From pjotr.public14 at thebird.nl Sun Mar 3 09:47:29 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 3 Mar 2013 15:47:29 +0100 Subject: [BioRuby] GSoC 2013 is ON Message-ID: <20130303144729.GE6566@thebird.nl> Game on! GSoC 2013 is ON. I am running with the OBF project administration this year for the Google Summer of code (GSoC). First and foremost I want to thank Robert Buels and others for making OBF/GSoC a success in the previous three years! This year, Robert, Chris Fields and Hilmar Lapp will act as backup administrators. The deadline for the OBF application for GSoC2013 as a mentoring organisation is Friday March 29! See http://www.google-melange.com/gsoc/events/google/gsoc2013 Similar to previous years, each Bio* project needs to update and add project ideas on the project's individual OBF wiki page and create links from the main OBF page at http://www.open-bio.org/wiki/Google_Summer_of_Code (we will update the main information on that page soon). So, for each of the OBF projects that wants to do GSoC again this year: 1. 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. For an example see http://bioruby.open-bio.org/wiki/Google_Summer_of_Code 2. Update the final list of project ideas on the main OBF GSoC page to match. http://www.open-bio.org/wiki/Google_Summer_of_Code 3. Register with gsoc at lists.open-bio.org 4. Announce it on that list when you are ready :) Anyone can submit a project idea! Former GSoC students are especially encouraged to contribute ideas to the mailing lists. Please have the updates done by Friday March 22nd. The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organisation again this year, so let's come up with some good ones! Pj. (Pjotr Prins) Important dates: * March 22nd: Finalise project ideas * March 29th: Deadline OBF mentoring organisation submission to Google http://www.open-bio.org/wiki/Google_Summer_of_Code From pjotr.public14 at thebird.nl Tue Mar 5 12:21:23 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 5 Mar 2013 18:21:23 +0100 Subject: [BioRuby] GSoC2013 Message-ID: <20130305172123.GA20241@thebird.nl> Hi everyone, It has been quiet the last months. Everyone must be busy. Meanwhile the biogems.info site shows that development continues :) We are starting to get ready to put up ideas for the Google Summer of Code. Do you have any coding that you want to be done under GSoC? Even if you don't want to be a primary mentor, we encourage floating ideas! Last year we had two D projects binding to Ruby. I would not mind doing the same with other languages. In particular binding languages on the JVM against JRuby would be interesting. One crazy idea I have is to bind Javascript/Coffescript against BioRuby on the JVM. But maybe that is a bit rich. Please post ideas here. Who needs work done? Pj. From pjotr.public14 at thebird.nl Thu Mar 7 07:08:50 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 7 Mar 2013 13:08:50 +0100 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <20130303144729.GE6566@thebird.nl> References: <20130303144729.GE6566@thebird.nl> Message-ID: <20130307120850.GA29190@thebird.nl> Note that proposals for GSoC can be for any Biogem work! Come on guys, you are not telling me that there are no ideas for student projects. A student will work almost 4 months for you. Writing a 2-paragraph proposal is easy! http://bioruby.open-bio.org/wiki/Google_Summer_of_Code How about an RDF backend for BioRuby? On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote: > Game on! GSoC 2013 is ON. I am running with the OBF project > administration this year for the Google Summer of code (GSoC). From joachim.baran at gmail.com Thu Mar 7 07:18:38 2013 From: joachim.baran at gmail.com (Joachim Baran) Date: Thu, 7 Mar 2013 07:18:38 -0500 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <20130307120850.GA29190@thebird.nl> References: <20130303144729.GE6566@thebird.nl> <20130307120850.GA29190@thebird.nl> Message-ID: <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> On 2013-03-07, at 7:08 AM, Pjotr Prins wrote: > Note that proposals for GSoC can be for any Biogem work! I would like to be able to discover biogems more easily. Having said that, I would like to be able to discover them at all! :P Right now, you either know what you are looking for, or, you probe the biogems.info listing. Wouldn't it be great if gems were categorized, searchable, and smartly linked together (as in: "related gems")? And it would be mega cool if BioRuby had a command line tool that could work together with such a new biogems.info feature. My two cents... Joachim From iainspeed at gmail.com Thu Mar 7 07:28:16 2013 From: iainspeed at gmail.com (Iain Barnett) Date: Thu, 7 Mar 2013 12:28:16 +0000 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> References: <20130303144729.GE6566@thebird.nl> <20130307120850.GA29190@thebird.nl> <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> Message-ID: <4DFF4C2D-6539-4EE4-B1F9-9A606A8CDCF5@gmail.com> I'd suggest contacting Ruby Toolbox and getting them to add a category. No point duplicating work that's already been done. https://www.ruby-toolbox.com/categories/by_name Regards, Iain On 7 Mar 2013, at 12:18, Joachim Baran wrote: > > On 2013-03-07, at 7:08 AM, Pjotr Prins wrote: >> Note that proposals for GSoC can be for any Biogem work! > I would like to be able to discover biogems more easily. Having said that, I would like to be able to discover them at all! :P > > Right now, you either know what you are looking for, or, you probe the biogems.info listing. > > Wouldn't it be great if gems were categorized, searchable, and smartly linked together (as in: "related gems")? > > And it would be mega cool if BioRuby had a command line tool that could work together with such a new biogems.info feature. > > My two cents... > Joachim > > > _______________________________________________ > 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 Mar 7 07:44:57 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 7 Mar 2013 13:44:57 +0100 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <4DFF4C2D-6539-4EE4-B1F9-9A606A8CDCF5@gmail.com> References: <20130303144729.GE6566@thebird.nl> <20130307120850.GA29190@thebird.nl> <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> <4DFF4C2D-6539-4EE4-B1F9-9A606A8CDCF5@gmail.com> Message-ID: <20130307124457.GA29323@thebird.nl> A 'bioinformatics' category would be good, indeed. Still I agree with Joachim that we can link that with the biogems.info website, and expand on that functionality. I was also thinking of tracking all OBF/GSoC projects on biogems.info this year. So all mentors can see activity in one page, as well as the BLOG entries. But that is not a student project ;) Pj. On Thu, Mar 07, 2013 at 12:28:16PM +0000, Iain Barnett wrote: > I'd suggest contacting Ruby Toolbox and getting them to add a category. No point duplicating work that's already been done. > > https://www.ruby-toolbox.com/categories/by_name > > Regards, > Iain > > On 7 Mar 2013, at 12:18, Joachim Baran wrote: > > > > > On 2013-03-07, at 7:08 AM, Pjotr Prins wrote: > >> Note that proposals for GSoC can be for any Biogem work! > > I would like to be able to discover biogems more easily. Having said that, I would like to be able to discover them at all! :P > > > > Right now, you either know what you are looking for, or, you probe the biogems.info listing. > > > > Wouldn't it be great if gems were categorized, searchable, and smartly linked together (as in: "related gems")? > > > > And it would be mega cool if BioRuby had a command line tool that could work together with such a new biogems.info feature. > > > > My two cents... > > Joachim > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > From dthorneycroft at gmail.com Thu Mar 7 14:30:42 2013 From: dthorneycroft at gmail.com (dave thorneycroft) Date: Thu, 7 Mar 2013 19:30:42 +0000 Subject: [BioRuby] Can I get more information on BioRuby Message-ID: Hello, I am a novice Ruby programmer, ex-biologist and experienced developer in other languages (sorry Adobe Flex), but I have seen the light and I want to contribute to BioRuby. I am looking through the BioRuby source code and find somethings confusing (of course I'm a novice !). Could anyone point me in the direction of any tutorials which wil help me get a better understanding of the code, I've seen the stuff on BioRuby.org. Anything that would explain but how its structured and coded not how to use it to solve a problem. A couple of things are really puzzling me right now. Number one, please don't laugh , where is the NCBIDB class located in the source (I see the GenBank class inherits NCBIDB ; but I cannot find the class source ?). NCBIDB is a class right ? Number two, could anyone explain how the Bio::FlatFile 'automagically' recognizes each database class? Any pointers would be great. Many thanks for your time, I really appreciate any comments. Regards Dave From rob.syme at gmail.com Fri Mar 8 00:11:42 2013 From: rob.syme at gmail.com (Rob Syme) Date: Fri, 8 Mar 2013 13:11:42 +0800 Subject: [BioRuby] Can I get more information on BioRuby In-Reply-To: References: Message-ID: Hi Dave Don't worry, these are appropriate questions for someone new to bioruby. Good on you for digging through the source code. The NCBIDB class is located at lib/bio/db.rb . Be sure to have a look at the top of the file for a great overview of how the database classes are constructed, written by ktym . To track down the method of autodetection, have a close look at the lib/bio/io/flatfile.rb and lib/bio/io/flatfile/autodetection.rb . *Step 1) Check to see if a dbclass has been provided* If no database class is provided to Bio::FlatFile.open, it falls through to _open_file(dbclass, filename, *arg), where dbclass is nil, which then creates a new Bio::FlatFile instance with the first argument (dbclass) as nil. If you look at the FlatFile initialize method, you'll see that the autodetect method is calledif dbclass is nil. Inside the autodetect method, a new Autodetect object is created which does the work you are interested in. Note that the class method "default" is called, which returns an Autodetect object, but does a lot of setting up first . *Step 2) Set up the default FlatFile::Autodetect object* The setup is mainly concerned with adding a large number of RuleTemplate instances to the @elements array. Each detectable format type has it's own RuleTemplate. The RuleTemplates provide three key pieces of information: - a name - a list of rules that are less important(checked later) that the current rule - a guess method, which, when given a string, returns a dbclass if the string looks like it belongs to that particular rule. There are different types of RuleTemplates. The simplest is a RegRegexp, which has a very simple guess method, which simply matches the given string given to a regular expression . The RuleTemplates also need a list of rules that are less important so that the final array of rules can be topologically sorted, returning a list rules with the most important at the top. There is a large array created in Autodetect.make_default which contains a bunch of rules that are added to the @elements array (to be tsorted later). *Step 3) Go through the first 31 lines, and match against each of the RuleTemplates* Way back in the FlatFile#autodetect method, a dbclass is pulled out of the FlatFile::Autodetect#autodetect_flatfile method . The FlatFile's BufferedInputSteam that was created earlier is pulled out so that the Autodetect object can peek inside. It then iterates over the first 31 lines of the file, taking each line and trying it out against each rule. If the guess returns non-nil (it will be a dbclass), that dbclass bubbles all the way back up to the autodetect method in FlatFile . I hope that's right - I've not contributed any code here. I might be way off. It does raise the question "How do I get a new dbclass to be recognised by FlatFile.open?" I'm not really sure, but I'm confident there will be someone here who does know. Any takers? -r * * On Fri, Mar 8, 2013 at 3:30 AM, dave thorneycroft wrote: > Hello, > > I am a novice Ruby programmer, ex-biologist and experienced developer in > other languages (sorry Adobe Flex), but I have seen the light and I want > to contribute to BioRuby. I am looking through the BioRuby source code and > find somethings confusing (of course I'm a novice !). Could anyone point > me in the direction of any tutorials which wil help me get a better > understanding of the code, I've seen the stuff on BioRuby.org. Anything > that would explain but how its structured and coded not how to use it to > solve a problem. > > A couple of things are really puzzling me right now. > > Number one, please don't laugh , where is the NCBIDB class located in the > source (I see the GenBank class inherits NCBIDB ; but I cannot find the > class source ?). NCBIDB is a class right ? > Number two, could anyone explain how the Bio::FlatFile 'automagically' > recognizes each database class? > > Any pointers would be great. Many thanks for your time, I really > appreciate any comments. > > Regards > Dave > _______________________________________________ > 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 Mar 11 05:26:56 2013 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 11 Mar 2013 10:26:56 +0100 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <20130303144729.GE6566@thebird.nl> References: <20130303144729.GE6566@thebird.nl> Message-ID: <1FD33CEA-1F51-4CBD-8D1D-DE11312255B9@ingm.org> I'm alive :-D we'll start thinking something picking up idea from our daily work. On Mar 3, 2013, at 3:47 PM, Pjotr Prins wrote: > Game on! GSoC 2013 is ON. I am running with the OBF project > administration this year for the Google Summer of code (GSoC). > First and foremost I want to thank Robert Buels and others for making > OBF/GSoC a success in the previous three years! This year, Robert, Chris > Fields and Hilmar Lapp will act as backup administrators. > > The deadline for the OBF application for GSoC2013 as a mentoring > organisation is Friday March 29! See > > http://www.google-melange.com/gsoc/events/google/gsoc2013 > > Similar to previous years, each Bio* project needs to update and add project > ideas on the project's individual OBF wiki page and create links from the main > OBF page at > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > (we will update the main information on that page soon). > > So, for each of the OBF projects that wants to do GSoC again this > year: > > 1. 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. For an example see > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code > > 2. Update the final list of project ideas on the main OBF GSoC page > to match. > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > 3. Register with gsoc at lists.open-bio.org > > 4. Announce it on that list when you are ready :) > > Anyone can submit a project idea! Former GSoC students are especially > encouraged to contribute ideas to the mailing lists. > > Please have the updates done by Friday March 22nd. The number and quality of > the project ideas are part of the evaluation process for whether OBF is > accepted as a Summer of Code organisation again this year, so let's come up > with some good ones! > > Pj. (Pjotr Prins) > > Important dates: > > * March 22nd: Finalise project ideas > * March 29th: Deadline OBF mentoring organisation submission to Google > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > > _______________________________________________ > 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 Mar 11 17:49:19 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 11 Mar 2013 22:49:19 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 Message-ID: <20130311214919.GA17212@thebird.nl> I was wondering if anyone is interested in a Ruby/Python/Perl browser graphics/animation generator with D3 Javascript output? The idea is to take existing figures for biological results and working them on to the web with some level of clickable interaction. If you have existing graphics in gnuplot or R, they could be candidates. It could be a GSoC project. Pj. From john.woods at marcottelab.org Mon Mar 11 18:20:07 2013 From: john.woods at marcottelab.org (John Woods) Date: Mon, 11 Mar 2013 17:20:07 -0500 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: <20130311214919.GA17212@thebird.nl> References: <20130311214919.GA17212@thebird.nl> Message-ID: There's been some talk about this on the SciRuby list. We have Rubyvis, but some people are interested in doing something D3-based. On Mon, Mar 11, 2013 at 4:49 PM, Pjotr Prins wrote: > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 mail at michaelbarton.me.uk Mon Mar 11 18:45:01 2013 From: mail at michaelbarton.me.uk (Michael Barton) Date: Mon, 11 Mar 2013 18:45:01 -0400 Subject: [BioRuby] Rails for genomics Message-ID: I'm still actively developing genomer and just pushed out a new version this morning thanks to some user feedback. I've also been updating the website with more videos on how to finish a genome too. Genomer is entirely written in Ruby and I wondered if adding more features to genomer, perhaps in response to the recent assemblathon 2 paper, would be of interest to the BioRuby community as a GSoC project. The website is here - http://next.gs/ From georgkam at gmail.com Tue Mar 12 01:36:40 2013 From: georgkam at gmail.com (George Githinji) Date: Tue, 12 Mar 2013 08:36:40 +0300 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: <20130311214919.GA17212@thebird.nl> References: <20130311214919.GA17212@thebird.nl> Message-ID: Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and https://github.com/chmille4/Scribl. On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins wrote: > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 -- --------------- Sincerely George Skype: george_g2 Blog: http://www.biorelated.com/ Twitter: http://twitter.com/#!/george_l From rob.syme at gmail.com Tue Mar 12 01:57:30 2013 From: rob.syme at gmail.com (Rob Syme) Date: Tue, 12 Mar 2013 13:57:30 +0800 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: @George, the canvas rendering would probably make certain types of animation more difficult than an svg/d3 plot. Then again, canvas rendering gives you enormous flexibility. I quite like genometools (no affiliation or collaboration), perhaps we could just piggy-back on the svg generated by their annotationsketch module? The ruby/python/lua/C APIs already exists (and are quite good). It just depends on how broad the project becomes. There are certainly be many classes plots that wouldn't be possible using only this approach. At the very least, we could take design notes from these guys. To my eyes, it has a great clean aesthetic. -r On Tue, Mar 12, 2013 at 1:36 PM, George Githinji wrote: > Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and > https://github.com/chmille4/Scribl. > > On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins > wrote: > > I was wondering if anyone is interested in a Ruby/Python/Perl browser > > graphics/animation generator with D3 Javascript output? The idea is to > > take existing figures for biological results and working them on to > > the web with some level of clickable interaction. > > > > If you have existing graphics in gnuplot or R, they could be > > candidates. > > > > It could be a GSoC 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 > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://www.biorelated.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 georgkam at gmail.com Tue Mar 12 02:14:14 2013 From: georgkam at gmail.com (George Githinji) Date: Tue, 12 Mar 2013 09:14:14 +0300 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: @rob d3 would probably be a better fit for complicated plots. (graph layouts,circos plots, hive-plots?) But I would be happy to see something that integrates easily with jQuery or uses a similar approach to render the graphics or could be easily extended with plugins. I also remembered that once upon a time we had bio::graphics http://bio-graphics.rubyforge.org written largely by Jan. The big challenge for this was the heavy dependency on - cairo (cairographics.org), to do the actual drawing. - pango (www.pango.org), to do the high level text drawing. and it was also a little trick it make it work on Windows. It also has not been updated for years. On Tue, Mar 12, 2013 at 8:57 AM, Rob Syme wrote: > @George, the canvas rendering would probably make certain types of animation > more difficult than an svg/d3 plot. Then again, canvas rendering gives you > enormous flexibility. > > I quite like genometools (no affiliation or collaboration), perhaps we could > just piggy-back on the svg generated by their annotationsketch module? The > ruby/python/lua/C APIs already exists (and are quite good). It just depends > on how broad the project becomes. There are certainly be many classes plots > that wouldn't be possible using only this approach. > > At the very least, we could take design notes from these guys. To my eyes, > it has a great clean aesthetic. > > -r > > > On Tue, Mar 12, 2013 at 1:36 PM, George Githinji wrote: >> >> Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and >> https://github.com/chmille4/Scribl. >> >> On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins >> wrote: >> > I was wondering if anyone is interested in a Ruby/Python/Perl browser >> > graphics/animation generator with D3 Javascript output? The idea is to >> > take existing figures for biological results and working them on to >> > the web with some level of clickable interaction. >> > >> > If you have existing graphics in gnuplot or R, they could be >> > candidates. >> > >> > It could be a GSoC 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 >> >> >> >> -- >> --------------- >> Sincerely >> George >> Skype: george_g2 >> Blog: http://www.biorelated.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 > > -- --------------- Sincerely George Skype: george_g2 Blog: http://www.biorelated.com/ Twitter: http://twitter.com/#!/george_l From matteo.picciolini at gmail.com Tue Mar 12 05:23:55 2013 From: matteo.picciolini at gmail.com (Matteo Picciolini) Date: Tue, 12 Mar 2013 10:23:55 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: Hi , i think that a biogem D3 generetor is a good project to start . I'm using D3 for transcripts annotation rendering and the result is really nice . 2013/3/12 George Githinji > @rob d3 would probably be a better fit for complicated plots. (graph > layouts,circos plots, hive-plots?) But I would be happy to see > something that integrates easily with jQuery or uses a similar > approach to render the graphics or could be easily extended with > plugins. > > I also remembered that once upon a time we had bio::graphics > http://bio-graphics.rubyforge.org written largely by Jan. > > The big challenge for this was the heavy dependency on > - cairo (cairographics.org), to do the actual drawing. > - pango (www.pango.org), to do the high level text drawing. > and it was also a little trick it make it work on Windows. > > It also has not been updated for years. > > On Tue, Mar 12, 2013 at 8:57 AM, Rob Syme wrote: > > @George, the canvas rendering would probably make certain types of > animation > > more difficult than an svg/d3 plot. Then again, canvas rendering gives > you > > enormous flexibility. > > > > I quite like genometools (no affiliation or collaboration), perhaps we > could > > just piggy-back on the svg generated by their annotationsketch module? > The > > ruby/python/lua/C APIs already exists (and are quite good). It just > depends > > on how broad the project becomes. There are certainly be many classes > plots > > that wouldn't be possible using only this approach. > > > > At the very least, we could take design notes from these guys. To my > eyes, > > it has a great clean aesthetic. > > > > -r > > > > > > On Tue, Mar 12, 2013 at 1:36 PM, George Githinji > wrote: > >> > >> Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and > >> https://github.com/chmille4/Scribl. > >> > >> On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins < > pjotr.public14 at thebird.nl> > >> wrote: > >> > I was wondering if anyone is interested in a Ruby/Python/Perl browser > >> > graphics/animation generator with D3 Javascript output? The idea is to > >> > take existing figures for biological results and working them on to > >> > the web with some level of clickable interaction. > >> > > >> > If you have existing graphics in gnuplot or R, they could be > >> > candidates. > >> > > >> > It could be a GSoC 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 > >> > >> > >> > >> -- > >> --------------- > >> Sincerely > >> George > >> Skype: george_g2 > >> Blog: http://www.biorelated.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 > > > > > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://www.biorelated.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 Tue Mar 12 07:51:18 2013 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 12 Mar 2013 12:51:18 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: <20130311214919.GA17212@thebird.nl> References: <20130311214919.GA17212@thebird.nl> Message-ID: I had a student working on that some months ago, you can find the github repo here: the idea was to convert rubyvis to D3 https://github.com/dafian/RubyD3 On Mar 11, 2013, at 10:49 PM, Pjotr Prins wrote: > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 pjotr.public14 at thebird.nl Wed Mar 13 17:28:20 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 13 Mar 2013 22:28:20 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: <20130313212820.GA26350@thebird.nl> I have added a project proposal: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Create_a_D3_based_graphics_package_for_Bioinformatics Who wants to mentor? I know one co-mentor who is very interested. Pj. On Tue, Mar 12, 2013 at 12:51:18PM +0100, Raoul Bonnal wrote: > I had a student working on that some months ago, > you can find the github repo here: > the idea was to convert rubyvis to D3 > > > https://github.com/dafian/RubyD3 > > > On Mar 11, 2013, at 10:49 PM, Pjotr Prins wrote: > > > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 pjotr.public14 at thebird.nl Wed Mar 13 17:29:44 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 13 Mar 2013 22:29:44 +0100 Subject: [BioRuby] Another proposal Message-ID: <20130313212944.GB26350@thebird.nl> To build up on biogems.info functionality: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Create_a_dynamic_and_social_web_portal_for_Bioinformatics_packages Motto: if you are not on the web you don't exist (thanks Marjan!) Pj. From bonnal at ingm.org Fri Mar 22 10:04:18 2013 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 22 Mar 2013 15:04:18 +0100 Subject: [BioRuby] Another proposal In-Reply-To: <20130313212944.GB26350@thebird.nl> References: <20130313212944.GB26350@thebird.nl> Message-ID: <7073CAAE-0D16-4728-9A97-AB20A7F2D279@ingm.org> Another proposal http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Machine_Learning_.26_Data_Mining_Algorithms_for_Ruby On Mar 13, 2013, at 10:29 PM, Pjotr Prins wrote: > To build up on biogems.info functionality: > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Create_a_dynamic_and_social_web_portal_for_Bioinformatics_packages > > Motto: if you are not on the web you don't exist (thanks Marjan!) > > 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 pjotr.public14 at thebird.nl Sun Mar 24 03:52:07 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 24 Mar 2013 08:52:07 +0100 Subject: [BioRuby] Another proposal In-Reply-To: <7073CAAE-0D16-4728-9A97-AB20A7F2D279@ingm.org> References: <20130313212944.GB26350@thebird.nl> <7073CAAE-0D16-4728-9A97-AB20A7F2D279@ingm.org> Message-ID: <20130324075207.GB7300@thebird.nl> There is one week left for adding project ideas! On Fri, Mar 22, 2013 at 03:04:18PM +0100, Raoul Bonnal wrote: > Another proposal > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code# > Machine_Learning_.26_Data_Mining_Algorithms_for_Ruby > > > On Mar 13, 2013, at 10:29 PM, Pjotr Prins wrote: > > > To build up on biogems.info functionality: > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code# > Create_a_dynamic_and_social_web_portal_for_Bioinformatics_packages > > Motto: if you are not on the web you don't exist (thanks Marjan!) > > 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 pjotr.public14 at thebird.nl Thu Mar 28 06:25:51 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 28 Mar 2013 11:25:51 +0100 Subject: [BioRuby] IRC Message-ID: <20130328102551.GA23080@thebird.nl> In the context of GSoC we will be on IRC the coming period. Join #bioruby on irc.freenode.net Pj. From pjotr.public14 at thebird.nl Sat Mar 30 05:34:42 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 30 Mar 2013 10:34:42 +0100 Subject: [BioRuby] GSoC Message-ID: <20130330093442.GA31537@thebird.nl> We have completed the list of project ideas at: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code Please check if something excites you enough to co-mentor an (interesting and talented) student! The full list of project ideas and more information about the GSoC program can be found at http://www.open-bio.org/wiki/Google_Summer_of_Code Pj. From pjotr.public14 at thebird.nl Sun Mar 3 14:47:29 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 3 Mar 2013 15:47:29 +0100 Subject: [BioRuby] GSoC 2013 is ON Message-ID: <20130303144729.GE6566@thebird.nl> Game on! GSoC 2013 is ON. I am running with the OBF project administration this year for the Google Summer of code (GSoC). First and foremost I want to thank Robert Buels and others for making OBF/GSoC a success in the previous three years! This year, Robert, Chris Fields and Hilmar Lapp will act as backup administrators. The deadline for the OBF application for GSoC2013 as a mentoring organisation is Friday March 29! See http://www.google-melange.com/gsoc/events/google/gsoc2013 Similar to previous years, each Bio* project needs to update and add project ideas on the project's individual OBF wiki page and create links from the main OBF page at http://www.open-bio.org/wiki/Google_Summer_of_Code (we will update the main information on that page soon). So, for each of the OBF projects that wants to do GSoC again this year: 1. 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. For an example see http://bioruby.open-bio.org/wiki/Google_Summer_of_Code 2. Update the final list of project ideas on the main OBF GSoC page to match. http://www.open-bio.org/wiki/Google_Summer_of_Code 3. Register with gsoc at lists.open-bio.org 4. Announce it on that list when you are ready :) Anyone can submit a project idea! Former GSoC students are especially encouraged to contribute ideas to the mailing lists. Please have the updates done by Friday March 22nd. The number and quality of the project ideas are part of the evaluation process for whether OBF is accepted as a Summer of Code organisation again this year, so let's come up with some good ones! Pj. (Pjotr Prins) Important dates: * March 22nd: Finalise project ideas * March 29th: Deadline OBF mentoring organisation submission to Google http://www.open-bio.org/wiki/Google_Summer_of_Code From pjotr.public14 at thebird.nl Tue Mar 5 17:21:23 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 5 Mar 2013 18:21:23 +0100 Subject: [BioRuby] GSoC2013 Message-ID: <20130305172123.GA20241@thebird.nl> Hi everyone, It has been quiet the last months. Everyone must be busy. Meanwhile the biogems.info site shows that development continues :) We are starting to get ready to put up ideas for the Google Summer of Code. Do you have any coding that you want to be done under GSoC? Even if you don't want to be a primary mentor, we encourage floating ideas! Last year we had two D projects binding to Ruby. I would not mind doing the same with other languages. In particular binding languages on the JVM against JRuby would be interesting. One crazy idea I have is to bind Javascript/Coffescript against BioRuby on the JVM. But maybe that is a bit rich. Please post ideas here. Who needs work done? Pj. From pjotr.public14 at thebird.nl Thu Mar 7 12:08:50 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 7 Mar 2013 13:08:50 +0100 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <20130303144729.GE6566@thebird.nl> References: <20130303144729.GE6566@thebird.nl> Message-ID: <20130307120850.GA29190@thebird.nl> Note that proposals for GSoC can be for any Biogem work! Come on guys, you are not telling me that there are no ideas for student projects. A student will work almost 4 months for you. Writing a 2-paragraph proposal is easy! http://bioruby.open-bio.org/wiki/Google_Summer_of_Code How about an RDF backend for BioRuby? On Sun, Mar 03, 2013 at 03:47:29PM +0100, Pjotr Prins wrote: > Game on! GSoC 2013 is ON. I am running with the OBF project > administration this year for the Google Summer of code (GSoC). From joachim.baran at gmail.com Thu Mar 7 12:18:38 2013 From: joachim.baran at gmail.com (Joachim Baran) Date: Thu, 7 Mar 2013 07:18:38 -0500 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <20130307120850.GA29190@thebird.nl> References: <20130303144729.GE6566@thebird.nl> <20130307120850.GA29190@thebird.nl> Message-ID: <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> On 2013-03-07, at 7:08 AM, Pjotr Prins wrote: > Note that proposals for GSoC can be for any Biogem work! I would like to be able to discover biogems more easily. Having said that, I would like to be able to discover them at all! :P Right now, you either know what you are looking for, or, you probe the biogems.info listing. Wouldn't it be great if gems were categorized, searchable, and smartly linked together (as in: "related gems")? And it would be mega cool if BioRuby had a command line tool that could work together with such a new biogems.info feature. My two cents... Joachim From iainspeed at gmail.com Thu Mar 7 12:28:16 2013 From: iainspeed at gmail.com (Iain Barnett) Date: Thu, 7 Mar 2013 12:28:16 +0000 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> References: <20130303144729.GE6566@thebird.nl> <20130307120850.GA29190@thebird.nl> <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> Message-ID: <4DFF4C2D-6539-4EE4-B1F9-9A606A8CDCF5@gmail.com> I'd suggest contacting Ruby Toolbox and getting them to add a category. No point duplicating work that's already been done. https://www.ruby-toolbox.com/categories/by_name Regards, Iain On 7 Mar 2013, at 12:18, Joachim Baran wrote: > > On 2013-03-07, at 7:08 AM, Pjotr Prins wrote: >> Note that proposals for GSoC can be for any Biogem work! > I would like to be able to discover biogems more easily. Having said that, I would like to be able to discover them at all! :P > > Right now, you either know what you are looking for, or, you probe the biogems.info listing. > > Wouldn't it be great if gems were categorized, searchable, and smartly linked together (as in: "related gems")? > > And it would be mega cool if BioRuby had a command line tool that could work together with such a new biogems.info feature. > > My two cents... > Joachim > > > _______________________________________________ > 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 Mar 7 12:44:57 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 7 Mar 2013 13:44:57 +0100 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <4DFF4C2D-6539-4EE4-B1F9-9A606A8CDCF5@gmail.com> References: <20130303144729.GE6566@thebird.nl> <20130307120850.GA29190@thebird.nl> <2CA03F4A-20A5-4E72-902F-0E036A89907D@gmail.com> <4DFF4C2D-6539-4EE4-B1F9-9A606A8CDCF5@gmail.com> Message-ID: <20130307124457.GA29323@thebird.nl> A 'bioinformatics' category would be good, indeed. Still I agree with Joachim that we can link that with the biogems.info website, and expand on that functionality. I was also thinking of tracking all OBF/GSoC projects on biogems.info this year. So all mentors can see activity in one page, as well as the BLOG entries. But that is not a student project ;) Pj. On Thu, Mar 07, 2013 at 12:28:16PM +0000, Iain Barnett wrote: > I'd suggest contacting Ruby Toolbox and getting them to add a category. No point duplicating work that's already been done. > > https://www.ruby-toolbox.com/categories/by_name > > Regards, > Iain > > On 7 Mar 2013, at 12:18, Joachim Baran wrote: > > > > > On 2013-03-07, at 7:08 AM, Pjotr Prins wrote: > >> Note that proposals for GSoC can be for any Biogem work! > > I would like to be able to discover biogems more easily. Having said that, I would like to be able to discover them at all! :P > > > > Right now, you either know what you are looking for, or, you probe the biogems.info listing. > > > > Wouldn't it be great if gems were categorized, searchable, and smartly linked together (as in: "related gems")? > > > > And it would be mega cool if BioRuby had a command line tool that could work together with such a new biogems.info feature. > > > > My two cents... > > Joachim > > > > > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > From dthorneycroft at gmail.com Thu Mar 7 19:30:42 2013 From: dthorneycroft at gmail.com (dave thorneycroft) Date: Thu, 7 Mar 2013 19:30:42 +0000 Subject: [BioRuby] Can I get more information on BioRuby Message-ID: Hello, I am a novice Ruby programmer, ex-biologist and experienced developer in other languages (sorry Adobe Flex), but I have seen the light and I want to contribute to BioRuby. I am looking through the BioRuby source code and find somethings confusing (of course I'm a novice !). Could anyone point me in the direction of any tutorials which wil help me get a better understanding of the code, I've seen the stuff on BioRuby.org. Anything that would explain but how its structured and coded not how to use it to solve a problem. A couple of things are really puzzling me right now. Number one, please don't laugh , where is the NCBIDB class located in the source (I see the GenBank class inherits NCBIDB ; but I cannot find the class source ?). NCBIDB is a class right ? Number two, could anyone explain how the Bio::FlatFile 'automagically' recognizes each database class? Any pointers would be great. Many thanks for your time, I really appreciate any comments. Regards Dave From rob.syme at gmail.com Fri Mar 8 05:11:42 2013 From: rob.syme at gmail.com (Rob Syme) Date: Fri, 8 Mar 2013 13:11:42 +0800 Subject: [BioRuby] Can I get more information on BioRuby In-Reply-To: References: Message-ID: Hi Dave Don't worry, these are appropriate questions for someone new to bioruby. Good on you for digging through the source code. The NCBIDB class is located at lib/bio/db.rb . Be sure to have a look at the top of the file for a great overview of how the database classes are constructed, written by ktym . To track down the method of autodetection, have a close look at the lib/bio/io/flatfile.rb and lib/bio/io/flatfile/autodetection.rb . *Step 1) Check to see if a dbclass has been provided* If no database class is provided to Bio::FlatFile.open, it falls through to _open_file(dbclass, filename, *arg), where dbclass is nil, which then creates a new Bio::FlatFile instance with the first argument (dbclass) as nil. If you look at the FlatFile initialize method, you'll see that the autodetect method is calledif dbclass is nil. Inside the autodetect method, a new Autodetect object is created which does the work you are interested in. Note that the class method "default" is called, which returns an Autodetect object, but does a lot of setting up first . *Step 2) Set up the default FlatFile::Autodetect object* The setup is mainly concerned with adding a large number of RuleTemplate instances to the @elements array. Each detectable format type has it's own RuleTemplate. The RuleTemplates provide three key pieces of information: - a name - a list of rules that are less important(checked later) that the current rule - a guess method, which, when given a string, returns a dbclass if the string looks like it belongs to that particular rule. There are different types of RuleTemplates. The simplest is a RegRegexp, which has a very simple guess method, which simply matches the given string given to a regular expression . The RuleTemplates also need a list of rules that are less important so that the final array of rules can be topologically sorted, returning a list rules with the most important at the top. There is a large array created in Autodetect.make_default which contains a bunch of rules that are added to the @elements array (to be tsorted later). *Step 3) Go through the first 31 lines, and match against each of the RuleTemplates* Way back in the FlatFile#autodetect method, a dbclass is pulled out of the FlatFile::Autodetect#autodetect_flatfile method . The FlatFile's BufferedInputSteam that was created earlier is pulled out so that the Autodetect object can peek inside. It then iterates over the first 31 lines of the file, taking each line and trying it out against each rule. If the guess returns non-nil (it will be a dbclass), that dbclass bubbles all the way back up to the autodetect method in FlatFile . I hope that's right - I've not contributed any code here. I might be way off. It does raise the question "How do I get a new dbclass to be recognised by FlatFile.open?" I'm not really sure, but I'm confident there will be someone here who does know. Any takers? -r * * On Fri, Mar 8, 2013 at 3:30 AM, dave thorneycroft wrote: > Hello, > > I am a novice Ruby programmer, ex-biologist and experienced developer in > other languages (sorry Adobe Flex), but I have seen the light and I want > to contribute to BioRuby. I am looking through the BioRuby source code and > find somethings confusing (of course I'm a novice !). Could anyone point > me in the direction of any tutorials which wil help me get a better > understanding of the code, I've seen the stuff on BioRuby.org. Anything > that would explain but how its structured and coded not how to use it to > solve a problem. > > A couple of things are really puzzling me right now. > > Number one, please don't laugh , where is the NCBIDB class located in the > source (I see the GenBank class inherits NCBIDB ; but I cannot find the > class source ?). NCBIDB is a class right ? > Number two, could anyone explain how the Bio::FlatFile 'automagically' > recognizes each database class? > > Any pointers would be great. Many thanks for your time, I really > appreciate any comments. > > Regards > Dave > _______________________________________________ > 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 Mar 11 09:26:56 2013 From: bonnal at ingm.org (Raoul Bonnal) Date: Mon, 11 Mar 2013 10:26:56 +0100 Subject: [BioRuby] GSoC 2013 is ON In-Reply-To: <20130303144729.GE6566@thebird.nl> References: <20130303144729.GE6566@thebird.nl> Message-ID: <1FD33CEA-1F51-4CBD-8D1D-DE11312255B9@ingm.org> I'm alive :-D we'll start thinking something picking up idea from our daily work. On Mar 3, 2013, at 3:47 PM, Pjotr Prins wrote: > Game on! GSoC 2013 is ON. I am running with the OBF project > administration this year for the Google Summer of code (GSoC). > First and foremost I want to thank Robert Buels and others for making > OBF/GSoC a success in the previous three years! This year, Robert, Chris > Fields and Hilmar Lapp will act as backup administrators. > > The deadline for the OBF application for GSoC2013 as a mentoring > organisation is Friday March 29! See > > http://www.google-melange.com/gsoc/events/google/gsoc2013 > > Similar to previous years, each Bio* project needs to update and add project > ideas on the project's individual OBF wiki page and create links from the main > OBF page at > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > (we will update the main information on that page soon). > > So, for each of the OBF projects that wants to do GSoC again this > year: > > 1. 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. For an example see > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code > > 2. Update the final list of project ideas on the main OBF GSoC page > to match. > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > 3. Register with gsoc at lists.open-bio.org > > 4. Announce it on that list when you are ready :) > > Anyone can submit a project idea! Former GSoC students are especially > encouraged to contribute ideas to the mailing lists. > > Please have the updates done by Friday March 22nd. The number and quality of > the project ideas are part of the evaluation process for whether OBF is > accepted as a Summer of Code organisation again this year, so let's come up > with some good ones! > > Pj. (Pjotr Prins) > > Important dates: > > * March 22nd: Finalise project ideas > * March 29th: Deadline OBF mentoring organisation submission to Google > > http://www.open-bio.org/wiki/Google_Summer_of_Code > > > _______________________________________________ > 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 Mar 11 21:49:19 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Mon, 11 Mar 2013 22:49:19 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 Message-ID: <20130311214919.GA17212@thebird.nl> I was wondering if anyone is interested in a Ruby/Python/Perl browser graphics/animation generator with D3 Javascript output? The idea is to take existing figures for biological results and working them on to the web with some level of clickable interaction. If you have existing graphics in gnuplot or R, they could be candidates. It could be a GSoC project. Pj. From john.woods at marcottelab.org Mon Mar 11 22:20:07 2013 From: john.woods at marcottelab.org (John Woods) Date: Mon, 11 Mar 2013 17:20:07 -0500 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: <20130311214919.GA17212@thebird.nl> References: <20130311214919.GA17212@thebird.nl> Message-ID: There's been some talk about this on the SciRuby list. We have Rubyvis, but some people are interested in doing something D3-based. On Mon, Mar 11, 2013 at 4:49 PM, Pjotr Prins wrote: > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 mail at michaelbarton.me.uk Mon Mar 11 22:45:01 2013 From: mail at michaelbarton.me.uk (Michael Barton) Date: Mon, 11 Mar 2013 18:45:01 -0400 Subject: [BioRuby] Rails for genomics Message-ID: I'm still actively developing genomer and just pushed out a new version this morning thanks to some user feedback. I've also been updating the website with more videos on how to finish a genome too. Genomer is entirely written in Ruby and I wondered if adding more features to genomer, perhaps in response to the recent assemblathon 2 paper, would be of interest to the BioRuby community as a GSoC project. The website is here - http://next.gs/ From georgkam at gmail.com Tue Mar 12 05:36:40 2013 From: georgkam at gmail.com (George Githinji) Date: Tue, 12 Mar 2013 08:36:40 +0300 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: <20130311214919.GA17212@thebird.nl> References: <20130311214919.GA17212@thebird.nl> Message-ID: Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and https://github.com/chmille4/Scribl. On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins wrote: > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 -- --------------- Sincerely George Skype: george_g2 Blog: http://www.biorelated.com/ Twitter: http://twitter.com/#!/george_l From rob.syme at gmail.com Tue Mar 12 05:57:30 2013 From: rob.syme at gmail.com (Rob Syme) Date: Tue, 12 Mar 2013 13:57:30 +0800 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: @George, the canvas rendering would probably make certain types of animation more difficult than an svg/d3 plot. Then again, canvas rendering gives you enormous flexibility. I quite like genometools (no affiliation or collaboration), perhaps we could just piggy-back on the svg generated by their annotationsketch module? The ruby/python/lua/C APIs already exists (and are quite good). It just depends on how broad the project becomes. There are certainly be many classes plots that wouldn't be possible using only this approach. At the very least, we could take design notes from these guys. To my eyes, it has a great clean aesthetic. -r On Tue, Mar 12, 2013 at 1:36 PM, George Githinji wrote: > Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and > https://github.com/chmille4/Scribl. > > On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins > wrote: > > I was wondering if anyone is interested in a Ruby/Python/Perl browser > > graphics/animation generator with D3 Javascript output? The idea is to > > take existing figures for biological results and working them on to > > the web with some level of clickable interaction. > > > > If you have existing graphics in gnuplot or R, they could be > > candidates. > > > > It could be a GSoC 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 > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://www.biorelated.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 georgkam at gmail.com Tue Mar 12 06:14:14 2013 From: georgkam at gmail.com (George Githinji) Date: Tue, 12 Mar 2013 09:14:14 +0300 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: @rob d3 would probably be a better fit for complicated plots. (graph layouts,circos plots, hive-plots?) But I would be happy to see something that integrates easily with jQuery or uses a similar approach to render the graphics or could be easily extended with plugins. I also remembered that once upon a time we had bio::graphics http://bio-graphics.rubyforge.org written largely by Jan. The big challenge for this was the heavy dependency on - cairo (cairographics.org), to do the actual drawing. - pango (www.pango.org), to do the high level text drawing. and it was also a little trick it make it work on Windows. It also has not been updated for years. On Tue, Mar 12, 2013 at 8:57 AM, Rob Syme wrote: > @George, the canvas rendering would probably make certain types of animation > more difficult than an svg/d3 plot. Then again, canvas rendering gives you > enormous flexibility. > > I quite like genometools (no affiliation or collaboration), perhaps we could > just piggy-back on the svg generated by their annotationsketch module? The > ruby/python/lua/C APIs already exists (and are quite good). It just depends > on how broad the project becomes. There are certainly be many classes plots > that wouldn't be possible using only this approach. > > At the very least, we could take design notes from these guys. To my eyes, > it has a great clean aesthetic. > > -r > > > On Tue, Mar 12, 2013 at 1:36 PM, George Githinji wrote: >> >> Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and >> https://github.com/chmille4/Scribl. >> >> On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins >> wrote: >> > I was wondering if anyone is interested in a Ruby/Python/Perl browser >> > graphics/animation generator with D3 Javascript output? The idea is to >> > take existing figures for biological results and working them on to >> > the web with some level of clickable interaction. >> > >> > If you have existing graphics in gnuplot or R, they could be >> > candidates. >> > >> > It could be a GSoC 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 >> >> >> >> -- >> --------------- >> Sincerely >> George >> Skype: george_g2 >> Blog: http://www.biorelated.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 > > -- --------------- Sincerely George Skype: george_g2 Blog: http://www.biorelated.com/ Twitter: http://twitter.com/#!/george_l From matteo.picciolini at gmail.com Tue Mar 12 09:23:55 2013 From: matteo.picciolini at gmail.com (Matteo Picciolini) Date: Tue, 12 Mar 2013 10:23:55 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: Hi , i think that a biogem D3 generetor is a good project to start . I'm using D3 for transcripts annotation rendering and the result is really nice . 2013/3/12 George Githinji > @rob d3 would probably be a better fit for complicated plots. (graph > layouts,circos plots, hive-plots?) But I would be happy to see > something that integrates easily with jQuery or uses a similar > approach to render the graphics or could be easily extended with > plugins. > > I also remembered that once upon a time we had bio::graphics > http://bio-graphics.rubyforge.org written largely by Jan. > > The big challenge for this was the heavy dependency on > - cairo (cairographics.org), to do the actual drawing. > - pango (www.pango.org), to do the high level text drawing. > and it was also a little trick it make it work on Windows. > > It also has not been updated for years. > > On Tue, Mar 12, 2013 at 8:57 AM, Rob Syme wrote: > > @George, the canvas rendering would probably make certain types of > animation > > more difficult than an svg/d3 plot. Then again, canvas rendering gives > you > > enormous flexibility. > > > > I quite like genometools (no affiliation or collaboration), perhaps we > could > > just piggy-back on the svg generated by their annotationsketch module? > The > > ruby/python/lua/C APIs already exists (and are quite good). It just > depends > > on how broad the project becomes. There are certainly be many classes > plots > > that wouldn't be possible using only this approach. > > > > At the very least, we could take design notes from these guys. To my > eyes, > > it has a great clean aesthetic. > > > > -r > > > > > > On Tue, Mar 12, 2013 at 1:36 PM, George Githinji > wrote: > >> > >> Have you had a look at Scribl? http://chmille4.github.com/Scribl/ and > >> https://github.com/chmille4/Scribl. > >> > >> On Tue, Mar 12, 2013 at 12:49 AM, Pjotr Prins < > pjotr.public14 at thebird.nl> > >> wrote: > >> > I was wondering if anyone is interested in a Ruby/Python/Perl browser > >> > graphics/animation generator with D3 Javascript output? The idea is to > >> > take existing figures for biological results and working them on to > >> > the web with some level of clickable interaction. > >> > > >> > If you have existing graphics in gnuplot or R, they could be > >> > candidates. > >> > > >> > It could be a GSoC 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 > >> > >> > >> > >> -- > >> --------------- > >> Sincerely > >> George > >> Skype: george_g2 > >> Blog: http://www.biorelated.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 > > > > > > > > -- > --------------- > Sincerely > George > Skype: george_g2 > Blog: http://www.biorelated.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 Tue Mar 12 11:51:18 2013 From: bonnal at ingm.org (Raoul Bonnal) Date: Tue, 12 Mar 2013 12:51:18 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: <20130311214919.GA17212@thebird.nl> References: <20130311214919.GA17212@thebird.nl> Message-ID: I had a student working on that some months ago, you can find the github repo here: the idea was to convert rubyvis to D3 https://github.com/dafian/RubyD3 On Mar 11, 2013, at 10:49 PM, Pjotr Prins wrote: > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 pjotr.public14 at thebird.nl Wed Mar 13 21:28:20 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 13 Mar 2013 22:28:20 +0100 Subject: [BioRuby] BioRuby Grapics generator for D3 In-Reply-To: References: <20130311214919.GA17212@thebird.nl> Message-ID: <20130313212820.GA26350@thebird.nl> I have added a project proposal: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Create_a_D3_based_graphics_package_for_Bioinformatics Who wants to mentor? I know one co-mentor who is very interested. Pj. On Tue, Mar 12, 2013 at 12:51:18PM +0100, Raoul Bonnal wrote: > I had a student working on that some months ago, > you can find the github repo here: > the idea was to convert rubyvis to D3 > > > https://github.com/dafian/RubyD3 > > > On Mar 11, 2013, at 10:49 PM, Pjotr Prins wrote: > > > I was wondering if anyone is interested in a Ruby/Python/Perl browser > graphics/animation generator with D3 Javascript output? The idea is to > take existing figures for biological results and working them on to > the web with some level of clickable interaction. > > If you have existing graphics in gnuplot or R, they could be > candidates. > > It could be a GSoC 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 pjotr.public14 at thebird.nl Wed Mar 13 21:29:44 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 13 Mar 2013 22:29:44 +0100 Subject: [BioRuby] Another proposal Message-ID: <20130313212944.GB26350@thebird.nl> To build up on biogems.info functionality: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Create_a_dynamic_and_social_web_portal_for_Bioinformatics_packages Motto: if you are not on the web you don't exist (thanks Marjan!) Pj. From bonnal at ingm.org Fri Mar 22 14:04:18 2013 From: bonnal at ingm.org (Raoul Bonnal) Date: Fri, 22 Mar 2013 15:04:18 +0100 Subject: [BioRuby] Another proposal In-Reply-To: <20130313212944.GB26350@thebird.nl> References: <20130313212944.GB26350@thebird.nl> Message-ID: <7073CAAE-0D16-4728-9A97-AB20A7F2D279@ingm.org> Another proposal http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Machine_Learning_.26_Data_Mining_Algorithms_for_Ruby On Mar 13, 2013, at 10:29 PM, Pjotr Prins wrote: > To build up on biogems.info functionality: > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code#Create_a_dynamic_and_social_web_portal_for_Bioinformatics_packages > > Motto: if you are not on the web you don't exist (thanks Marjan!) > > 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 pjotr.public14 at thebird.nl Sun Mar 24 07:52:07 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 24 Mar 2013 08:52:07 +0100 Subject: [BioRuby] Another proposal In-Reply-To: <7073CAAE-0D16-4728-9A97-AB20A7F2D279@ingm.org> References: <20130313212944.GB26350@thebird.nl> <7073CAAE-0D16-4728-9A97-AB20A7F2D279@ingm.org> Message-ID: <20130324075207.GB7300@thebird.nl> There is one week left for adding project ideas! On Fri, Mar 22, 2013 at 03:04:18PM +0100, Raoul Bonnal wrote: > Another proposal > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code# > Machine_Learning_.26_Data_Mining_Algorithms_for_Ruby > > > On Mar 13, 2013, at 10:29 PM, Pjotr Prins wrote: > > > To build up on biogems.info functionality: > > http://bioruby.open-bio.org/wiki/Google_Summer_of_Code# > Create_a_dynamic_and_social_web_portal_for_Bioinformatics_packages > > Motto: if you are not on the web you don't exist (thanks Marjan!) > > 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 pjotr.public14 at thebird.nl Thu Mar 28 10:25:51 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 28 Mar 2013 11:25:51 +0100 Subject: [BioRuby] IRC Message-ID: <20130328102551.GA23080@thebird.nl> In the context of GSoC we will be on IRC the coming period. Join #bioruby on irc.freenode.net Pj. From pjotr.public14 at thebird.nl Sat Mar 30 09:34:42 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 30 Mar 2013 10:34:42 +0100 Subject: [BioRuby] GSoC Message-ID: <20130330093442.GA31537@thebird.nl> We have completed the list of project ideas at: http://bioruby.open-bio.org/wiki/Google_Summer_of_Code Please check if something excites you enough to co-mentor an (interesting and talented) student! The full list of project ideas and more information about the GSoC program can be found at http://www.open-bio.org/wiki/Google_Summer_of_Code Pj.