal_2012 > > > -- > Ra > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Fri Feb 17 17:25:18 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 17 Feb 2012 18:25:18 +0100 Subject: [BioRuby] Restyling BioRuby.org Message-ID: <20120217172518.GB16813@thebird.nl> A question for everyone: What would you like to a fresh BioRuby.org to be? Myself, I am thinking we need to retool the site for inexperienced programmers. That means accentuating Tutorials and examples, as Michael Barton suggested. What do you think? And please, also let some respond that have not mailed to this list before! We are here to hear you! From cjfields at illinois.edu Fri Feb 17 17:26:32 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 17 Feb 2012 17:26:32 +0000 Subject: [BioRuby] Beautiful code for Bioinformatics In-Reply-To: <20120217083854.GA11837@thebird.nl> References: <20120213103408.GA4358@thebird.nl> <20120214082432.GA12201@thebird.nl> <20120217083854.GA11837@thebird.nl> Message-ID: <491E0F71-F8C9-40C6-9074-E0E7F566D52D@illinois.edu> I think understanding concepts in classic and modern programming languages, and their advantages and disadvantages, is considerably more important than the language itself. VM's like JVM, Mono, Parrot, etc allow one to cross over from one language to another (sometimes within the same module space), so the adage about which lang is best seems very trite now. Anyway, anytime I see someone pipe up (on SO, reddit, etc) with a big trolly 'lang A is better than lang B' thread, I invariably find the most interesting responses are from those who can clearly point out the advantages and disadvantages of both languages. Inevitably the conclusion is every language has its flaws, the choice is very much based on one's opinions, and that concepts and specifications are way more important to know than specific implementations of them (and knowledge of such allows one to migrate more effortlessly between languages). (my rant for the day, sorry, need coffee) chris On Feb 17, 2012, at 2:38 AM, Pjotr Prins wrote: > On Fri, Feb 17, 2012 at 10:32:38AM +0300, George Githinji wrote: >> Tango development might not have stopped and tango has now been ported >> to D2 see this announcement >> http://forum.dlang.org/thread/jgagrl$1ta5$1 at digitalmars.com > > Indeed. Even if Tango had been dropped, it would not be a good reason > to say D has 'issues'. Saying that software libraries are not > maintained is rubbish - how many Ruby modules do you think are not > maintained? > > ... > I believe multi-language programming is necessary for big data > analysis. The reason is parallel computing and efficient data > structures. You may want to read our book chapter on language > bindings in > > Sharing programming resources between Bio* projects through remote > procedure call and native call stack strategies > > by Pjotr Prins, Naohisa Goto, Andrew Yates, Laurent Gautier, Scooter > Willis, Christopher Fields and Toshiaki Katayama > > chapter 21 in Evolutionary Genomics: statistical and computational > methods, ed. Anisimova M. within Meth. Mol. Biol. Series of > Humana-Springer 2012 > > coming out in a month from now :). Notice the authors are from Perl, Python, > Java and Ruby communities. > > Pj. From p.j.a.cock at googlemail.com Fri Feb 17 22:40:29 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 17 Feb 2012 22:40:29 +0000 Subject: [BioRuby] Fwd: [Utilities-announce] NCBI E-Utilities Update In-Reply-To: References: Message-ID: Hi all, Just FYI, the following was also changed in this week's Entrez update to EFetch 2.0 (see forwarded email below). This was breaking some Biopython scripts - depending on how they passed in the id parameters. It turns out we relied on the undocumented and now withdrawn form in one of our examples, so some users had copied this style. Biopython 1.59 will solve this. I know BioJava is looking at the more publicised changes to retmode - I don't know if BioPerl or BioRuby was affected. Regards, Peter ---------- Forwarded message ---------- From: Date: Fri, Feb 17, 2012 at 7:09 PM Subject: [Utilities-announce] NCBI E-Utilities Update To: NLM/NCBI List utilities-announce The most recent NCBI E-Utilities update includes a more stringent check for correct URL parameters. EFetch URLs with multiple IDs must be entered as: id=1,2,3 EFetch no longer accepts invalid URL parameters, e.g., id=1&id=2&id=3 Please see the online E-Utilities help for additional information: http://www.ncbi.nlm.nih.gov/books/NBK25500/ EFetch online help: http://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.EFetch Thank you. _______________________________________________ Utilities-announce mailing list http://www.ncbi.nlm.nih.gov/mailman/listinfo/utilities-announce From cjfields at illinois.edu Sat Feb 18 02:54:44 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Sat, 18 Feb 2012 02:54:44 +0000 Subject: [BioRuby] [Bioperl-l] Fwd: [Utilities-announce] NCBI E-Utilities Update In-Reply-To: References: Message-ID: On Feb 17, 2012, at 4:40 PM, Peter Cock wrote: > Hi all, > > Just FYI, the following was also changed in this week's Entrez > update to EFetch 2.0 (see forwarded email below). > > This was breaking some Biopython scripts - depending on how > they passed in the id parameters. It turns out we relied on the > undocumented and now withdrawn form in one of our examples, > so some users had copied this style. Biopython 1.59 will solve > this. > > I know BioJava is looking at the more publicised changes to > retmode - I don't know if BioPerl or BioRuby was affected. No, I checked the BioPerl modules against regression tests today after seeing the announcement. Seems everything is fine; the main issue on NCBI's end that seemed to break things was how multiple IDs were joined. > Regards, > > Peter chris From pjotr.public14 at thebird.nl Sun Feb 19 08:56:12 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 19 Feb 2012 09:56:12 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120217172518.GB16813@thebird.nl> References: <20120217172518.GB16813@thebird.nl> Message-ID: <20120219085612.GA29424@thebird.nl> On Fri, Feb 17, 2012 at 06:25:18PM +0100, Pjotr Prins wrote: > What would you like to a fresh BioRuby.org to be? > > Myself, I am thinking we need to retool the site for inexperienced > programmers. That means accentuating Tutorials and examples, as > Michael Barton suggested. > > What do you think? > > And please, also let some respond that have not mailed to this list > before! We are here to hear you! With an embarrassing 0 (zero) responses, I can conclude there is either no interest in this matter, or no one considers it his/her business. That is sad. Open source software matters. Web presence matters. So let me take you by the hand and draw a vision :). I think programming for Biology (which I call big B) is important for the future of humanity, and the broader world we live in. We are the ones that have to unlock the potential of big data. As I see it around me, scientists are generating data at an incredible rate. Now the data analysis is the bottle neck, there are plenty of indications. For example, we have a programming course here at our biology university which was never really popular. This year the attendance tripled, and includes a number of Ph.D. students! I.e. the research groups are feeling the pinch. There are not enough people to analyse the data. It gets worse. What I see is that the universities train people to the level they can script a bit, and use existing tools. For example for genome assembly. The problem is that these tools work for the general case. With different experimental design and setups the data may contain more valuable information, i.e. there is often opportunity for harvesting more information - which never gets done. And we do not scale. Each of us is too busy, even to write to a mailing list and participate in mentoring students in the Google Summer of Code (GSoC). Are we being responsible scientific citizens here? I think not. Are most of us true participants in Bio*. I think not. This ML and GSoC is about all Bio* projects (BioRuby, Biopython, BioPerl, Bioconductor...). The programming languages are tools that we should use to not only analyse our own data, but also to give back to others so we can maximize the scientific potential. You are using open source software (OSS). I bet you have benefited from Bio*. We are asking to give back some of your time. Everyone can do it in a different way. Ben Woodcroft has created many small plugins of his coding efforts. That is greatness in my opinion. Raoul spent many weeks of his free time to create the Biogems tool and make it possible for people to share code. That is greatness in my opinion. So how can you participate and be great? First by discussing ideas on the mailing list. Discuss what you want out of the BioRuby web presence. Any idea will do. An active mailing list will help young developers find us. Adding projects to GSoC will help young developers find us. I don't think mentoring GSoC students necessarily leads to long term committers, but that is not the point. The point is to move science as a whole forward. The universities train people to use tools and maybe script them together. We here, are the select crowd of real software afficiendos in Biology. I think there is only one conclusion possible, if we are not to sink in a cynical mire. If you understand and benefit from *our* OSS, don't go the way alone. Don't just take and not give. Help us materialize that potential of young developers. They are out there, and we need them to find us. I am asking: What do you think? How can we accommodate this goal using the tools we have. Pj. From pjotr.public14 at thebird.nl Sun Feb 19 09:31:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 19 Feb 2012 10:31:54 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120217172103.GA16813@thebird.nl> References: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> <20120217172103.GA16813@thebird.nl> Message-ID: <20120219093154.GA1030@thebird.nl> I added the following GSoC proposal: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Testing_framework_for_biogem_plugins Testing framework for biogem plugins Rationale Biogems are Ruby gems that are created by independent authors, see the publication. Designing an automated testing frame work for different versions of Ruby is critical for the successful use of Ruby in bioinformatics. Gems should be tested on release, but also when tagged on github Approach We integrate facilities of http://biogems.info/, http://rubygems.org/ and http://github.com/ to automatically test gems that get released in the public domain. We can make use of open-bio's testing framework to test individual gems, or crowd sourcing setups, such as http://test.rubygems.org/ to test gems in different setups. Next we program the http://biogems.info/ website to show the test results in easy way. Difficulty and needed skills Ruby scripting, and affinity for web integration, some web programming including Ruby, HTML (HAML), CSS and Javascript (Coffee) The project requires Mentors Pjotr Prins, Raoul Bonnal, Peter Cock (confirm) From pjotr.public14 at thebird.nl Sun Feb 19 09:45:21 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 19 Feb 2012 10:45:21 +0100 Subject: [BioRuby] Google Summer of Code project ideas In-Reply-To: <20120219093154.GA1030@thebird.nl> References: <20120216161451.GA6031@bartonh-mbp-01.uanet.edu> <20120217172103.GA16813@thebird.nl> <20120219093154.GA1030@thebird.nl> Message-ID: <20120219094521.GA1154@thebird.nl> Another one :) Restyling BioRuby.org Rationale BioRuby.org is a portal for getting appropriate information on Ruby-related software development to bioinformatics software developers. The current portal discourages both experienced and inexperienced software developers from digging deeper, and finding solutions to typical bioinformatics problems. Approach We want to restyle the portal so it becomes an interactive environment, encourages people to participate and put information in, and information gets easier to find. The restyling is about web design, and programming an interactive website in Ruby, using Ruby on Rails and other tools, such as markdown, haml, sass, staticmatic, etc. Also the idea is to use existing webservices, such has github gists, rubydoc.info, e.g. example, and embed them into the site - rather than recreating all these services from scratch. We would like to create a collection of code snippets and documentation that is easy to navigate and add to. It should be even less effort than maintaining a Wiki. Also code snippets should be able to run online - and prove they are correct. The total design should also be useful for other Bio* projectcs, such as BioPerl. It is possible to get a scientific paper out of this work. Difficulty and needed skills Affinity for web design, accessibility of information, web programming in Ruby. Perhaps Javascript and Coffeescript. The project requires Some Ruby experience, experience in web design Mentors Raoul Bonnal, Pjotr Prins, Toshiaki Katayama (confirm) http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Restyling_BioRuby.org From hlapp at drycafe.net Sun Feb 19 23:27:00 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Sun, 19 Feb 2012 18:27:00 -0500 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120219085612.GA29424@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> Message-ID: <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> On Feb 19, 2012, at 3:56 AM, Pjotr Prins wrote: > With an embarrassing 0 (zero) responses, I can conclude there is > either no interest in this matter, or no one considers it his/her > business. Or that nobody else has as much time on their hands :-) -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From pjotr.public14 at thebird.nl Mon Feb 20 09:51:29 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 20 Feb 2012 10:51:29 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> Message-ID: <20120220095129.GA10167@thebird.nl> On Sun, Feb 19, 2012 at 06:27:00PM -0500, Hilmar Lapp wrote: > > On Feb 19, 2012, at 3:56 AM, Pjotr Prins wrote: > > > With an embarrassing 0 (zero) responses, I can conclude there is > > either no interest in this matter, or no one considers it his/her > > business. > > Or that nobody else has as much time on their hands :-) Which somewhat proves my point. We need fresh blood. I must admit I have not been good at nurturing this myself, but now I have seen the light :). Questions that keep going through my mind are: 1. Where is our leadership? This is not unique to BioRuby. The other projects suffer similar problems. Perhaps, in bioinformatics (the small b), people get too busy too quickly, and sitting leadership starts being the cause of inertia. 2. Is this the time fork the BioRuby project? I have been thinking this for many years ;). Forking the code is one thing - as noted before, we can and should strip out modules into Biogems. Forking the project is not possible, unless the domain gets released. Do we want a bioruby2.org? 3. How are we going to revamp our web presence? With Biogems.info we show that a change in this can have real effect on contributions. Here we have raised that we can take the web presence to a new level. 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* projects? It is appears to me that sitting leadership is reluctant to give away their positions. I have discussed this with Chris Fields last year. We agreed that there are also few to take over the helm. So... 5. how do we nurture future leadership? I am old and cynical enough to know people mostly work for their own direct benefit (their itch, so tho speak) in OSS, or anywhere else. Still, I am going to poke and prod for some time, to see if we can make change. I believe Bio* projects are at fork in the road. Which one are we going to take? Should BioRuby exist as it is, or should we use it as a breeding ground for young developers. Same question really for BioPython and BioPerl. The BioRuby community is almost in a coma, I think. Despite 180 readers of the ML. I see the same people engaging, and interestingly, a significant number of messages from Biopython and BioPerl leadership. Thank you for that. BioRuby is just coming out of its shell, and you are helping. 6. What is needed to get BioRuby out of the comatose state? With BioRuby we have had lively discussions before, but they tend to peter out. We can reason about this, but I think it goes back to leadership again. Please note that I have no ambition in taking on a leadership role. That would also be too contentious ;). That is not what I am trying to achieve here. But I would certainly like to make the leadership more fluent, responsive, and rotating. Pj. From ngoto at gen-info.osaka-u.ac.jp Mon Feb 20 10:37:07 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 20 Feb 2012 19:37:07 +0900 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120219085612.GA29424@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> Message-ID: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Hi, On Sun, 19 Feb 2012 09:56:12 +0100 Pjotr Prins wrote: > With an embarrassing 0 (zero) responses, I can conclude there is > either no interest in this matter, or no one considers it his/her > business. That is sad. Open source software matters. Web presence > matters. I think requesting for writing responses for the mail posted on Friday night in the weekend is too hurry. I personally don't feel strong dissatisfaction with the current http://bioruby.org/ website, although I agree it is not the best ideal state, and I don't have strong motivation to discuss about the topic unless new website candidate is sent by someone. So, please send new site html contents. Current contents is now on th GitHub. https://github.com/ngoto/bioruby.org-webpage Writing new pages without using current contents is also welcomed. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From francesco.strozzi at gmail.com Mon Feb 20 11:22:23 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 20 Feb 2012 12:22:23 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: Hi all, coming back to the website restyle. If I could suggest a new look, I really like the layout of http://jruby.org . You have 3-4 main sections just at the first page, very clear and very visible. There we could place sections like "Why Ruby?" (as in JRuby) to show the pros and avantages of Ruby (or why we love it and use it in Bioinformatics). A second section like "Use it", with clear and coincise info on how to start using BioRuby and a reference to the most updated/most recent official documentation (e.g. point to github / wiki etc.). A last third section "Contribute" that describe the BioRuby code organization, the repository and the BioGems/plugins system. Just under these 3 main sections you can have one or two areas with "Recent news", Tweets that mention BioRuby and/or OpenBio projects in general, plus maybe a feed or even a calendar with conferences, events, hackathons where BioRuby and OpenBio people meets and presents stuff. This to show the community activity, plus also some links to point to the ML and IRC. That's my view so far, I think there is room for discussion. Cheers -- Francesco From pjotr.public14 at thebird.nl Mon Feb 20 11:40:06 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 20 Feb 2012 12:40:06 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120220114006.GA13746@thebird.nl> Hi Naohisa, > I personally don't feel strong dissatisfaction with the current > http://bioruby.org/ website, although I agree it is not the > best ideal state, Good. > and I don't have strong motivation to discuss about the topic unless > new website candidate is sent by someone. Bad. This is bad, because you are asking for someone to do (a lot of) work, without any guarantee that it will be used. Do you see why no one will respond to this query? Leadership sets the tone of things. What are your ideas, to start with? It is not a discussion per se. > So, please send new site html contents. > Current contents is now on th GitHub. > https://github.com/ngoto/bioruby.org-webpage > Writing new pages without using current contents is also welcomed. Better. Based on this response, my questions are: 1. Who is in charge of the website - is it You? So you are effectively Mr BioRuby now? 2. What is the process to get the new website approved? 3. Can it be a democratic process? I doubt you will approve of just any new website :) Pj. From ngoto at gen-info.osaka-u.ac.jp Mon Feb 20 13:49:47 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 20 Feb 2012 22:49:47 +0900 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220114006.GA13746@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> <20120220114006.GA13746@thebird.nl> Message-ID: <20120220134948.878861CBC4B1@idnmail.gen-info.osaka-u.ac.jp> Hi Pjotr, On Mon, 20 Feb 2012 12:40:06 +0100 Pjotr Prins wrote: > Bad. > > This is bad, because you are asking for someone to do (a lot of) > work, without any guarantee that it will be used. Do you see why no > one will respond to this query? I understand hard work (and/or money) would be needed for restyling bioruby.org. > Leadership sets the tone of things. What are your ideas, to start > with? It is not a discussion per se. I think there may be some starting points. * Edting current site gradually, accumulating small changes * Paying money to professional web designers * Waiting for someone to bring new website Indeed, I don't have enough motivation about all of the above. In my todo list, the priority is low. > > So, please send new site html contents. > > Current contents is now on th GitHub. > > https://github.com/ngoto/bioruby.org-webpage > > Writing new pages without using current contents is also welcomed. > > Better. > > Based on this response, my questions are: > > 1. Who is in charge of the website - is it You? So you are > effectively Mr BioRuby now? Currently, only Toshiaki can update the website. Usually I send him modified html files when releasing new version of bioruby. > 2. What is the process to get the new website approved? > > 3. Can it be a democratic process? Nothing decided. Maybe vote in this mailing list? > I doubt you will approve of just any new website :) Don't worry :) Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From hlapp at drycafe.net Mon Feb 20 18:01:30 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Mon, 20 Feb 2012 13:01:30 -0500 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220095129.GA10167@thebird.nl> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> <20120220095129.GA10167@thebird.nl> Message-ID: <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> On Feb 20, 2012, at 4:51 AM, Pjotr Prins wrote: > 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* projects? How would the OBF do that? In the present relationship between the OBF umbrella and its member projects, the OBF takes a completely hands-off approach with respect to how each of the member projects organize themselves. The OBF doesn't meddle in matters of its member project communities that concern the respective member project. As a consequence, the OBF by definition neither encourages nor discourages inertia in its member projects. Instead the OBF leaves it to each member project how inert or not they want to be. I think this is different, for better or worse, from the relationship between the Apache Foundation and Apache projects, and we've had some of that discussion (such as, is it better or worse) as a result of Ross Gardler's talk at BOSC a while ago. Personally, I am open to OBF changing the nature of that relationship, but I think the drive to do that would have to come with very broad community support that cuts across our projects, rather than top-down. > It is appears to me that sitting leadership is reluctant to give away their positions. I'm not sure - I can imagine that Chris F would more than happily turn over release and other leadership to someone else if they stepped up. I think volunteers taking leadership and responsibility is fundamentally at odds with the loosey-goosey fork-patch-pull request micro-contribution model that reins supreme on Github. While that model has done lots of good in terms of lowering the barrier to contribution, we must not forget that taking leadership and responsibility is not a micro-contribution, and by nature not low-barrier. Hence, cultivating a large following of micro-contributors is by no means prone to give you an ample resource for future leadership. Sorry if that's not what you wanted to hear. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From mictadlo at gmail.com Tue Feb 21 05:41:07 2012 From: mictadlo at gmail.com (Mic) Date: Tue, 21 Feb 2012 15:41:07 +1000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> <20120220095129.GA10167@thebird.nl> <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> Message-ID: BioRuby must become faster in next generation sequence time. Some of the mailing list member like D very much. How about BioD or BioGO or BioVala instead of a BioRuby fork? On Tue, Feb 21, 2012 at 4:01 AM, Hilmar Lapp wrote: > > On Feb 20, 2012, at 4:51 AM, Pjotr Prins wrote: > > > 4. One for you Hilmar: does the OBF actually encourage inertia in the > Bio* projects? > > How would the OBF do that? > > In the present relationship between the OBF umbrella and its member > projects, the OBF takes a completely hands-off approach with respect to how > each of the member projects organize themselves. The OBF doesn't meddle in > matters of its member project communities that concern the respective > member project. As a consequence, the OBF by definition neither encourages > nor discourages inertia in its member projects. Instead the OBF leaves it > to each member project how inert or not they want to be. > > I think this is different, for better or worse, from the relationship > between the Apache Foundation and Apache projects, and we've had some of > that discussion (such as, is it better or worse) as a result of Ross > Gardler's talk at BOSC a while ago. Personally, I am open to OBF changing > the nature of that relationship, but I think the drive to do that would > have to come with very broad community support that cuts across our > projects, rather than top-down. > > > It is appears to me that sitting leadership is reluctant to give away > their positions. > > I'm not sure - I can imagine that Chris F would more than happily turn > over release and other leadership to someone else if they stepped up. I > think volunteers taking leadership and responsibility is fundamentally at > odds with the loosey-goosey fork-patch-pull request micro-contribution > model that reins supreme on Github. While that model has done lots of good > in terms of lowering the barrier to contribution, we must not forget that > taking leadership and responsibility is not a micro-contribution, and by > nature not low-barrier. Hence, cultivating a large following of > micro-contributors is by no means prone to give you an ample resource for > future leadership. > > Sorry if that's not what you wanted to hear. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Feb 21 08:52:29 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Feb 2012 09:52:29 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120221085229.GA21491@thebird.nl> Francesco, All valid points. I also like the design - very Ruby. Pj. On Mon, Feb 20, 2012 at 12:22:23PM +0100, Francesco Strozzi wrote: > Hi all, > coming back to the website restyle. If I could suggest a new look, I really > like the layout of http://jruby.org . You have 3-4 main sections just at > the first page, very clear and very visible. There we could place sections > like "Why Ruby?" (as in JRuby) to show the pros and avantages of Ruby (or > why we love it and use it in Bioinformatics). A second section like "Use > it", with clear and coincise info on how to start using BioRuby and a > reference to the most updated/most recent official documentation (e.g. > point to github / wiki etc.). A last third section "Contribute" that > describe the BioRuby code organization, the repository and the > BioGems/plugins system. > > Just under these 3 main sections you can have one or two areas with "Recent > news", Tweets that mention BioRuby and/or OpenBio projects in general, plus > maybe a feed or even a calendar with conferences, events, hackathons where > BioRuby and OpenBio people meets and presents stuff. This to show the > community activity, plus also some links to point to the ML and IRC. > > That's my view so far, I think there is room for discussion. > > Cheers > > -- > > Francesco > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Tue Feb 21 09:04:52 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Feb 2012 10:04:52 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <2D5BEEDF-5FB6-4FAC-A704-725EC22B85D0@drycafe.net> <20120220095129.GA10167@thebird.nl> <7F834D4B-DB91-43BA-93FD-3E1DA0310C18@drycafe.net> Message-ID: <20120221090452.GB21491@thebird.nl> Hi Mic, On Tue, Feb 21, 2012 at 03:41:07PM +1000, Mic wrote: > BioRuby must become faster in next generation sequence time. > Some of the mailing list member like D very much. How about BioD or BioGO > or BioVala instead of a BioRuby fork? It is a very good idea to start a new project. Still we need to work on BioRuby too. If you look at all the Bio* projects, you can see that the statically typed languages don't do that well, including BioJava. Dynamically typed languages have a lower threshold, and give instant gratification. That is the key to understanding success in bioinformatics ;). We do, however, need fast back-end stuff. BioRuby needs to allow for that (and we do in biogems), so the broader user base only needs to know Ruby (or Python, or whatever). We'll see more bindings to these other languages. A new BioD project - I am sure someone will start - should aim to provide that. Focussing on D bioinformatics alone, however, will render you a small community. Check out the committers of BioJava, BioC, BioC++, etc. It is my experience with BioScala too. Not to stop anyone, just saying that Ruby, Python, Perl and R will remain mainstream for years to come. Pj. From bonnal at ingm.org Tue Feb 21 11:29:53 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 21 Feb 2012 12:29:53 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220095129.GA10167@thebird.nl> Message-ID: Hi Pjotr, Hilmar and others, On 20/02/12 10.51, "Pjotr Prins" wrote: > On Sun, Feb 19, 2012 at 06:27:00PM -0500, Hilmar Lapp wrote: > 1. Where is our leadership? > > This is not unique to BioRuby. The other projects suffer similar > problems. Perhaps, in bioinformatics (the small b), people get too > busy too quickly, and sitting leadership starts being the cause of > inertia. > > 2. Is this the time fork the BioRuby project? > > I have been thinking this for many years ;). Forking the code is one > thing - as noted before, we can and should strip out modules into > Biogems. Forking the project is not possible, unless the domain gets > released. Do we want a bioruby2.org? At this time forking is not a solution, like creating another Bio language (as suggested by Mic with D) which is just used by a niche of developers. Why is not a solution ? A) Because I supposed we have no time to support a whole library from zero. B) It's not a founded project, so I can not spend time on it. Now I can justify the effort because I use it daily or for specific tasks but if I must spend time supporting people on things which are not relevant to my own work, that would be a real problem. In Boston (BOSC) (Apache talk) we discussed about the chance to be founded, but I can imagine is not easy. C) I think that extending or hacking bioruby with plugins is a good way to introduce new concept/design keeping compatibility when needed and most importantly publishing papers to be cited = Ruby more widespread in bioinformatics. Unfortunately bioruby by itself is not enough so we must provide support and contribute to SciRuby (just an example). C.1) everyone will contribute to its own field and is normal. D) WE NEED A ROAD MAP (is connected to point 3) I would put a link ( Ruby for Science Alliance ) to friend projects like SciRuby :-) > 3. How are we going to revamp our web presence? > > With Biogems.info we show that a change in this can have real > effect on contributions. Here we have raised that we can take the > web presence to a new level. Publications, ML activities, IRC meetings, ROAD Map is the only way I see. So in a new BioRuby site, as Francesco suggested, calendar/events etc.. Is more than welcome. > 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* > projects? > > It is appears to me that sitting leadership is reluctant to > give away their positions. I have discussed this with Chris Fields > last year. We agreed that there are also few to take over the helm. > So... I don't see how OBF could push the projects, in case of founds they would be distributed equally? We are good people so we are working together promoting our language helping the others. During the last BioHackathon the most astonishing things was seeing Bio Perl/Ruby/Python/Java working (really) together, it was great. > 5. how do we nurture future leadership? > > I am old and cynical enough to know people mostly work for their own > direct benefit (their itch, so tho speak) in OSS, or anywhere else. > Still, I am going to poke and prod for some time, to see if we can > make change. I believe Bio* projects are at fork in the road. Which > one are we going to take? > Should BioRuby exist as it is, or should we > use it as a breeding ground for young developers. Same question really > for BioPython and BioPerl. Not very clear, at least to me. > The BioRuby community is almost in a coma, I think. Despite 180 > readers of the ML. I see the same people engaging, and interestingly, > a significant number of messages from Biopython and BioPerl > leadership. Thank you for that. BioRuby is just coming out of its > shell, and you are helping. > 6. What is needed to get BioRuby out of the comatose state? > > With BioRuby we have had lively discussions before, but they tend to > peter out. We can reason about this, but I think it goes back to > leadership again. I don't know how to solve this issue... The democratic process you suggested some time ago ? Which is the workload, which is the coding power we have ? Which are the languages we can rely on for performances (it means which is the knowledge of the people around here )? Do we want to support Jruby? Suppose we now need a new feature in BioRuby, which one ? Do we want to participate to GSoC ? YES and we MUST there is no doubt and we NEED to write good proposals but everything should be made as a community not only as a group of passionate developers. LANGUAGES: D or Scala, I don't know that I'm just curious and eager to learn. Most of my work is managing large scale data and interconnecting them extracting information etc... I would say, why not Hadoop ? We are just a piece of a bigger ecosystem, the problem is that most of the time "setting up" each piece is a pain in the ass. WEBSITE Proposals: Why not create and post images, an image per page. Is a usual approach for proposing new layouts. We are growing and this kind of discussions are a natural process. -- Ra From pjotr.public14 at thebird.nl Tue Feb 21 17:31:21 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 21 Feb 2012 18:31:21 +0100 Subject: [BioRuby] Developing a VISION Message-ID: <20120221173121.GA28249@thebird.nl> I guess this is a good moment to work on a VISION for BioRuby. A VISION may lead to a ROADMAP. See if you like the following... # BioRuby Vision Here BioRuby is defined as the wider eco-system of Ruby in bioinformatics. This includes the BioRuby project, biogems, and external libraries and tools which can interoperate with Ruby. Note that for Ruby one can equally use Python or Perl. ## Challenges in Computational Biology At this point in time a number of challenges in computational biology are recognised: 1. Big data: bioinformatics software needs to address performance and efficiency required for TB analysis 2. Biological analysis: we need to find ways of making analysis software available to users not so proficient in programming software 3. Education: more biologists need to become software engineers, from entry level all the way to expert BioRuby is the natural place to look for a concerted drive in addressing these challenges, as it has a thriving community, software engineering expertise, and people working in all three areas of challenge. ## Vision statement: BioRuby should focus on inexperienced developers Experienced people tend to be very busy in their jobs. Experienced developers do not scale that well. Young people are less experienced, but have the time and energy to make a difference. Experienced developers were once inexperienced too. This leads to a natural conclusion that BioRuby should focus on inexperienced developers. Realisation: We need to find ways of making BioRuby cool (something RoR handles very well), we need to have young people engage with us, we need to pull them into BioRuby with a good web presence. Talented developers like challenges, so we should set challenges and make sure there is the proper guidance. Questions on the mailing list should be rapidly responded to, always in a positive fashion. Rapidly means within hours, not within days. The IRC channel should be monitored at all time. GSoC is an almost free way of attracting talent, and deserves the effort of mentoring GSoC students. ## Vision statement: BioRuby aims for distributed development Distributed development puts power into the hands of developers, and makes sure they get the credits. Dependencies are clear, and modules are easily replaced and upgraded. Realisation: We have Biogem, which is a powerful tool in making distributed development possible. Anyone can create a biogem. The current BioRuby source base, meanwhile, is bloated, and confusing to newcomers. The code base needs to be reduced, and modules have to be moved into biogems. These biogems may gain new ownership, or may disappear over time. RoR shows the way of reducing complexity, and striving for logical organisation of pluggable modules. External dependencies, such as FFI, need to be implemented in independent biogems. We will have biogems for the JVM and native Ruby. The core BioRuby gem itself should be platform independent. more to come... From cjfields at illinois.edu Tue Feb 21 18:54:00 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 21 Feb 2012 18:54:00 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: Message-ID: <8B427626-EEDB-4ED9-94DE-2F0D99F14866@illinois.edu> On Feb 21, 2012, at 5:29 AM, Raoul Bonnal wrote: > Hi Pjotr, Hilmar and others, > ... > >> 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* >> projects? >> >> It is appears to me that sitting leadership is reluctant to >> give away their positions. I have discussed this with Chris Fields >> last year. We agreed that there are also few to take over the helm. >> So... > I don't see how OBF could push the projects, in case of founds they would be > distributed equally? We are good people so we are working together promoting > our language helping the others. During the last BioHackathon the most > astonishing things was seeing Bio Perl/Ruby/Python/Java working (really) > together, it was great. Bioinformatics problems span languages >> 5. how do we nurture future leadership? >> >> I am old and cynical enough to know people mostly work for their own >> direct benefit (their itch, so tho speak) in OSS, or anywhere else. >> Still, I am going to poke and prod for some time, to see if we can >> make change. I believe Bio* projects are at fork in the road. Which >> one are we going to take? > >> Should BioRuby exist as it is, or should we >> use it as a breeding ground for young developers. Same question really >> for BioPython and BioPerl. > Not very clear, at least to me. > >> The BioRuby community is almost in a coma, I think. Despite 180 >> readers of the ML. I see the same people engaging, and interestingly, >> a significant number of messages from Biopython and BioPerl >> leadership. Thank you for that. BioRuby is just coming out of its >> shell, and you are helping. > > >> 6. What is needed to get BioRuby out of the comatose state? >> >> With BioRuby we have had lively discussions before, but they tend to >> peter out. We can reason about this, but I think it goes back to >> leadership again. > I don't know how to solve this issue... The democratic process you suggested > some time ago ? Which is the workload, which is the coding power we have ? > Which are the languages we can rely on for performances (it means which is > the knowledge of the people around here )? Do we want to support Jruby? > Suppose we now need a new feature in BioRuby, which one ? Do we want to > participate to GSoC ? YES and we MUST there is no doubt and we NEED to write > good proposals but everything should be made as a community not only as a > group of passionate developers. > > > LANGUAGES: > D or Scala, I don't know that I'm just curious and eager to learn. Most of > my work is managing large scale data and interconnecting them extracting > information etc... I would say, why not Hadoop ? > We are just a piece of a bigger ecosystem, the problem is that most of the > time "setting up" each piece is a pain in the ass. > > WEBSITE Proposals: > Why not create and post images, an image per page. Is a usual approach for > proposing new layouts. > > > We are growing and this kind of discussions are a natural process. > -- > Ra > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From cjfields at illinois.edu Tue Feb 21 19:10:41 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Tue, 21 Feb 2012 19:10:41 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <8B427626-EEDB-4ED9-94DE-2F0D99F14866@illinois.edu> References: <8B427626-EEDB-4ED9-94DE-2F0D99F14866@illinois.edu> Message-ID: <492B88CE-FC32-4AEE-B4A6-0F688DC50D85@illinois.edu> Um, that was sent a little early :P Saw a unicorn and distractedly hit the 'send'... On Feb 21, 2012, at 12:54 PM, Christopher Fields wrote: > On Feb 21, 2012, at 5:29 AM, Raoul Bonnal wrote: > >> Hi Pjotr, Hilmar and others, >> ... >> >>> 4. One for you Hilmar: does the OBF actually encourage inertia in the Bio* >>> projects? >>> >>> It is appears to me that sitting leadership is reluctant to >>> give away their positions. I have discussed this with Chris Fields >>> last year. We agreed that there are also few to take over the helm. >>> So... >> I don't see how OBF could push the projects, in case of founds they would be >> distributed equally? We are good people so we are working together promoting >> our language helping the others. During the last BioHackathon the most >> astonishing things was seeing Bio Perl/Ruby/Python/Java working (really) >> together, it was great. > > Bioinformatics problems span languages My point being, cross-pollination of projects with common problems makes sense. >>> 5. how do we nurture future leadership? >>> >>> I am old and cynical enough to know people mostly work for their own >>> direct benefit (their itch, so tho speak) in OSS, or anywhere else. >>> Still, I am going to poke and prod for some time, to see if we can >>> make change. I believe Bio* projects are at fork in the road. Which >>> one are we going to take? >> >>> Should BioRuby exist as it is, or should we >>> use it as a breeding ground for young developers. Same question really >>> for BioPython and BioPerl. >> Not very clear, at least to me. You can probably have it every way, make a toolkit that the community can use and have it be a means to bring in additional developers to attempt to add or improve upon functionality. That's how I got involved with bioperl. >>> The BioRuby community is almost in a coma, I think. Despite 180 >>> readers of the ML. I see the same people engaging, and interestingly, >>> a significant number of messages from Biopython and BioPerl >>> leadership. Thank you for that. BioRuby is just coming out of its >>> shell, and you are helping. There is a favorite term of mine that was coined back in the early Perl days, 'being Warnocked': http://en.wikipedia.org/wiki/Warnock's_dilemma Lack of a response to a question could mean a lot of things. If you absolutely need a response, an email thread may not be the best option (maybe a survey?) >>> 6. What is needed to get BioRuby out of the comatose state? >>> >>> With BioRuby we have had lively discussions before, but they tend to >>> peter out. We can reason about this, but I think it goes back to >>> leadership again. >> I don't know how to solve this issue... The democratic process you suggested >> some time ago ? Which is the workload, which is the coding power we have ? >> Which are the languages we can rely on for performances (it means which is >> the knowledge of the people around here )? Do we want to support Jruby? >> Suppose we now need a new feature in BioRuby, which one ? Do we want to >> participate to GSoC ? YES and we MUST there is no doubt and we NEED to write >> good proposals but everything should be made as a community not only as a >> group of passionate developers. Developers tend to work hard on projects they are passionate about; if the website project or others aren't gathering input, it's possibly b/c there isn't anyone passionate about it. Or as Naohisa indicated, there hasn't been enough time to adequately respond. As mentioned above, everyone has a day $job and can't dedicate a lot of time to discussions. >> LANGUAGES: >> D or Scala, I don't know that I'm just curious and eager to learn. Most of >> my work is managing large scale data and interconnecting them extracting >> information etc... I would say, why not Hadoop ? >> We are just a piece of a bigger ecosystem, the problem is that most of the >> time "setting up" each piece is a pain in the ass. >> >> WEBSITE Proposals: >> Why not create and post images, an image per page. Is a usual approach for >> proposing new layouts. >> >> >> We are growing and this kind of discussions are a natural process. >> -- >> Ra Yes, but I think you have to balance that with actual work (code). Theoreticals and pet projects work only up to a point, you have to both establish a project's usefulness to the community, and even then sometimes the community doesn't immediately pick it up. chris From p.j.a.cock at googlemail.com Wed Feb 22 13:27:22 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 22 Feb 2012 13:27:22 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Mon, Feb 20, 2012 at 10:37 AM, Naohisa GOTO wrote: > Hi, > > On Sun, 19 Feb 2012 09:56:12 +0100 > Pjotr Prins wrote: > >> With an embarrassing 0 (zero) responses, I can conclude there is >> either no interest in this matter, or no one considers it his/her >> business. That is sad. Open source software matters. Web presence >> matters. > > I think requesting for writing responses for the mail posted > on Friday night in the weekend is too hurry. +1 I'm sure some people wouldn't even have seen Pjotr's email until Monday. Personally I saw this thread but was tied up with a workshop on Monday & Tuesday so didn't reply immediately. > I personally don't feel strong dissatisfaction with the current > http://bioruby.org/ website, although I agree it is not the > best ideal state, and I don't have strong motivation to discuss > about the topic unless new website candidate is sent by someone. I quite like the style of the current BioRuby.org page - there are two issues here, style and content. Obviously they are linked and the technical side will restrain the style and things like the ability to embed Twitter feeds or RSS. In terms of style, most of the Bio* home pages are simply wiki pages - usually protected to prevent vandalism, while most of the Bio* wiki pages are able to be edited by any registered account. This made it easy for anyone to create an alternative home page for discussion, and for that to be adopted. That's how we did the last major restructuring of the Biopython home page on our wiki, http://biopython.org/wiki/Main_Page > So, please send new site html contents. > Current contents is now on th GitHub. > https://github.com/ngoto/bioruby.org-webpage > Writing new pages without using current contents is also welcomed. That is interesting - I know other major open source projects have or are moving their home pages to github like this. For developers this isn't a major barrier to contribution - you can fork it and build an alterative webpage proposal. Pjotr wrote: >> Myself, I am thinking we need to retool the site >> for inexperienced programmers. That means >> accentuating Tutorials and examples, as >> Michael Barton suggested. We had similar concerns with Biopython's homepage and the current rather minimal page is attempting to highlight this kind of thing and make it obvious. While tutorial links are on the BioPerl, BioJava and BioRuby home pages, and near the start, I personally I find they are lost in an overly full page. (Constructive criticism/feedback on the Biopython website is also welcome) Another issue is keeping the content fresh. I notice that the Biopython, BioPerl and BioRuby homepage all have an embedded news feed top right from the OBF news server (filtering on the project category). This is great but relies on regular content appearing on the news server. I've tried to write blog posts on new or forthcoming features for Biopython, and suggested this would be a nice thing for all our developers to do. Another idea is community updates posts, perhaps monthly - something BioPerl used to do by email some years ago. The trouble is you need someone keen and committed to keep this going - although they don't have to be a developer so this is a nice way of trying to broaden community participation, We might be able to embed a Twitter feed on the home pages too... Regards, Peter From p.j.a.cock at googlemail.com Wed Feb 22 13:33:18 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 22 Feb 2012 13:33:18 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock wrote: > > We might be able to embed a Twitter feed on the > home pages too... > Looks like you can get an RSS feed easily enough, e.g. http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby That can be embedded in MediaWiki but it isn't very pretty. Peter From pjotr.public14 at thebird.nl Wed Feb 22 16:56:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 22 Feb 2012 17:56:27 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120221173121.GA28249@thebird.nl> References: <20120221173121.GA28249@thebird.nl> Message-ID: <20120222165627.GA1210@thebird.nl> ## Vision statement: BioRuby is about beauty Ruby is a language that encourages writing 'beautiful code'. RoR is often praised for its solutions and minimalism. It is no accident that many new ideas in agile software development are quickly taken up, or even originate in the the Ruby community. For example Cucumber feature DSL is a typical Ruby idea. BioRuby, however, shows little of this excitement. Let us have more focus on beautiful code and taking up behaviour driven development. Realisation: We should show many examples on how to design software properly, and redesign BioRuby to match that expectation. From georgkam at gmail.com Wed Feb 22 17:37:18 2012 From: georgkam at gmail.com (George Githinji) Date: Wed, 22 Feb 2012 20:37:18 +0300 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: +1 On Wed, Feb 22, 2012 at 7:56 PM, Pjotr Prins wrote: > ## Vision statement: BioRuby is about beauty > > Ruby is a language that encourages writing 'beautiful code'. RoR is often > praised for its solutions and minimalism. It is no accident that many new ideas > in agile software development are quickly taken up, or even originate in the > the Ruby community. For example Cucumber feature DSL is a typical Ruby idea. > BioRuby, however, shows little of this excitement. Let us have more focus > on beautiful code and taking up behaviour driven development. > > Realisation: > > We should show many examples on how to design software properly, and redesign > BioRuby to match that expectation. > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From hlapp at drycafe.net Wed Feb 22 22:17:05 2012 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 22 Feb 2012 17:17:05 -0500 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: <9340D5B7-C1E0-4965-B4A3-A9BC2AC4E1D2@drycafe.net> On Feb 22, 2012, at 11:56 AM, Pjotr Prins wrote: > ## Vision statement: BioRuby is about beauty Perl is, too, actually. The beauty of getting things done. Some beauty may be more difficult to see than another, but that doesn't make it any less beautiful :-) -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From mictadlo at gmail.com Wed Feb 22 23:27:03 2012 From: mictadlo at gmail.com (Mic) Date: Thu, 23 Feb 2012 09:27:03 +1000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: I thought BioRuby would run with JRuby. How far is Rubinus and support for it? There is a Ruby like language on to of erlang http://reia-lang.org/ which support erlang's famous concurrent programming. On Wed, Feb 22, 2012 at 11:33 PM, Peter Cock wrote: > On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock > wrote: > > > > We might be able to embed a Twitter feed on the > > home pages too... > > > > Looks like you can get an RSS feed easily enough, e.g. > > http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython > > http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl > > http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby > > That can be embedded in MediaWiki but it isn't very pretty. > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From georgkam at gmail.com Thu Feb 23 05:41:29 2012 From: georgkam at gmail.com (George Githinji) Date: Thu, 23 Feb 2012 08:41:29 +0300 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: Now let us get discuss the issues regarding actually restyling the bioruby.org site. If we were to restyle bioruby.org., What is the community's preferred way of doing it? 1. Using an existing Ruby framework i) Rails ii) Sinatra iii) Others (specify) 2. Getting together some static pages without utilizing a framework. Some considerations: 1. Who hosts the Bioruby.org site This is important so as to access the nature and the ease of deployment. Also should bioruby.org be hosted on a cloud infrastructure like heroku? What are the pros and cons? 2. Who owns the bioruby.org domain name? aka who pays and registers this domain every year and why? Is this person willing to surrender the domain ownership to the community? Would he perform the registration on behalf of the community ? 3. For a while now, bioruby.org redirects to http://bioruby.open-bio.org/. Which of the two is the more appropriate 'home' url? On Thu, Feb 23, 2012 at 2:27 AM, Mic wrote: > I thought BioRuby would run with JRuby. How far is Rubinus and support for > it? There is a Ruby like language on to of erlang ?http://reia-lang.org/ which > support erlang's famous concurrent programming. > > On Wed, Feb 22, 2012 at 11:33 PM, Peter Cock wrote: > >> On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock >> wrote: >> > >> > We might be able to embed a Twitter feed on the >> > home pages too... >> > >> >> Looks like you can get an RSS feed easily enough, e.g. >> >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython >> >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl >> >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby >> >> That can be embedded in MediaWiki but it isn't very pretty. >> >> Peter >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From pjotr.public14 at thebird.nl Thu Feb 23 07:35:37 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 23 Feb 2012 08:35:37 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120223073537.GB4065@thebird.nl> Today we will be on IRC. Pj. On Thu, Feb 23, 2012 at 08:41:29AM +0300, George Githinji wrote: > Now let us get discuss the issues regarding actually restyling the > bioruby.org site. > > If we were to restyle bioruby.org., What is the community's preferred > way of doing it? > 1. Using an existing Ruby framework > i) Rails > ii) Sinatra > iii) Others (specify) > > 2. Getting together some static pages without utilizing a framework. > > Some considerations: > 1. Who hosts the Bioruby.org site > This is important so as to access the nature and the ease of > deployment. Also should bioruby.org be hosted on a cloud > infrastructure like heroku? What are the pros and cons? > > 2. Who owns the bioruby.org domain name? aka who pays and registers > this domain every year and why? > Is this person willing to surrender the domain ownership to the > community? Would he perform the registration on behalf of the > community ? > > 3. For a while now, bioruby.org redirects to > http://bioruby.open-bio.org/. Which of the two is the more > appropriate 'home' url? > > > > > > On Thu, Feb 23, 2012 at 2:27 AM, Mic wrote: > > I thought BioRuby would run with JRuby. How far is Rubinus and support for > > it? There is a Ruby like language on to of erlang ?http://reia-lang.org/ which > > support erlang's famous concurrent programming. > > > > On Wed, Feb 22, 2012 at 11:33 PM, Peter Cock wrote: > > > >> On Wed, Feb 22, 2012 at 1:27 PM, Peter Cock > >> wrote: > >> > > >> > We might be able to embed a Twitter feed on the > >> > home pages too... > >> > > >> > >> Looks like you can get an RSS feed easily enough, e.g. > >> > >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=biopython > >> > >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioperl > >> > >> http://api.twitter.com/1/statuses/user_timeline.rss?screen_name=bioruby > >> > >> That can be embedded in MediaWiki but it isn't very pretty. > >> > >> Peter > >> _______________________________________________ > >> BioRuby Project - http://www.bioruby.org/ > >> BioRuby mailing list > >> BioRuby at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://biorelated.wordpress.com/ > Twitter: http://twitter.com/#!/george_l > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Thu Feb 23 08:40:14 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Thu, 23 Feb 2012 08:40:14 +0000 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <941C9523-3B11-434D-B04B-35BC170A209E@googlemail.com> Hi George, On 23 Feb 2012, at 05:41, George Githinji wrote: > Some considerations: > 1. Who hosts the Bioruby.org site > This is important so as to access the nature and the ease of > deployment. Also should bioruby.org be hosted on a cloud > infrastructure like heroku? What are the pros and cons? Currently most Bio* project homepages are hosted on an OBF server - see www.open-bio.org - with donated bandwidth. I understand that the BioRuby homepage is hosted on Github (see earlier in this thread). Some OBF machines are in the cloud, specifically the buildbot server runs on an Amazon instance. > 2. Who owns the bioruby.org domain name? aka who pays and registers > this domain every year and why? > Is this person willing to surrender the domain ownership to the > community? Would he perform the registration on behalf of the > community ? Currently the OBF (at least, they do for most of the Bio* projects) which is on behalf of the community. I assume the same applies to the BioRuby.org domain. > 3. For a while now, bioruby.org redirects to > http://bioruby.open-bio.org/. Which of the two is the more > appropriate 'home' url? Why exactly that happens I don't know, it doesn't happen for BioPerl.org or Biopython.org for instance. It could be linked to the GitHub hosting and domain records - it can probably be tweaked. Peter (Biopython, also OBF board member) From ngoto at gen-info.osaka-u.ac.jp Thu Feb 23 12:16:11 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Thu, 23 Feb 2012 21:16:11 +0900 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <941C9523-3B11-434D-B04B-35BC170A209E@googlemail.com> References: <941C9523-3B11-434D-B04B-35BC170A209E@googlemail.com> Message-ID: <20120223211611.6787.EEF6E030@gen-info.osaka-u.ac.jp> Hi Peter, > I understand that the BioRuby homepage is hosted on > Github (see earlier in this thread). No, not hosted on GitHub. The GitHub URL in the previous mail https://github.com/ngoto/bioruby.org-webpage is my personal copy of http://bioruby.org web contents. I've push them to GitHub for smooth collaboration. The contents should be copied to real servers by hand. http://bioruby.org/ is now redirection to http://bioruby.open-bio.org/, provided by a domain name registerer. Previously, http://bioruby.org/ was hosted on the University of Tokyo and http://bioruby.open-bio.org/ was a mirror site of http://bioruby.org/, but due to the machine replacement and administration changes in the university, it was changed to the redirection. We provided some server-side services in http://bioruby.org/ server, e.g. BioFetch service http://bioruby.org/cgi-bin/biofetch.rb. That was a reason why we could not migrate to OBF server and kept bioruby.open-bio.org as a mirror server. -- Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Thu Feb 23 12:27:39 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 23 Feb 2012 13:27:39 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120217172518.GB16813@thebird.nl> <20120219085612.GA29424@thebird.nl> <20120220103708.25B9A1CBC3F9@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <20120223122739.GA7421@thebird.nl> On Thu, Feb 23, 2012 at 09:27:03AM +1000, Mic wrote: > I thought BioRuby would run with JRuby. How far is Rubinus and support for > it? There is a Ruby like language on to of erlang > [1]http://reia-lang.org/ which support erlang's famous concurrent > programming. Reia too different a dialect. Rubinius should work. Pj. From bonnal at ingm.org Thu Feb 23 14:50:01 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 23 Feb 2012 15:50:01 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: <20120223122739.GA7421@thebird.nl> Message-ID: George have summarised some of the points raised during irc meeting: here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling About :" support example code snippets that can be run from the browser * it would be great if we had a set of tutorials that users can follow in the browser" A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I think Katayama did it. From marian.povolny at gmail.com Thu Feb 23 17:28:23 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Thu, 23 Feb 2012 18:28:23 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: <20120223122739.GA7421@thebird.nl> Message-ID: Hi all, Looking at the "Audience" section on the http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling page, is there a real need for a separate treatment of Computer Science and Ruby background? What different paths would those two groups go to get into bioinformatics using BioRuby? Except for learning Ruby frirst :) And also, I think there is one category of audience missing: BioRuby developers :) -- Marjan Povolni On Thu, Feb 23, 2012 at 3:50 PM, Raoul Bonnal wrote: > George have summarised some of the points raised during irc meeting: > here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling > > About :" support example code snippets that can be run from the browser > * it would be great if we had a set of tutorials that users can follow in > the browser" > A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I > think Katayama did it. > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From bonnal at ingm.org Thu Feb 23 17:38:56 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Thu, 23 Feb 2012 18:38:56 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: Message-ID: Actually no need, may be .... What about a kind of logo with: BioRuby boosted by FFI, that could be interesting for CS which can incorporate their algorithm written in C/C++ (whatever language) into Ruby. BioRuby developers could be ?redirected? to biogems.info/tutorial or incorporate it into the site. If I remember correctly Jan wrote guide lines on howto use git for developing bioruby, that kind of docs could be used as inspiration for the new docs. http://saaientist.blogspot.com/2008/06/bioruby-with-git-how-would-that-work. html http://nsaunders.wordpress.com/2011/08/05/bioruby-development-feedback-on-us ing-git/ http://lists.open-bio.org/pipermail/bioruby/2008-September/000700.html On 23/02/12 18.28, "Marjan Povolni" wrote: > Hi all, > > Looking at the "Audience" section on > the?http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling?page, is there a > real need for a separate treatment of Computer Science and Ruby background? > > > What different paths would those two groups go to get into bioinformatics > using BioRuby? Except for learning Ruby frirst :) > > And also, I think there is one category of audience missing: BioRuby > developers :) > > -- > Marjan Povolni > > On Thu, Feb 23, 2012 at 3:50 PM, Raoul Bonnal wrote: >> George have summarised some of the points raised during irc meeting: >> here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling >> >> About :" support example code snippets that can be run from the browser >> * it would be great if we had a set of tutorials that users can follow in >> the browser" >> A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, ?I >> think Katayama did it. >> >> >> >> _______________________________________________ >> BioRuby Project - http://www.bioruby.org/ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby > > From pjotr.public14 at thebird.nl Thu Feb 23 18:37:51 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 23 Feb 2012 19:37:51 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: <20120223183751.GA10920@thebird.nl> ## Vision statement: BioRuby is for biologists Ruby is a language which shines in creating simple DSL's for end-users. Great examples are Cucumber, Chef and bio-ngs. BioRuby needs to build out this concept of creating 'simple' work flows in the form of DSLs. The other area is in creating web sites. Many papers publish simple web sites presenting some algorithm (some of these papers get embarrassingly high impact). BioRuby should present a quick way of building websites - probably on top of RoR. Realisation: Biogem has some facility for that, but it should be much easier and obvious. Combining RoR with DSL's could make BioRuby a preferred environment for both publications and education. From yannick.wurm at unil.ch Thu Feb 23 18:37:25 2012 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Thu, 23 Feb 2012 18:37:25 +0000 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: References: Message-ID: <11659791-F673-4D2B-B444-EB6A47ABB326@unil.ch> On 23 Feb 2012, at 17:00, bioruby-request at lists.open-bio.org wrote: > George have summarised some of the points raised during irc meeting: > here at http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling > > About :" support example code snippets that can be run from the browser > * it would be great if we had a set of tutorials that users can follow in > the browser" > A starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I > think Katayama did it. Apologies for chiming in a bit late. I fully agree that having something along these lines set up can greatly facilitate bioruby adoption. * people should be able to test it without having to install anything. (I recently tried running the BioRubyOnRails & failed). * http://rubular.com/ (used for learning & testing regexps) provides good inspiration. * making it idiot-proof (e.g. having an "upload flatfile" button... and then autogenerating the appropriate file loading code) can help further... Cheers, yannick ---- Yannick Wurm Ants, Genomes & Evolution ? y.wurm at qmul.ac.uk ? skype:yannickwurm ? +44 207 882 3049 5.03A Fogg ? School of Biological & Chemical Sciences ? Queen Mary, University of London ? Mile End Road ? E1 4NX London ? UK From marian.povolny at gmail.com Thu Feb 23 20:03:53 2012 From: marian.povolny at gmail.com (Marjan Povolni) Date: Thu, 23 Feb 2012 21:03:53 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: References: Message-ID: > > > BioRuby developers could be ?redirected? to biogems.info/tutorial or > incorporate it into the site. If I remember correctly Jan wrote guide lines > on howto use git for developing bioruby, that kind of docs could be used as > inspiration for the new docs. > > > http://saaientist.blogspot.com/2008/06/bioruby-with-git-how-would-that-work.html > > http://nsaunders.wordpress.com/2011/08/05/bioruby-development-feedback-on-using-git/ > http://lists.open-bio.org/pipermail/bioruby/2008-September/000700.html > > That sounds like a page for potential contributors, with instructions on how to contribute. That should definitely be a part of the new website. Is there anything else the active developers could use in their development effort, or maybe something to stay in touch with the community and what are others doing? Any ideas? Or is the ML doing a good job? I would also like to see a similar page like the GSoC page on wiki, but incorporated into the new site, maybe even with a link like "Need a challenge?" on the front page, or the page for contributors. The purpose would be to list feature descriptions that somebody would like to see implemented but has no time to do it, but still would be available for some mentoring. I can see myself handing out the link to my future students which would like to learn more, or get some experience while doing something useful. Would anybody in the developer community be interested in supporting something like this? Or would the mentoring part be too much work? -- Marjan Povolni From bonnal at ingm.org Fri Feb 24 07:37:50 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 24 Feb 2012 08:37:50 +0100 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: <11659791-F673-4D2B-B444-EB6A47ABB326@unil.ch> Message-ID: On 23/02/12 19.37, "Yannick Wurm" wrote: > On 23 Feb 2012, at 17:00, bioruby-request at lists.open-bio.org wrote: > George > have summarised some of the points raised during irc meeting: > here at > http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling > > About :" support > example code snippets that can be run from the browser > * it would be great > if we had a set of tutorials that users can follow in > the browser" > A > starting point is http://bioruby.open-bio.org/wiki/BioRubyOnRails, I > think > Katayama did it. Apologies for chiming in a bit late. I fully agree that > having something along these lines set up can greatly facilitate bioruby > adoption. * people should be able to test it without having to install > anything. (I recently tried running the BioRubyOnRails & failed). * It was developed a long time ago and Ror is great but life time cycle of each release is very short. >* making it idiot-proof (e.g. having an "upload flatfile" > button... and then autogenerating the appropriate file loading code) can help > further... Good point we could also present a set of tutorials/docs related with the file type uploaded: ok you uploaded this filetime and now the related docs is 1,2,3,4...n From bonnal at ingm.org Fri Feb 24 07:51:01 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 24 Feb 2012 08:51:01 +0100 Subject: [BioRuby] Restyling BioRuby.org In-Reply-To: Message-ID: +1 Mentoring is not too much work if the mentor has interest :-) I would call that page ?BioRuby Lab?. In this page I would rank the projects accomplished, these projects could be used by universities to offer stages for students (Francesco and Me, we are doing in this way) I?d like to have a page with the developers with an image and brief description of his/her research/interest with all contact information (twitter,email,irc,skype,G+). On 23/02/12 21.03, "Marjan Povolni" wrote: >> >> BioRuby developers could be ?redirected? to biogems.info/tutorial >> or incorporate it into the site. If I >> remember correctly Jan wrote guide lines on howto use git for developing >> bioruby, that kind of docs could be used as inspiration for the new docs. >> >> http://saaientist.blogspot.com/2008/06/bioruby-with-git-how-would-that-work.h >> tml >> http://nsaunders.wordpress.com/2011/08/05/bioruby-development-feedback-on-usi >> ng-git/ >> http://lists.open-bio.org/pipermail/bioruby/2008-September/000700.html >> > ? > That sounds like a page for potential contributors, with instructions on how > to contribute. That should definitely be a part of the new website. > > Is there anything else the active developers could use in their development > effort, or maybe something to stay in touch with the community and what are > others doing? Any ideas? Or is the ML doing a good job?? > > I would also like to see a similar page like the GSoC page on wiki, but > incorporated into the new site, maybe even with a link like "Need a > challenge?" on the front page, or the page for contributors. The purpose would > be to list feature descriptions that somebody would like to see implemented > but has no time to do it, but still would be available for some mentoring. I > can see myself handing out the link to my future students which would like to > learn more, or get some experience while doing something useful. Would anybody > in the developer community be interested in supporting something like this? Or > would the mentoring part be too much work? > > -- > Marjan Povolni > From bonnal at ingm.org Fri Feb 24 07:59:31 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 24 Feb 2012 08:59:31 +0100 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: <11659791-F673-4D2B-B444-EB6A47ABB326@unil.ch> Message-ID: ++1 On 23/02/12 19.37, "Yannick Wurm" wrote: > * making it idiot-proof This is a key point, user experience is everything. From pjotr.public14 at thebird.nl Fri Feb 24 16:11:11 2012 From: pjotr.public14 at thebird.nl (pjotr.public14 at thebird.nl) Date: Fri, 24 Feb 2012 17:11:11 +0100 Subject: [BioRuby] New age BioRuby Message-ID: <20120224161111.GB18826@thebird.nl> Hi everyone, We are happy to announce a new age BioRuby. This is BioRuby in the broadest sense, which includes gems and web presence. As a group, we have decided to take BioRuby into a new age, and change the way we approach community and newcomers. This we will do at four levels: (1) Democracy First of all, for new age BioRuby the decision making process will be transparent and democratic. To guard the democratic process we are forming a panel of active major BioRuby committers, including Pjotr, Raoul and Francesco. The panel will act as a monitor. Other active major BioRuby and biogem committers are welcome to join the panel. (2) Web presence The web presence needs to change to appeal to a new generation of coders. We are committed to changing that. (3) BioRuby gems The recently published Biogem system has introduced the plug-in approach and we think has a natural evolving process that BioRuby needs to be adapted for the new generation of tools. We will take on moving functionality into gems, creating a modular setup, and reducing the existing BioRuby source to a skeleton framework. The old BioRuby will continue to exist for reasons of backward compatibility. Until someone else is elected by the community, the panel will be responsible for the new BioRuby code base, and Pjotr will be in charge of coordinating the effort. (4) New talent The new age of BioRuby is really about nurturing new talent. This means giving away responsibilities to the next generation. We will rotate leadership for projects on a regular basis. To achieve our ends we will put together a VISION statement for BioRuby, as well as a road map. Pj, Ra & Fra From ktym at hgc.jp Fri Feb 24 22:34:48 2012 From: ktym at hgc.jp (Toshiaki Katayama) Date: Sat, 25 Feb 2012 07:34:48 +0900 Subject: [BioRuby] New age BioRuby In-Reply-To: <20120224161111.GB18826@thebird.nl> References: <20120224161111.GB18826@thebird.nl> Message-ID: <44451BFF-5016-4BAB-98F5-49166C57985C@hgc.jp> Hello Pjotr, I felt your recent statements sent to me and on this list were not fair. I believe everyone naturally has rights and freedom to try any changes on the code base. You can propose it when you implemented. You can also propose new web site candidate when it is ready. I have been a web maintainer for the historical reasons (as I paid for past 10 years and maintained the computer resources in my institution and on the open-bio.org). I tried to cover all aspects of the BioRuby related web resources when I designed the current site. I can admit we need to update the site and happy to see the alternative candidates, but I personally think what actually we need is not that superficial but the contents which kindly describes the usage of the BioRuby for scientific purposes (and future plans, maybe). The founder of the BioRuby had been responsible on the functionality and stability of the BioRuby over 10 years and have never been non-democratic. We welcomed contributors like you and gave privileges as a committer. However, you had never committed the process of the release management which actually is a hard and sometimes painful task. Dr. Goto has been done a great job on this as a release manager for many years as he understand all modules in the BioRuby code base so that he could pay careful attention to keep the library very stable and also to keep backward compatibilities. I respect him as he has been an only person who dedicated on this procedure because no one else have volunteered for the task until now. We invited you to Japan and discussed many aspects of the BioRuby which finally resulted as the Biogem system. Before we get there, we started from open CVS repository then moved to SVN but both still had some barrier to join the development process, therefore we moved to the GitHub so that everyone can fork and contribute without any privileges given in advance. (Other Open Bio* groups followed the same way.) This means real democracy had been maintained as much as we can. Finally, with Biogem, anyone can develop and release bioinformatics modules without bothered by the release cycle of the stable core. I believe that this system was a milestone where most democratic development process had been firstly introduced among the Open Bio* projects. Given said that, I don't intend to block your motivations to make the BioRuby better. Rather, I hope you to push your plans in a fruitful way. I just wish that people on this list won't misunderstand the founders of this project wrongly. We had paid tons of efforts to cross the chasm as innovators. We may already have reached the early majority stage with the help of early adopters like you and good others on this list. If so, now is the time to change the scene as you described. I may have missed several mails recently posted on this list or sent personally to me as I had been quite busy. Sorry about that. Despite the long message of this mail, it is easy for me to catch up with short e-mails, basically. Thanks. ;) P.S. I have several plans to develop (Bio)Ruby/Rails or Node.js based semantic DB applications starting from this spring. Is there anyone who are interested in to work with us in Japan? We may be able to employ some developers. Regards, Toshiaki Katayama On 2012/02/25, at 1:11, pjotr.public14 at thebird.nl wrote: > Hi everyone, > > We are happy to announce a new age BioRuby. This is BioRuby in the > broadest sense, which includes gems and web presence. As a group, we > have decided to take BioRuby into a new age, and change the way we > approach community and newcomers. This we will do at four levels: > > > (1) Democracy > > First of all, for new age BioRuby the decision making process will be > transparent and democratic. To guard the democratic process we are > forming a panel of active major BioRuby committers, including Pjotr, > Raoul and Francesco. The panel will act as a monitor. Other active > major BioRuby and biogem committers are welcome to join the panel. > > > (2) Web presence > > The web presence needs to change to appeal to a new generation of > coders. We are committed to changing that. > > > (3) BioRuby gems > > The recently published Biogem system has introduced the plug-in > approach and we think has a natural evolving process that BioRuby > needs to be adapted for the new generation of tools. We will take on > moving functionality into gems, creating a modular setup, and reducing > the existing BioRuby source to a skeleton framework. The old BioRuby > will continue to exist for reasons of backward compatibility. Until > someone else is elected by the community, the panel will be > responsible for the new BioRuby code base, and Pjotr will be in charge > of coordinating the effort. > > > (4) New talent > > The new age of BioRuby is really about nurturing new talent. This > means giving away responsibilities to the next generation. We will > rotate leadership for projects on a regular basis. > > To achieve our ends we will put together a VISION statement for > BioRuby, as well as a road map. > > > Pj, Ra & Fra > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From p.j.a.cock at googlemail.com Fri Feb 24 23:51:13 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Fri, 24 Feb 2012 23:51:13 +0000 Subject: [BioRuby] Nightly build testing Message-ID: Hello all, My apologies, the buildbot server has been offline over a week. It had run out of disk space (too many log files), solved now: http://testing.open-bio.org/bioruby/ I intend to setup a Windows XP (32bit) machine as another build slave next week - there was a permissions problem running the BioRuby tests under Windows but that was fixed. Regards, Peter P.S. Who should the failure emails be sent to? Initially at least there may be quite a few - so this mailing list does not seem appropriate: http://lists.open-bio.org/pipermail/bioruby/2011-December/001996.html From pjotr.public14 at thebird.nl Sat Feb 25 08:18:36 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 25 Feb 2012 09:18:36 +0100 Subject: [BioRuby] New age BioRuby In-Reply-To: <44451BFF-5016-4BAB-98F5-49166C57985C@hgc.jp> References: <20120224161111.GB18826@thebird.nl> <44451BFF-5016-4BAB-98F5-49166C57985C@hgc.jp> Message-ID: <20120225081836.GB24046@thebird.nl> On Sat, Feb 25, 2012 at 07:34:48AM +0900, Toshiaki Katayama wrote: > Hello Pjotr, > > I felt your recent statements sent to me and on this list were not > fair. I believe everyone naturally has rights and freedom to try > any changes on the code base. You can propose it when you > implemented. You can also propose new web site candidate when it is > ready. I have been a web maintainer for the historical reasons (as I > paid for past 10 years and maintained the computer resources in my > institution and on the open-bio.org). I tried to cover all aspects > of the BioRuby related web resources when I designed the current > site. I can admit we need to update the site and happy to see the > alternative candidates, but I personally think what actually we need > is not that superficial but the contents which kindly describes the > usage of the BioRuby for scientific purposes (and future plans, > maybe). > > The founder of the BioRuby had been responsible on the functionality > and stability of the BioRuby over 10 years and have never been > non-democratic. We welcomed contributors like you and gave > privileges as a committer. However, you had never committed the > process of the release management which actually is a hard and > sometimes painful task. Dr. Goto has been done a great job on this > as a release manager for many years as he understand all modules in > the BioRuby code base so that he could pay careful attention to keep > the library very stable and also to keep backward compatibilities. > I respect him as he has been an only person who dedicated on this > procedure because no one else have volunteered for the task until > now. > > We invited you to Japan and discussed many aspects of the BioRuby > which finally resulted as the Biogem system. Before we get there, we > started from open CVS repository then moved to SVN but both still > had some barrier to join the development process, therefore we moved > to the GitHub so that everyone can fork and contribute without any > privileges given in advance. (Other Open Bio* groups followed the > same way.) This means real democracy had been maintained as much as > we can. Finally, with Biogem, anyone can develop and release > bioinformatics modules without bothered by the release cycle of the > stable core. I believe that this system was a milestone where most > democratic development process had been firstly introduced among the > Open Bio* projects. > > Given said that, I don't intend to block your motivations to make > the BioRuby better. Rather, I hope you to push your plans in a > fruitful way. > > I just wish that people on this list won't misunderstand the > founders of this project wrongly. We had paid tons of efforts to > cross the chasm as innovators. I think no one on this list disagrees with the above. I would be the last one not to recognize your and Naohisa's inputs and achievements. I thank you for inviting us to Japan, for encouraging plugins. And basically I thank you for being you. I hope that is clear enough. > We may already have reached the early majority stage with the help > of early adopters like you and good others on this list. If so, now > is the time to change the scene as you described. We as BioRuby have been innovative, and attract some really good people. We should continue pushing for innovation, including the processes that encourage innovation. Also, it is very important that people who put in a lot of energy get the right credit for their work, and get encouraged to keep putting in a lot of work. We have erected a panel to ascertain that we continue the line of innovation, including total encouragement to new comers and old hands. That takes a lot of time and energy, and needs total commitment. By erecting the panel we have *committed* ourselves. Together with you we can define the exact remit of the panel. In fact, you should be on the panel. In my opinion the remit of the panel is to ascertain the code base, chosen technologies, website, web presence etc. represent the interests of the community. I am not saying it was not handled properly before, but I am saying it can be improved. By having a body of dedicated people, and open discussion, we can move forward. We also have to think about developing leadership. You have been doing this job for over 10 years. I don't expect you to think you will be project leader in another 10 year's time. Personally I think no one should be leading for a really long time. People get very busy - which is a natural progression in science. The panel should put the processes in place to nurture new leadership. The first job of the panel is to exactly define its remit for the coming years. We have made a start in that earlier announcement. Thanks for response Toshiaki. We all have the interest of BioRuby at heart, so let's keep on innovating and keep BioRuby going as the most exciting Bio* project! Pj. From pjotr.public14 at thebird.nl Sat Feb 25 08:42:00 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 25 Feb 2012 09:42:00 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120222165627.GA1210@thebird.nl> References: <20120221173121.GA28249@thebird.nl> <20120222165627.GA1210@thebird.nl> Message-ID: <20120225084200.GA28069@thebird.nl> ## Vision statement: BioRuby is agile The Ruby community is always working on agile processes. BioRuby can benefit from behaviour driven development (BDD), specifications, doctests and integration and unit testing. Realisation: In addition to unit testing we should concentrate on introducing Rspec, Cucumber, rubydoctests across the board. Also we should use the continuous integration testing by services such as travis-ci (I have a writeup on the latter soon) and perhaps use the OBF test services for stable plugins. From bonnal at ingm.org Sat Feb 25 09:16:21 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 25 Feb 2012 10:16:21 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120225084200.GA28069@thebird.nl> Message-ID: +1 On 25/02/12 09.42, "Pjotr Prins" wrote: > ## Vision statement: BioRuby is agile > > The Ruby community is always working on agile processes. BioRuby can > benefit from behaviour driven development (BDD), specifications, > doctests and integration and unit testing. > > Realisation: > > In addition to unit testing we should concentrate on introducing > Rspec, Cucumber, rubydoctests across the board. Also we should use the > continuous integration testing by services such as travis-ci (I have a > writeup on the latter soon) and perhaps use the OBF test services for > stable plugins. From p.j.a.cock at googlemail.com Sat Feb 25 09:35:31 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 25 Feb 2012 09:35:31 +0000 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120225084200.GA28069@thebird.nl> Message-ID: On Saturday, February 25, 2012, Raoul Bonnal wrote: > +1 > > > On 25/02/12 09.42, "Pjotr Prins" > > wrote: > > > ## Vision statement: BioRuby is agile > > > > The Ruby community is always working on agile processes. BioRuby can > > benefit from behaviour driven development (BDD), specifications, > > doctests and integration and unit testing. > > > > Realisation: > > > > In addition to unit testing we should concentrate on introducing > > Rspec, Cucumber, rubydoctests across the board. Also we should use the > > continuous integration testing by services such as travis-ci (I have a > > writeup on the latter soon) and perhaps use the OBF test services for > > stable plugins. > Without an extensive testing process like this, I struggle to see how a dynamic range of plugins from different authors can keep interoperability - so this sounds good. As we've discussed, the buildbot system as we're using it on the OBF testing service is more suited to testing one code base under a single repository. So another +1 for looking at automated testing of all the biogem packages. It will be a lot of work though... But should pay off :) Peter From georgkam at gmail.com Sat Feb 25 10:15:20 2012 From: georgkam at gmail.com (George Githinji) Date: Sat, 25 Feb 2012 13:15:20 +0300 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120225084200.GA28069@thebird.nl> Message-ID: +1 On Sat, Feb 25, 2012 at 12:35 PM, Peter Cock wrote: > On Saturday, February 25, 2012, Raoul Bonnal wrote: > >> +1 >> >> >> On 25/02/12 09.42, "Pjotr Prins" > >> wrote: >> >> > ## Vision statement: BioRuby is agile >> > >> > The Ruby community is always working on agile processes. BioRuby can >> > benefit from behaviour driven development (BDD), specifications, >> > doctests and integration and unit testing. >> > >> > Realisation: >> > >> > In addition to unit testing we should concentrate on introducing >> > Rspec, Cucumber, rubydoctests across the board. Also we should use the >> > continuous integration testing by services such as travis-ci (I have a >> > writeup on the latter soon) and perhaps use the OBF test services for >> > stable plugins. >> > > Without an extensive testing process like this, I struggle to see > how a dynamic range of plugins from different authors can keep > interoperability - so this sounds good. As we've discussed, the > buildbot system as we're using it on the OBF testing service is > more suited to testing one code base under a single repository. > > So another +1 for looking at automated testing of all the biogem > packages. It will be a lot of work though... But should pay off :) > > Peter > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ Twitter: http://twitter.com/#!/george_l From bonnal at ingm.org Sat Feb 25 13:49:03 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 25 Feb 2012 14:49:03 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: Message-ID: Something we need and I need to figure out how to do is, check the plugins? interdependencies/dependencies and notify to the author, ml or the web site the need to update them; maybe would be useful to test the plugin with upgraded dependencies and let that know to the developers. This would be useful because gems are updated frequently and if the developer maintains a lot of plugins it?s a mess follow everything ( at least for me). PS: If you need to mirror the test bots I can see if there are machines available here, do they require a lot of resources ? On 25/02/12 10.35, "Peter Cock" wrote: > > > On Saturday, February 25, 2012, Raoul Bonnal wrote: >> +1 >> >> >> On 25/02/12 09.42, "Pjotr Prins" > >> wrote: >> >>> > ## Vision statement: BioRuby is agile >>> > >>> > The Ruby community is always working on agile processes. BioRuby can >>> > benefit from behaviour driven development (BDD), specifications, >>> > doctests and integration and unit testing. >>> > >>> > Realisation: >>> > >>> > In addition to unit testing we should concentrate on introducing >>> > Rspec, Cucumber, rubydoctests across the board. Also we should use the >>> > continuous integration testing by services such as travis-ci (I have a >>> > writeup on the latter soon) and perhaps use the OBF test services for >>> > stable plugins. > ? > Without an extensive testing process like this, I struggle to see > how a dynamic range of plugins from different authors can keep > interoperability - so this sounds good. As we've discussed, the > buildbot system as we're using it on the OBF testing service is > more?suited to testing one code base under a single repository. > > So another +1 for looking at automated testing of all the biogem > packages. It will be a lot of work though... But should pay off :) > > Peter > From bonnal at ingm.org Sat Feb 25 16:41:16 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Sat, 25 Feb 2012 17:41:16 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: Message-ID: Found a candidate https://gemnasium.com/ On 25/02/12 14.49, "Raoul Bonnal" wrote: > Something we need and I need to figure out how to do is, check the > plugins? interdependencies/dependencies and notify to the author, ml or the > web site the need to update them; maybe would be useful to test the plugin > with upgraded dependencies and let that know to the developers. This would > be useful because gems are updated frequently and if the developer maintains > a lot of plugins it?s a mess follow everything ( at least for me). > > PS: If you need to mirror the test bots I can see if there are machines > available here, do they require a lot of resources ? > > > On 25/02/12 10.35, "Peter Cock" wrote: > >> >> >> On Saturday, February 25, 2012, Raoul Bonnal wrote: >>> +1 >>> >>> >>> On 25/02/12 09.42, "Pjotr Prins" > >>> wrote: >>> >>>>> ## Vision statement: BioRuby is agile >>>>> >>>>> The Ruby community is always working on agile processes. BioRuby can >>>>> benefit from behaviour driven development (BDD), specifications, >>>>> doctests and integration and unit testing. >>>>> >>>>> Realisation: >>>>> >>>>> In addition to unit testing we should concentrate on introducing >>>>> Rspec, Cucumber, rubydoctests across the board. Also we should use the >>>>> continuous integration testing by services such as travis-ci (I have a >>>>> writeup on the latter soon) and perhaps use the OBF test services for >>>>> stable plugins. >> ? >> Without an extensive testing process like this, I struggle to see >> how a dynamic range of plugins from different authors can keep >> interoperability - so this sounds good. As we've discussed, the >> buildbot system as we're using it on the OBF testing service is >> more?suited to testing one code base under a single repository. >> >> So another +1 for looking at automated testing of all the biogem >> packages. It will be a lot of work though... But should pay off :) >> >> Peter >> > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From francesco.strozzi at gmail.com Sat Feb 25 17:43:23 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Sat, 25 Feb 2012 18:43:23 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: Message-ID: Seems very nice and has a direct integration with Github +1 On Sat, Feb 25, 2012 at 17:41, Raoul Bonnal wrote: > Found a candidate https://gemnasium.com/ > > > On 25/02/12 14.49, "Raoul Bonnal" wrote: > > > Something we need and I need to figure out how to do is, check the > > plugins? interdependencies/dependencies and notify to the author, ml or > the > > web site the need to update them; maybe would be useful to test the > plugin > > with upgraded dependencies and let that know to the developers. This > would > > be useful because gems are updated frequently and if the developer > maintains > > a lot of plugins it?s a mess follow everything ( at least for me). > > > > PS: If you need to mirror the test bots I can see if there are machines > > available here, do they require a lot of resources ? > > > > > > On 25/02/12 10.35, "Peter Cock" wrote: > > > >> > >> > >> On Saturday, February 25, 2012, Raoul Bonnal wrote: > >>> +1 > >>> > >>> > >>> On 25/02/12 09.42, "Pjotr Prins" > > >>> wrote: > >>> > >>>>> ## Vision statement: BioRuby is agile > >>>>> > >>>>> The Ruby community is always working on agile processes. BioRuby can > >>>>> benefit from behaviour driven development (BDD), specifications, > >>>>> doctests and integration and unit testing. > >>>>> > >>>>> Realisation: > >>>>> > >>>>> In addition to unit testing we should concentrate on introducing > >>>>> Rspec, Cucumber, rubydoctests across the board. Also we should use > the > >>>>> continuous integration testing by services such as travis-ci (I have > a > >>>>> writeup on the latter soon) and perhaps use the OBF test services for > >>>>> stable plugins. > >> > >> Without an extensive testing process like this, I struggle to see > >> how a dynamic range of plugins from different authors can keep > >> interoperability - so this sounds good. As we've discussed, the > >> buildbot system as we're using it on the OBF testing service is > >> more suited to testing one code base under a single repository. > >> > >> So another +1 for looking at automated testing of all the biogem > >> packages. It will be a lot of work though... But should pay off :) > >> > >> Peter > >> > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Francesco From pjotr.public14 at thebird.nl Sat Feb 25 18:00:07 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 25 Feb 2012 19:00:07 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: Message-ID: <20120225180006.GA29616@thebird.nl> Lots of new projects listed by some fstrozzi ;j On Sat, Feb 25, 2012 at 06:43:23PM +0100, Francesco Strozzi wrote: > Seems very nice and has a direct integration with Github > > +1 > > On Sat, Feb 25, 2012 at 17:41, Raoul Bonnal wrote: > > > Found a candidate https://gemnasium.com/ > > > > > > On 25/02/12 14.49, "Raoul Bonnal" wrote: > > > > > Something we need and I need to figure out how to do is, check the > > > plugins? interdependencies/dependencies and notify to the author, ml or > > the > > > web site the need to update them; maybe would be useful to test the > > plugin > > > with upgraded dependencies and let that know to the developers. This > > would > > > be useful because gems are updated frequently and if the developer > > maintains > > > a lot of plugins it?s a mess follow everything ( at least for me). > > > > > > PS: If you need to mirror the test bots I can see if there are machines > > > available here, do they require a lot of resources ? > > > > > > > > > On 25/02/12 10.35, "Peter Cock" wrote: > > > > > >> > > >> > > >> On Saturday, February 25, 2012, Raoul Bonnal wrote: > > >>> +1 > > >>> > > >>> > > >>> On 25/02/12 09.42, "Pjotr Prins" > > > >>> wrote: > > >>> > > >>>>> ## Vision statement: BioRuby is agile > > >>>>> > > >>>>> The Ruby community is always working on agile processes. BioRuby can > > >>>>> benefit from behaviour driven development (BDD), specifications, > > >>>>> doctests and integration and unit testing. > > >>>>> > > >>>>> Realisation: > > >>>>> > > >>>>> In addition to unit testing we should concentrate on introducing > > >>>>> Rspec, Cucumber, rubydoctests across the board. Also we should use > > the > > >>>>> continuous integration testing by services such as travis-ci (I have > > a > > >>>>> writeup on the latter soon) and perhaps use the OBF test services for > > >>>>> stable plugins. > > >> > > >> Without an extensive testing process like this, I struggle to see > > >> how a dynamic range of plugins from different authors can keep > > >> interoperability - so this sounds good. As we've discussed, the > > >> buildbot system as we're using it on the OBF testing service is > > >> more suited to testing one code base under a single repository. > > >> > > >> So another +1 for looking at automated testing of all the biogem > > >> packages. It will be a lot of work though... But should pay off :) > > >> > > >> Peter > > >> > > > > > > > > > _______________________________________________ > > > BioRuby Project - http://www.bioruby.org/ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > -- > > Francesco > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From p.j.a.cock at googlemail.com Sat Feb 25 22:45:23 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Sat, 25 Feb 2012 22:45:23 +0000 Subject: [BioRuby] Developing a VISION In-Reply-To: References: Message-ID: On Sat, Feb 25, 2012 at 1:49 PM, Raoul Bonnal wrote: > > PS: If you need to mirror the test bots I can see if there are machines > available here, do they require a lot of resources ? > Yes, more buildslave machines would be good, and the load isn't very high. We should probably move this to a new thread (or resume one of the old ones). Peter From francesco.strozzi at gmail.com Mon Feb 27 09:38:58 2012 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Mon, 27 Feb 2012 10:38:58 +0100 Subject: [BioRuby] Ruby VideoCasts Message-ID: Hi all, I've just discovered this nice index of some of the best videocasts talking about Ruby and Rails, all available in the same place and tagged by arguments. http://showmedo.com/videotutorials/ruby Cheers -- Francesco From pjotr.public14 at thebird.nl Mon Feb 27 09:55:25 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 10:55:25 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120225084200.GA28069@thebird.nl> Message-ID: <20120227095525.GA12126@thebird.nl> Continuous integration testing is very useful for biogems/plugins. The Ruby community has come up with travis-ci, which is integrated into github! Any time code is submitted to github, the automated testing on different platforms kicks in. Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 gem for integrated testing. See https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > +1 > > > On 25/02/12 09.42, "Pjotr Prins" wrote: > > > ## Vision statement: BioRuby is agile > > > > The Ruby community is always working on agile processes. BioRuby can > > benefit from behaviour driven development (BDD), specifications, > > doctests and integration and unit testing. > > > > Realisation: > > > > In addition to unit testing we should concentrate on introducing > > Rspec, Cucumber, rubydoctests across the board. Also we should use the > > continuous integration testing by services such as travis-ci (I have a > > writeup on the latter soon) and perhaps use the OBF test services for > > stable plugins. > > From bonnal at ingm.org Mon Feb 27 10:19:26 2012 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 27 Feb 2012 11:19:26 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120227095525.GA12126@thebird.nl> Message-ID: Cool Pjotr, I could add this feature/tempalte to biogem I'll open an issue/request On 27/02/12 10.55, "Pjotr Prins" wrote: > Continuous integration testing is very useful for biogems/plugins. The > Ruby community has come up with travis-ci, which is integrated into > github! Any time code is submitted to github, the automated testing on > different platforms kicks in. > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > gem for integrated testing. See > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: >> +1 >> >> >> On 25/02/12 09.42, "Pjotr Prins" wrote: >> >>> ## Vision statement: BioRuby is agile >>> >>> The Ruby community is always working on agile processes. BioRuby can >>> benefit from behaviour driven development (BDD), specifications, >>> doctests and integration and unit testing. >>> >>> Realisation: >>> >>> In addition to unit testing we should concentrate on introducing >>> Rspec, Cucumber, rubydoctests across the board. Also we should use the >>> continuous integration testing by services such as travis-ci (I have a >>> writeup on the latter soon) and perhaps use the OBF test services for >>> stable plugins. >> >> From pjotr.public14 at thebird.nl Mon Feb 27 10:33:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 11:33:27 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120227095525.GA12126@thebird.nl> Message-ID: <20120227103327.GB12848@thebird.nl> Excellent idea. On Mon, Feb 27, 2012 at 11:19:26AM +0100, Raoul Bonnal wrote: > Cool Pjotr, I could add this feature/tempalte to biogem I'll open an > issue/request > > > On 27/02/12 10.55, "Pjotr Prins" wrote: > > > Continuous integration testing is very useful for biogems/plugins. The > > Ruby community has come up with travis-ci, which is integrated into > > github! Any time code is submitted to github, the automated testing on > > different platforms kicks in. > > > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > > gem for integrated testing. See > > > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > >> +1 > >> > >> > >> On 25/02/12 09.42, "Pjotr Prins" wrote: > >> > >>> ## Vision statement: BioRuby is agile > >>> > >>> The Ruby community is always working on agile processes. BioRuby can > >>> benefit from behaviour driven development (BDD), specifications, > >>> doctests and integration and unit testing. > >>> > >>> Realisation: > >>> > >>> In addition to unit testing we should concentrate on introducing > >>> Rspec, Cucumber, rubydoctests across the board. Also we should use the > >>> continuous integration testing by services such as travis-ci (I have a > >>> writeup on the latter soon) and perhaps use the OBF test services for > >>> stable plugins. > >> > >> > > From rob.syme at gmail.com Mon Feb 27 10:44:26 2012 From: rob.syme at gmail.com (Rob Syme) Date: Mon, 27 Feb 2012 18:44:26 +0800 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120227103327.GB12848@thebird.nl> References: <20120227095525.GA12126@thebird.nl> <20120227103327.GB12848@thebird.nl> Message-ID: Very nice. Does this make the open-bio testing apparatus redundant (for our purposes)? -r On Feb 27, 2012 6:33 PM, "Pjotr Prins" wrote: > Excellent idea. > > On Mon, Feb 27, 2012 at 11:19:26AM +0100, Raoul Bonnal wrote: > > Cool Pjotr, I could add this feature/tempalte to biogem I'll open an > > issue/request > > > > > > On 27/02/12 10.55, "Pjotr Prins" wrote: > > > > > Continuous integration testing is very useful for biogems/plugins. The > > > Ruby community has come up with travis-ci, which is integrated into > > > github! Any time code is submitted to github, the automated testing on > > > different platforms kicks in. > > > > > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > > > gem for integrated testing. See > > > > > > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > > > > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > > >> +1 > > >> > > >> > > >> On 25/02/12 09.42, "Pjotr Prins" wrote: > > >> > > >>> ## Vision statement: BioRuby is agile > > >>> > > >>> The Ruby community is always working on agile processes. BioRuby can > > >>> benefit from behaviour driven development (BDD), specifications, > > >>> doctests and integration and unit testing. > > >>> > > >>> Realisation: > > >>> > > >>> In addition to unit testing we should concentrate on introducing > > >>> Rspec, Cucumber, rubydoctests across the board. Also we should use > the > > >>> continuous integration testing by services such as travis-ci (I have > a > > >>> writeup on the latter soon) and perhaps use the OBF test services for > > >>> stable plugins. > > >> > > >> > > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr.public14 at thebird.nl Mon Feb 27 10:58:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 11:58:27 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: References: <20120227095525.GA12126@thebird.nl> <20120227103327.GB12848@thebird.nl> Message-ID: <20120227105827.GA13537@thebird.nl> On Mon, Feb 27, 2012 at 06:44:26PM +0800, Rob Syme wrote: > Very nice. > Does this make the open-bio testing apparatus redundant (for our > purposes)? > -r For the biogems: yes, I think so. For the large BioRuby library, and perhaps a few meta-biogems (bio-core) the open-bio setup is very useful. Pj. From pjotr.public14 at thebird.nl Mon Feb 27 11:14:13 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 12:14:13 +0100 Subject: [BioRuby] Developing a VISION In-Reply-To: <20120227095525.GA12126@thebird.nl> References: <20120225084200.GA28069@thebird.nl> <20120227095525.GA12126@thebird.nl> Message-ID: <20120227111413.GA13769@thebird.nl> bioruby-gff3-plugin now runs on ruby 1.8.7 ruby 1.9.2 jruby 1.9 mode rubinius 1.9 mode http://travis-ci.org/#!/pjotrp/bioruby-gff3-plugin the changes were in the tests only :). Tested without even installing Rubinius. This is almost miraculous stuff. You can see the power of the Travis Ruby stack - including webserver, rvm, vagrant etc. etc. I hope that Travis-ci will stay. Pj. On Mon, Feb 27, 2012 at 10:55:25AM +0100, Pjotr Prins wrote: > Continuous integration testing is very useful for biogems/plugins. The > Ruby community has come up with travis-ci, which is integrated into > github! Any time code is submitted to github, the automated testing on > different platforms kicks in. > > Here we set out to set up travis-ci with a biogem. I chose my bio-gff3 > gem for integrated testing. See > > https://github.com/pjotrp/bioruby-gem/blob/master/doc/integration-testing.md > > On Sat, Feb 25, 2012 at 10:16:21AM +0100, Raoul Bonnal wrote: > > +1 > > > > > > On 25/02/12 09.42, "Pjotr Prins" wrote: > > > > > ## Vision statement: BioRuby is agile > > > > > > The Ruby community is always working on agile processes. BioRuby can > > > benefit from behaviour driven development (BDD), specifications, > > > doctests and integration and unit testing. > > > > > > Realisation: > > > > > > In addition to unit testing we should concentrate on introducing > > > Rspec, Cucumber, rubydoctests across the board. Also we should use the > > > continuous integration testing by services such as travis-ci (I have a > > > writeup on the latter soon) and perhaps use the OBF test services for > > > stable plugins. > > > > > From pjotr.public14 at thebird.nl Mon Feb 27 11:55:44 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 12:55:44 +0100 Subject: [BioRuby] Travis-ci on biogems.info Message-ID: <20120227115544.GA14668@thebird.nl> Will pick up the Travis-ci build status: fail|passing|unknown. http://www.biogems.info/ (master branch of each repo only). Pj. From p.j.a.cock at googlemail.com Mon Feb 27 12:41:15 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Mon, 27 Feb 2012 12:41:15 +0000 Subject: [BioRuby] Failure: test_output_fasta(Bio::FuncTestSequenceOutputEMBL) In-Reply-To: References: Message-ID: On Fri, Nov 25, 2011 at 2:32 PM, Peter Cock wrote: > Hello all, > > There seems to have been a new test failure or regression in Linux 64 Ruby 1.9, > > Revision 48bd150a6180d59879872bd85dd95c7ddf1a19c0 passed, > http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/22/steps/test/logs/stdio > commit 48bd150a6180d59879872bd85dd95c7ddf1a19c0 > Author: Naohisa Goto > Date: ? Tue Nov 22 17:32:23 2011 +0900 > Test bug fix: fixed incomplete Windows platform detection. > https://github.com/bioruby/bioruby/commit/48bd150a6180d59879872bd85dd95c7ddf1a19c0 > > Revision 688779e71a27e861fb01e07f816384561b8cfe45 failed, > http://testing.open-bio.org/bioruby/builders/Linux%2064%20-%20Ruby%201.9/builds/23/steps/test/logs/stdio > commit 688779e71a27e861fb01e07f816384561b8cfe45 > Author: Naohisa Goto > Date: ? Thu Nov 24 11:49:30 2011 +0900 > Rakefile: new tasks: test-all to run all tests, etc. > https://github.com/bioruby/bioruby/commit/688779e71a27e861fb01e07f816384561b8cfe45 > > ?1) Failure: > test_output_fasta(Bio::FuncTestSequenceOutputEMBL) > [/home/buildslave/BuildBot_BioRuby/lin1964/build/test/functional/bio/sequence/test_output_embl.rb:47]: > Exception raised: > <#>. > > I hope that helps and that someone can reproduce the failure locally. > If need be I can try to bisect the failure here. This issue doesn't happen on two other Ruby 1.9.3 machines (under Windows XP 32 bit, and a 32 bit Linux Machine). Can anyone else reproduce this, or might it be a problem specific to my 64 bit Linux machine? Peter From pjotr.public14 at thebird.nl Mon Feb 27 20:22:05 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 27 Feb 2012 21:22:05 +0100 Subject: [BioRuby] GSoC 2012 Message-ID: <20120227202205.GA17212@thebird.nl> We have listed the following GSoC projects at http://www.open-bio.org/wiki/Google_Summer_of_Code - Write the world's fastest parallelized GFF3/GTF parser in D, for Ruby FFI - Extend bio-alignment plug-in with Multiple Alignment Format -MAF- parser (FFI?) - Adding social networking functionality to BioRuby.org - Update bio-images a plugin to represent bio-object with cool images - Update to the Ruby Ensembl API Feel free to comment. The BioRuby panel. From yannick.wurm at unil.ch Tue Feb 28 11:28:32 2012 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Tue, 28 Feb 2012 11:28:32 +0000 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: References: Message-ID: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> On 24 Feb 2012, at 07:59, Raoul Bonnal wrote: > ++1 > > On 23/02/12 19.37, "Yannick Wurm" wrote: >> * making it idiot-proof > This is a key point, user experience is everything. Thanks Raoul. Yes, I think there is still a lot of potential for idiot-proofing (or should one say biologist-proofing??) at all levels between biological stuff and machines (most interfaces of PCR machines, robots, online bio* forms suck *really* *bad*!). Getting ruby/apple/google minimalist philosophies into things can only make the world a better place :) Thats the kind of idea driving our approach with our blast server/wrapper http://www.sequenceserver.com (still a work in progress - e.g. hoping to elminate the necessity of choosing blast algorithms soon - http://goo.gl/nP8u8 ) Have you watched some noobs code? I was surprised to see that some biopython users new to programming don't actually ever execute whole scripts. Instead, they use the python shell... and copy-paste individual lines or blocks of code from their MS Word document. Similarly to the manner in which most run analyses in R. Going line by line & seeing where things screw up definitely reduces the initial hurdle. I wish I had known about 'Bioruby in the shell' when I started... >> * people should be able to test it without having to install >> anything. (I recently tried running the BioRubyOnRails & failed). > *It was developed a long time ago and Ror is great but life time cycle of > each release is very short. Sure I understand. Noob's don't. Thus if it doenst work out of the box as advertised one should make it work or get rid of it. Making it work everywhere is likely quite intense. The best compromise might be to remove the biorubyonrails from the documentation in its current form, and instead set up an online server that people can simply use (without local install). Cheers yannick ps: don't forget to show you use ruby in Mike Barton's http://bioinfsurvey.org/ Yannick Wurm Ants, Genomes & Evolution ? y.wurm at qmul.ac.uk ? skype:yannickwurm ? +44 207 882 3049 5.03A Fogg ? School of Biological & Chemical Sciences ? Queen Mary, University of London ? Mile End Road ? E1 4NX London ? UK From pjotr.public14 at thebird.nl Tue Feb 28 16:43:56 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 28 Feb 2012 17:43:56 +0100 Subject: [BioRuby] BioRuby.org website Message-ID: <20120228164356.GB22204@thebird.nl> In preparation of changing the BioRuby.org website, we are adding feature requests, in the form of cucumber features. See https://github.com/pjotrp/NA-BioRuby.org Feel free to add your own! Example from https://github.com/pjotrp/NA-BioRuby.org/blob/master/features/main-page.feature Feature: BioRuby.org main page The BioRuby project main page is the entry page for new comers to the project. This page should be informative, without information overload. It should invite people to 'jump right in'. Rob Syme made one nice example: http://bioruby.open-bio.org/wiki/Bioruby_site_Re-styling In this feature we describe scenarios for a visiting biologist, bioinformatician, and (non-bio) Ruby coder. Scenario: Visiting biologist Given I visit the main BioRuby.org page When I view the area for Biology Then I should see that Ruby is easy to learn And I should see that BioRuby gives me much functionality When I click the topic Then I should be taken to an area suitable for biologists Scenario: Visiting bioinformatician Given I visit the main BioRuby.org page When I view the area for Bioinformatics Then I should see that Ruby is easy to learn And I should see that BioRuby gives me much functionality And I should see that Ruby offers modularity and agility When I click the topic Then I should be taken to an area suitable for bioinformaticians Scenario: Visiting Ruby coder Given I visit the main BioRuby.org page When I view the area for coders Then I should see that Bioinformatics is exciting And I should see that BioRuby gives me much functionality When I click the topic Then I should be taken to an area suitable for Ruby coders From russell.whitaker at gmail.com Tue Feb 28 16:59:51 2012 From: russell.whitaker at gmail.com (Russell Whitaker) Date: Tue, 28 Feb 2012 08:59:51 -0800 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> References: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> Message-ID: On Tue, Feb 28, 2012 at 3:28 AM, Yannick Wurm wrote: > > Have you watched some noobs code? I was surprised to see that some biopython users > new to programming don't actually ever execute whole scripts. Instead, they use the python shell... > and copy-paste individual lines or blocks of code from their MS Word document. Similarly to the > manner in which most run analyses in R. > Going line by line & seeing where things screw up definitely reduces the initial hurdle. > I wish I had known about 'Bioruby in the shell' when I started... > This isn't only a practice of novices: I've been doing software construction for a couple of decades, and I explore code this way all the time, e.g. inspecting the state of objects in the interactive interpreter shell, determining the specific types of exceptions thrown in corner cases while writing TDD/BDD test cases in parallel, etc. These novices are intuitively using their code exploration tools to understand the mechanics of what they're doing. By the way, I prefer the term "novice" to "noob" or even "newbie": the tone of "noob" - intentionally or not - seems to imply a bit of condescension toward those early in their personal learning curves, and could be considered exclusionary. -- Russell Whitaker http://twitter.com/OrthoNormalRuss / http://orthonormalruss.blogspot.com/ http://www.linkedin.com/pub/russell-whitaker/0/b86/329 From yannick.wurm at unil.ch Tue Feb 28 22:43:16 2012 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Tue, 28 Feb 2012 22:43:16 +0000 Subject: [BioRuby] BioRuby Digest, Vol 77, Issue 20 In-Reply-To: References: <42A3A21A-A061-4ABF-B72B-311CDDBEDB73@unil.ch> Message-ID: On 28 Feb 2012, at 16:59, Russell Whitaker wrote: > By the way, I prefer the term "novice" to "noob" or even "newbie": the > tone of "noob" - intentionally or not - seems to imply a bit of condescension toward > those early in their personal learning curves, and could be considered exclusionary. Sorry, you're right. I was just trying to be young by forgetting that nobody said "noob" back when I was one :p From pjotr.public14 at thebird.nl Wed Feb 29 08:30:39 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 09:30:39 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120228164356.GB22204@thebird.nl> References: <20120228164356.GB22204@thebird.nl> Message-ID: <20120229083039.GA26459@thebird.nl> Feature: BioRuby.org main page beautiful code BioRuby is about beautiful code. The BioRuby main page should show rotating examples of beautiful code. Initially this will be static, eventually people can run it in a sand box. The example should come with a short description, which can be expanded on in separate pages. Scenario: Each page visit shows a new example of beautiful code Given I visit the main BioRuby.org page When I view the area which shows beautiful code Then I should see that Ruby is for beauty And I should see that BioRuby gives me much functionality Scenario: Under the example we display an explanation Given I see the beautiful code box Then I should see an explanation Scenario: Display a More info link Given I see the beautiful code box When I view the area which shows beautiful code Then I should see a 'More info' link And it takes me to the relevant page Scenario: Display a RUN button Given I see the beautiful code box When I view the area which shows beautiful code Then I should see a RUN button And it should execute the code Scenario: Display an EDIT button Given I see the beautiful code box When I view the area which shows beautiful code Then I should see an EDIT button And it should allow editing the code https://github.com/pjotrp/NA-BioRuby.org/blob/master/features/main-page-beautiful-code.feature From pjotr.public14 at thebird.nl Wed Feb 29 09:02:33 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 10:02:33 +0100 Subject: [BioRuby] BioRuby.org website Message-ID: <20120229090233.GB27695@thebird.nl> Feature: BioRuby.org main page direct answer section The BioRuby project main page is the entry page for new comers to the project. Visitors who are not (yet) on IRC or the mailing list, should be encouraged to post questions and receive immediate answers. One way to achieve this would be a Jabber connection to a 'room' where BioRuby members connect. Similar to IRC, but available directly from the main page. This chat will not be logged, so spammers will have no benefit. Scenario: BioRuby.org newbie visitor with a question Given I visit the main BioRuby.org page and someone is online When I click the button for contacting BioRuby And someone is online Then I should be able to post a question And get an answer Scenario: BioRuby.org newbie visitor with a question (2) Given I visit the main BioRuby.org page and no one is online When I click the button for contacting BioRuby And no one is online Then I should be able to post a question with an E-mail address And get an answer over E-mail https://github.com/pjotrp/NA-BioRuby.org/blob/master/features/main-page-direct-answers.feature From p.j.a.cock at googlemail.com Wed Feb 29 10:12:51 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 29 Feb 2012 10:12:51 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120229090233.GB27695@thebird.nl> References: <20120229090233.GB27695@thebird.nl> Message-ID: On Wed, Feb 29, 2012 at 9:02 AM, Pjotr Prins wrote: > Feature: BioRuby.org main page direct answer section > > ?The BioRuby project main page is the entry page for new comers to > ?the project. Visitors who are not (yet) on IRC or the mailing list, > ?should be encouraged to post questions and receive immediate > ?answers. One way to achieve this would be a Jabber connection to a > ?'room' where BioRuby members connect. Similar to IRC, but available > ?directly from the main page. This chat will not be logged, so > ?spammers will have no benefit. > > ?Scenario: BioRuby.org newbie visitor with a question > ? ?Given I visit the main BioRuby.org page and someone is online > ? ?When I click the button for contacting BioRuby > ? ?And someone is online > ? ?Then I should be able to post a question > ? ?And get an answer Could you embed an IRC client into the browser page? > ?Scenario: BioRuby.org newbie visitor with a question (2) > ? ?Given I visit the main BioRuby.org page and no one is online > ? ?When I click the button for contacting BioRuby > ? ?And no one is online > ? ?Then I should be able to post a question with an E-mail address > ? ?And get an answer over E-mail You don't think giving them instructions on how to join the mailing list is good enough? How would you implement that email form idea - keeping in mind the newcomer would reasonably expect their query to be 'private' and not be sent to the public mailing list on their behalf? Peter From pjotr.public14 at thebird.nl Wed Feb 29 14:54:43 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 15:54:43 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: References: <20120229090233.GB27695@thebird.nl> Message-ID: <20120229145443.GA28775@thebird.nl> On Wed, Feb 29, 2012 at 10:12:51AM +0000, Peter Cock wrote: > On Wed, Feb 29, 2012 at 9:02 AM, Pjotr Prins wrote: > > Feature: BioRuby.org main page direct answer section > > > > ?The BioRuby project main page is the entry page for new comers to > > ?the project. Visitors who are not (yet) on IRC or the mailing list, > > ?should be encouraged to post questions and receive immediate > > ?answers. One way to achieve this would be a Jabber connection to a > > ?'room' where BioRuby members connect. Similar to IRC, but available > > ?directly from the main page. This chat will not be logged, so > > ?spammers will have no benefit. > > > > ?Scenario: BioRuby.org newbie visitor with a question > > ? ?Given I visit the main BioRuby.org page and someone is online > > ? ?When I click the button for contacting BioRuby > > ? ?And someone is online > > ? ?Then I should be able to post a question > > ? ?And get an answer > > Could you embed an IRC client into the browser page? I suppose so. One problem is that our IRC gets logged. > > ?Scenario: BioRuby.org newbie visitor with a question (2) > > ? ?Given I visit the main BioRuby.org page and no one is online > > ? ?When I click the button for contacting BioRuby > > ? ?And no one is online > > ? ?Then I should be able to post a question with an E-mail address > > ? ?And get an answer over E-mail > > You don't think giving them instructions on how to join the mailing > list is good enough? How would you implement that email form > idea - keeping in mind the newcomer would reasonably expect > their query to be 'private' and not be sent to the public mailing > list on their behalf? Exactly. We will have a limited number of people who receive these. Privacy is key (I did not mention that), so people feel free to ask any question, and a low threshold. Glad someone is reading my stuff ;) Pj. From p.j.a.cock at googlemail.com Wed Feb 29 15:29:14 2012 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Wed, 29 Feb 2012 15:29:14 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120229145443.GA28775@thebird.nl> References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> Message-ID: Pjotr wrote: >Peter wrote: >> Pjotr wrote: >> > ?Scenario: BioRuby.org newbie visitor with a question (2) >> > ? ?Given I visit the main BioRuby.org page and no one is online >> > ? ?When I click the button for contacting BioRuby >> > ? ?And no one is online >> > ? ?Then I should be able to post a question with an E-mail address >> > ? ?And get an answer over E-mail >> >> You don't think giving them instructions on how to join the mailing >> list is good enough? How would you implement that email form >> idea - keeping in mind the newcomer would reasonably expect >> their query to be 'private' and not be sent to the public mailing >> list on their behalf? > > Exactly. We will have a limited number of people who receive these. > > Privacy is key (I did not mention that), so people feel free to ask > any question, and a low threshold. > > Glad someone is reading my stuff ;) > > Pj. I can see why being able to ask questions "in private" might lower the barrier to entry, but you will need a dedicated (in the sense of committed) and patient team to handle those queries. Personally my preference is to encourage people to ask their questions on the mailing list in public (they can use a semi- anonymous email address if they like, assuming it doesn't get flagged as spam - I used to myself once). This means the entire development team and all the other users would see the question and might help, but also the fact that it is open means the question will be searchable by Google etc, and can spark useful discussions. Sites like http://biostar.stackexchange.com/ work in a similar open way but are more question & answer focused. Based on the tag usage this isn't yet very popular with BioRuby folk: http://biostar.stackexchange.com/questions/tagged/bioruby Do you feel that for many people the potential embarrassment of asking a 'silly question' puts people off asking 'in public'? Peter From pjotr.public14 at thebird.nl Wed Feb 29 15:33:54 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 16:33:54 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> Message-ID: <20120229153354.GA29186@thebird.nl> On Wed, Feb 29, 2012 at 03:29:14PM +0000, Peter Cock wrote: > I can see why being able to ask questions "in private" might > lower the barrier to entry, but you will need a dedicated (in the > sense of committed) and patient team to handle those queries. Yes. That is one of the intended tasks for the BioRuby panel. We already are more present on IRC. > Personally my preference is to encourage people to ask their > questions on the mailing list in public (they can use a semi- > anonymous email address if they like, assuming it doesn't > get flagged as spam - I used to myself once). This means > the entire development team and all the other users would > see the question and might help, but also the fact that it is > open means the question will be searchable by Google etc, > and can spark useful discussions. > > Sites like http://biostar.stackexchange.com/ work in a similar > open way but are more question & answer focused. Based > on the tag usage this isn't yet very popular with BioRuby folk: > http://biostar.stackexchange.com/questions/tagged/bioruby > > Do you feel that for many people the potential embarrassment > of asking a 'silly question' puts people off asking 'in public'? All these channels are very useful. And used by many. I simply want new comers to come in, and ask 'Why is Ruby preferred over, say, Perl?' - rather than have them dig around, so we can offer them an opiniated reply ;). Question from my end: Why not try? I am very much in favour of experiments. It is my nature. Pj. From cjfields at illinois.edu Wed Feb 29 16:13:55 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 29 Feb 2012 16:13:55 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> Message-ID: <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> On Feb 29, 2012, at 9:29 AM, Peter Cock wrote: > Pjotr wrote: >> Peter wrote: >>> Pjotr wrote: >>>> Scenario: BioRuby.org newbie visitor with a question (2) >>>> Given I visit the main BioRuby.org page and no one is online >>>> When I click the button for contacting BioRuby >>>> And no one is online >>>> Then I should be able to post a question with an E-mail address >>>> And get an answer over E-mail >>> >>> You don't think giving them instructions on how to join the mailing >>> list is good enough? How would you implement that email form >>> idea - keeping in mind the newcomer would reasonably expect >>> their query to be 'private' and not be sent to the public mailing >>> list on their behalf? >> >> Exactly. We will have a limited number of people who receive these. >> >> Privacy is key (I did not mention that), so people feel free to ask >> any question, and a low threshold. >> >> Glad someone is reading my stuff ;) >> >> Pj. > > I can see why being able to ask questions "in private" might > lower the barrier to entry, but you will need a dedicated (in the > sense of committed) and patient team to handle those queries. > > Personally my preference is to encourage people to ask their > questions on the mailing list in public (they can use a semi- > anonymous email address if they like, assuming it doesn't > get flagged as spam - I used to myself once). This means > the entire development team and all the other users would > see the question and might help, but also the fact that it is > open means the question will be searchable by Google etc, > and can spark useful discussions. > > Sites like http://biostar.stackexchange.com/ work in a similar > open way but are more question & answer focused. Based > on the tag usage this isn't yet very popular with BioRuby folk: > http://biostar.stackexchange.com/questions/tagged/bioruby The BioPerl folks don't monitor it much either. We should be promoting it more. > Do you feel that for many people the potential embarrassment > of asking a 'silly question' puts people off asking 'in public'? > > Peter Peter, I think you hit the nail on the head; allowing people to contact you (or other devs) privately means there is no cross-benefit to others. It makes more sense to promote the avenues already present (biostar, mail list, web site, IRC, etc) and encourage users to both search for answers and submit questions there. As an example, even though I currently oversee bioperl I certainly didn't write all the code (and I certainly don't want that distinction :). I always redirect users to the mail list, to the point I may actually cc the list in my response. The community benefits. All bioperl code specifically mentions who wrote and maintains the code, where to send questions, etc, and it's very possible the actual author (very likely not me) will respond if the question is asked where it is promoted to be asked. Asking me directly will not benefit anyone beyond having me redirect the question to an actual useful forum. Re: 'experimenting with this': that's a possibility, but then you run the risk of opening avenues for users that might be shut down later. chris From pjotr.public14 at thebird.nl Wed Feb 29 17:20:26 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 29 Feb 2012 18:20:26 +0100 Subject: [BioRuby] BioRuby.org website In-Reply-To: <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> Message-ID: <20120229172026.GA29664@thebird.nl> On Wed, Feb 29, 2012 at 04:13:55PM +0000, Fields, Christopher J wrote: > Re: 'experimenting with this': that's a possibility, but then you > run the risk of opening avenues for users that might be shut down > later. I don't see why everyone is overreacting. I am not proposing this as an alternative channel to the others you mention. It is just to provide direct access to the BioRuby authors. Very much like providing a phone or Skype number. Our normal response to a regular question would be to point users to IRC, the ML, stackexchange, whatever. Lowering all barriers to entry, without it costing too much, is our goal. If it turns out we get hammered with bad questions, or get irritated, or it does not work, we just shut it down. If it works and we get more people on IRC and our ML, everyone gains. Note btw that I am proposing this functionality, and others, will be made available to other Bio* projects. Pj. From cjfields at illinois.edu Wed Feb 29 18:02:09 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 29 Feb 2012 18:02:09 +0000 Subject: [BioRuby] BioRuby.org website In-Reply-To: <20120229172026.GA29664@thebird.nl> References: <20120229090233.GB27695@thebird.nl> <20120229145443.GA28775@thebird.nl> <098C48D9-F855-4E5A-B978-FE9B690B785D@illinois.edu> <20120229172026.GA29664@thebird.nl> Message-ID: <5ECDDDAF-98B7-453D-8928-F5C0E1A49377@illinois.edu> On Feb 29, 2012, at 11:20 AM, Pjotr Prins wrote: > On Wed, Feb 29, 2012 at 04:13:55PM +0000, Fields, Christopher J wrote: >> Re: 'experimenting with this': that's a possibility, but then you >> run the risk of opening avenues for users that might be shut down >> later. > > I don't see why everyone is overreacting. I am not proposing this as > an alternative channel to the others you mention. It is just to > provide direct access to the BioRuby authors. Very much like providing > a phone or Skype number. Our normal response to a regular question > would be to point users to IRC, the ML, stackexchange, whatever. > > Lowering all barriers to entry, without it costing too much, is our > goal. If it turns out we get hammered with bad questions, or get > irritated, or it does not work, we just shut it down. If it works and > we get more people on IRC and our ML, everyone gains. > > Note btw that I am proposing this functionality, and others, will be > made available to other Bio* projects. > > Pj. That's fine, I'm not saying "don't do it", just that (based on experience) users can feel a little burned when something they expect to work no longer does, and that spending time on this vs. coding is a tricky balance. If enough devs in the community can chip in and keep it up, more power to you. chris