From arareko at campus.iztacala.unam.mx Sat Mar 3 17:32:46 2007 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Sat, 03 Mar 2007 16:32:46 -0600 Subject: [BioRuby] [Bioperl-l] New Article on Approaches to Web Development for Bioinformatics In-Reply-To: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com> Message-ID: <45E9F78E.8040406@campus.iztacala.unam.mx> Hi Alex, I think you've put a very nice & concise introductory article. I'd like to comment a little on some sections I've read: * Introduction > "Given that you have an idea for analyzing or presenting data in a > particular was, a complete bioinformatics web application depends of > these basic pieces, which is what this article is all about: > > 1. A source of data... > 2. An application programming language... > 3. A web application platform... > 4. Optionally, a data store... > 5. Optionally, you would reuse software tools..." Even though you do a small mention about Web Services at the very end of the article (under Application Integration -> Programmatic Integration), I believe that Web Services can be another optional (or even basic) piece of a web application. In fact, many web applications consist only of Web Services without HTML user interfaces. * Application Development Languages > "There are many different programming platforms and tools available to > solve bioinformatics problems. It can be bewildering at first, but it > makes more sense to build on top of some of these tools rather than > build from scratch. Some the problems with using these tools for a > bioinformatics portal are > > 1. Many tools are written... > 2. Some tools have particular prerequisites... > 3. Many may not be in a form... > 4. The context that gives meaning... > > Standardization on a particular platform can help manageability but > for most organizations a compromise between standardization and > adoption of several different platforms will allow many people to > develop software in platforms that they are already comfortable with > and allow the reuse of a large amount of freely available software..." I would add to the problems list the fact that building web (or other kind of) applications on top of a platform whose codebase is evolving constantly, can make them very difficult to maintain. The case of EnsEMBL comes to my mind here: they opted to stick with BioPerl 1.2.3 as a core library and haven't moved onto a higher version of it because the EnsEMBL code is so vast, that a simple upgrade of BioPerl would break a lot of their code. AFAIK, it's because of this and the slowness at some parts of BioPerl that EnsEMBL is gradually saying goodbye to BioPerl. Also, I think that depending on the amount of available code you plan to import into your application, sometimes having a whole platform at the very bottom can add unnecessary extra weight to your application. More weight could be equal to less speed, this is critical in web development. * Application Integration -> Navigation > "The basic way that users will navigate into and around your > application should be using HTTP GET and POST requests with specific > URL's. Users bookmark these URL's and other applications will link to > them. Most applications developers did not realize it at first, but > these URL's are, in fact, an interface into your application that you > must maintain in a consistent way as you change and evolve your > software. Otherwise, they will find dead links..." Just as I clicked the bookmark button for your article :) The same principle could apply to its filenames. A URL of the form: http://medicalcomputing.net/tools_dna17.php is less indicative of the real content of the article and can mislead potential readers. Optimising the URL's will make them better to be indexed by search engines, something like: http://medicalcomputing.net/web-development-bioinformatics17.php would do the trick. To conclude my comments, I was surprised to see a section about BioPHP and not about other more-known toolkits like BioPython or BioRuby. What about their role in web development? Python is also a common language for web programming and with all the recent *hot* stuff like Ruby On Rails, it's very likely that both Bio* toolkits are more than ready for deploying web applications. I'm Cc'ing this to their respective mailing lists to see if someone wants to give you some feedback about them in order to complement your article. Other than that, I really liked your work :) Cheers, Mauricio. Alex Amies wrote: > I have written an article on Approaches to Web Development for > Bioinformatics at > > http://medicalcomputing.net/tools_dna1.php > > There is a fairly large section on BioPerl at > > http://medicalcomputing.net/tools_dna13.php > > I hope that someone gets something useful out of it. I also looking for > feedback on it and, in particular, please let me know about any mistakes in > it. > > The intent of the article is to give an overview of various approaches to > developing web based tools for bioinformatics. It describes the alternatives > at each layer of the system, including the data layer and sources of data, > the application programming layer, the web layer, and bioinformatics tools > and software libraries. > > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From phidippus at yahoo.com Tue Mar 6 11:42:03 2007 From: phidippus at yahoo.com (TO) Date: Tue, 6 Mar 2007 08:42:03 -0800 (PST) Subject: [BioRuby] ka/ks computation Message-ID: <885190.43458.qm@web56102.mail.re3.yahoo.com> Hello, I just started using BioRuby and like to compute Ka/Ks for pairs of sequences. Is there a function that is equivalent to dnds() of Matlab in BioRuby? http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ or could you instruct me some alternative way? Thank you for your help! TO ____________________________________________________________________________________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ From georgkam at gmail.com Wed Mar 7 02:50:05 2007 From: georgkam at gmail.com (george) Date: Tue, 06 Mar 2007 23:50:05 -0800 Subject: [BioRuby] Making Contributions Message-ID: <45EE6EAD.1010705@gmail.com> Hello Guys! I have been using ruby for 2 months now and i have loved its elegance. Previous i have been much of a perl guy and what i miss in ruby is the extensive bioinformatics library available in perl. However am grateful that ruby also has some bioinformatics library though the last release is over an year ago. Please is there any news of a major expected release for bioruby? How can i make some contributions? Am excited about rails and am developing on rails. i would be happy to contribute in a small way to the development of bioruby API on RoR framework. Thanks george From jdudley at stanford.edu Wed Mar 7 12:22:35 2007 From: jdudley at stanford.edu (Joel Dudley) Date: Wed, 7 Mar 2007 09:22:35 -0800 Subject: [BioRuby] Making Contributions In-Reply-To: <45EE6EAD.1010705@gmail.com> References: <45EE6EAD.1010705@gmail.com> Message-ID: Ditto for me as well. I'm using BioRuby and Ruby on Rails in translational genomics research. - Joel On Mar 6, 2007, at 11:50 PM, george wrote: > Hello Guys! > I have been using ruby for 2 months now and i have loved its elegance. > Previous i have been much of a perl guy and what i miss in ruby is the > extensive bioinformatics library available in perl. However am > grateful > that ruby also has some bioinformatics library though the last release > is over an year ago. > > Please is there any news of a major expected release for bioruby? How > can i make some contributions? Am excited about rails and am > developing > on rails. > i would be happy to contribute in a small way to the development of > bioruby API on RoR framework. > > Thanks > > george > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From s-merchant at northwestern.edu Thu Mar 8 10:42:06 2007 From: s-merchant at northwestern.edu (Sohel Merchant) Date: Thu, 8 Mar 2007 09:42:06 -0600 Subject: [BioRuby] Making Contributions In-Reply-To: References: <45EE6EAD.1010705@gmail.com> Message-ID: <000c01c76198$53f8dc50$c2987ca5@pc13> Hey Guys, It is very exciting to see a number of people using Ruby/Rails in the Bioinformatics community. Although, I have been primarily developing in Perl, I have started and am working on some new projects in Rails. I was wondering if any of you guys are planning to attend the Rails conference coming up in May 2007, we could have a BOF session. Cheers, Sohel Merchant. dictyBase -----Original Message----- From: bioruby-bounces at lists.open-bio.org [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Joel Dudley Sent: Wednesday, March 07, 2007 11:23 AM To: george Cc: bioruby at lists.open-bio.org Subject: Re: [BioRuby] Making Contributions Ditto for me as well. I'm using BioRuby and Ruby on Rails in translational genomics research. - Joel On Mar 6, 2007, at 11:50 PM, george wrote: > Hello Guys! > I have been using ruby for 2 months now and i have loved its elegance. > Previous i have been much of a perl guy and what i miss in ruby is the > extensive bioinformatics library available in perl. However am > grateful > that ruby also has some bioinformatics library though the last release > is over an year ago. > > Please is there any news of a major expected release for bioruby? How > can i make some contributions? Am excited about rails and am > developing > on rails. > i would be happy to contribute in a small way to the development of > bioruby API on RoR framework. > > Thanks > > george > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby _______________________________________________ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby From angel at mail.med.upenn.edu Thu Mar 8 11:26:11 2007 From: angel at mail.med.upenn.edu (Angel Pizarro) Date: Thu, 8 Mar 2007 11:26:11 -0500 Subject: [BioRuby] Making Contributions In-Reply-To: <000c01c76198$53f8dc50$c2987ca5@pc13> References: <45EE6EAD.1010705@gmail.com> <000c01c76198$53f8dc50$c2987ca5@pc13> Message-ID: Looks like it is sold out, so no ;) I made a small bioinf web application, you can take a look at the unfinished (but close!) product here http://wasabi.itmat.upenn.edu/zebrafish The schema behind the app is a stripped down biosql that has been railed ( e.g. plural names) The originating schema was populated using bioperl and the SQL scripts to ETL into the rails schema and augment with data types missing from biosql. Keyword searching is basic MySQL on the full text records and some additional annotations (GO, Ingenuity, etc) Source code will be avail upon request or publication. Whichever comes first! Other Ruby RoR projects I amworking on: - pure ruby mzXML/mzData reader (finished, but slow 221 seconds to read peaks from mzXML file) - fast (e.g. C ext wrapper on RAMP) read libs for mzXML/mzData format (working but unpolished, adds minimal overhead to straight RAMP access (21 seconds vs. 31 seconds for equiv readmzXML performance test) - MS1 signal processing and quantification (based on C++ code from OpenMS group) If anyone is is interested in these drop a line. -angel On 3/8/07, Sohel Merchant wrote: > > Hey Guys, > It is very exciting to see a number of people using Ruby/Rails in the > Bioinformatics community. Although, I have been primarily developing in > Perl, I have started and am working on some new projects in Rails. I was > wondering if any of you guys are planning to attend the Rails conference > coming up in May 2007, we could have a BOF session. > > Cheers, > Sohel Merchant. > dictyBase > > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Joel Dudley > Sent: Wednesday, March 07, 2007 11:23 AM > To: george > Cc: bioruby at lists.open-bio.org > Subject: Re: [BioRuby] Making Contributions > > Ditto for me as well. I'm using BioRuby and Ruby on Rails in > translational genomics research. > > - Joel > > On Mar 6, 2007, at 11:50 PM, george wrote: > > > Hello Guys! > > I have been using ruby for 2 months now and i have loved its elegance. > > Previous i have been much of a perl guy and what i miss in ruby is the > > extensive bioinformatics library available in perl. However am > > grateful > > that ruby also has some bioinformatics library though the last release > > is over an year ago. > > > > Please is there any news of a major expected release for bioruby? How > > can i make some contributions? Am excited about rails and am > > developing > > on rails. > > i would be happy to contribute in a small way to the development of > > bioruby API on RoR framework. > > > > Thanks > > > > george > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 From jdudley at stanford.edu Thu Mar 8 13:09:49 2007 From: jdudley at stanford.edu (Joel Dudley) Date: Thu, 8 Mar 2007 10:09:49 -0800 Subject: [BioRuby] Making Contributions In-Reply-To: <000c01c76198$53f8dc50$c2987ca5@pc13> References: <45EE6EAD.1010705@gmail.com> <000c01c76198$53f8dc50$c2987ca5@pc13> Message-ID: <07A48B9E-C0F3-4077-88C3-511CCB5298B6@stanford.edu> I would love to attend RailsConf but it looks like it already sold out. Hopefully some tickets will free up right before the conference. - Joel On Mar 8, 2007, at 7:42 AM, Sohel Merchant wrote: > Hey Guys, > It is very exciting to see a number of people using Ruby/Rails in > the > Bioinformatics community. Although, I have been primarily > developing in > Perl, I have started and am working on some new projects in Rails. > I was > wondering if any of you guys are planning to attend the Rails > conference > coming up in May 2007, we could have a BOF session. > > Cheers, > Sohel Merchant. > dictyBase From zagato.gekko at gmail.com Thu Mar 8 18:02:26 2007 From: zagato.gekko at gmail.com (Zagato) Date: Thu, 8 Mar 2007 18:02:26 -0500 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! Message-ID: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> Hello, i'm trying to decide between BioJava and BioRuby for a work, but i'm a newbie, and doesn't exists a "table" that explanis what is the better choice an what are the differences :'(. By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with BioRuby to get lineage to poulate a BioSQL database on Postgres, is this posibble?, how?. Exists a form to load the BioSQL database from a .gbk, and asn Files from a genome automagicaly :-p ? Thanks and any help it's aprecciate. Alan Jairo Acosta -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From jdudley at stanford.edu Thu Mar 8 18:17:05 2007 From: jdudley at stanford.edu (Joel Dudley) Date: Thu, 8 Mar 2007 15:17:05 -0800 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> Message-ID: You may find this link useful: http://sciruby.codeforpeople.com/sr.cgi/BioProjects - Joel On Mar 8, 2007, at 3:02 PM, Zagato wrote: > Hello, i'm trying to decide between BioJava and BioRuby for a work, > but i'm > a newbie, and doesn't exists a "table" that explanis what is the > better > choice an what are the differences :'(. > > By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with > BioRuby to get > lineage to poulate a BioSQL database on Postgres, is this > posibble?, how?. > Exists a form to load the BioSQL database from a .gbk, and asn > Files from a > genome automagicaly :-p ? > > Thanks and any help it's aprecciate. > > Alan Jairo Acosta > > -- > Farewell. > http://www.youtube.com/zagatogekko > ruby << __EOF__ > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > __EOF__ > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From zagato.gekko at gmail.com Fri Mar 9 09:53:32 2007 From: zagato.gekko at gmail.com (Zagato) Date: Fri, 9 Mar 2007 09:53:32 -0500 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> Message-ID: <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Thanks, it's a good start, for a newbie, but i still want to test, so i test BioRuby Vs BioJava, and BioRuby is more faster :D and less harder with the memory, i will try now with JRuby :-p, for enable JMS. In any case, i still want to know how to populate a BioSQL database with Ruby automatically and if i can read an ASN.1 file to extract the lineage. Lot of Thanks :D Alan Jairo Acosta On 3/8/07, Joel Dudley wrote: > > You may find this link useful: > > http://sciruby.codeforpeople.com/sr.cgi/BioProjects > > - Joel > > On Mar 8, 2007, at 3:02 PM, Zagato wrote: > > > Hello, i'm trying to decide between BioJava and BioRuby for a work, > > but i'm > > a newbie, and doesn't exists a "table" that explanis what is the > > better > > choice an what are the differences :'(. > > > > By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with > > BioRuby to get > > lineage to poulate a BioSQL database on Postgres, is this > > posibble?, how?. > > Exists a form to load the BioSQL database from a .gbk, and asn > > Files from a > > genome automagicaly :-p ? > > > > Thanks and any help it's aprecciate. > > > > Alan Jairo Acosta > > > > -- > > Farewell. > > http://www.youtube.com/zagatogekko > > ruby << __EOF__ > > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > > __EOF__ > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From mmhohman at northwestern.edu Tue Mar 13 01:23:11 2007 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Mon, 12 Mar 2007 22:23:11 -0700 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Message-ID: Hi Zagato, Why do you need to populate a BioSQL database, is the database an integration point with another BioSQL-compliant codebase? I have limited BioRuby expertise (what I know I know from writing unit tests for BioRuby long ago, and reading over the codebase just now), but AFAIK BioRuby does not support BioSQL, nor does it support ASN.1. You can however parse that genome in the GenBank file format as follows: genome = Bio::FlatFile.open(Bio::GenBank, "BA000002.gbk").entries[0] That returns you a Bio::GenBank object, which has the following methods you can play around with: ["acc_version", "accession", "accessions", "basecount", "circular", "comment", "common_name", "date", "definition", "division", "each_cds", "each_gene", "entry_id", "exists?", "features", "fetch", "get", "gi", "keywords", "length", "locus", "nalen", "naseq", "natype", "nid", "organism", "origin", "references", "segment", "seq", "seq_len", "source", "strand", "tags", "taxonomy", "vernacular_name", "version", "versions"] Hope that helps, Moses On Mar 9, 2007, at 6:53 AM, Zagato wrote: > Thanks, it's a good start, for a newbie, but i still want to test, > so i test > BioRuby Vs BioJava, and BioRuby is more faster :D and less harder > with the > memory, i will try now with JRuby :-p, for enable JMS. > In any case, i still want to know how to populate a BioSQL database > with > Ruby automatically and if i can read an ASN.1 file to extract the > lineage. > > Lot of Thanks :D > > Alan Jairo Acosta > > On 3/8/07, Joel Dudley wrote: >> >> You may find this link useful: >> >> http://sciruby.codeforpeople.com/sr.cgi/BioProjects >> >> - Joel >> >> On Mar 8, 2007, at 3:02 PM, Zagato wrote: >> >>> Hello, i'm trying to decide between BioJava and BioRuby for a work, >>> but i'm >>> a newbie, and doesn't exists a "table" that explanis what is the >>> better >>> choice an what are the differences :'(. >>> >>> By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with >>> BioRuby to get >>> lineage to poulate a BioSQL database on Postgres, is this >>> posibble?, how?. >>> Exists a form to load the BioSQL database from a .gbk, and asn >>> Files from a >>> genome automagicaly :-p ? >>> >>> Thanks and any help it's aprecciate. >>> >>> Alan Jairo Acosta >>> >>> -- >>> Farewell. >>> http://www.youtube.com/zagatogekko >>> ruby << __EOF__ >>> puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse >>> __EOF__ >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> > > > -- > Farewell. > http://www.youtube.com/zagatogekko > ruby << __EOF__ > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > __EOF__ > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From mh6 at sanger.ac.uk Tue Mar 13 08:57:21 2007 From: mh6 at sanger.ac.uk (Michael Han) Date: Tue, 13 Mar 2007 12:57:21 +0000 Subject: [BioRuby] db/embl/embl.rb Message-ID: Hi, I think the bioruby embl parser is slightly broken with the last EMBL format. I did some changes to the embl.rb that should fix it. Could someone have a look at the changes? thanks, Michael ---------------------- db/embl/embl.rb ---------- # added the new fields to the id_line parser def id_line(key=nil) unless @data['ID'] tmp = Hash.new idline = fetch('ID').split(/; +/) tmp['ENTRY_NAME'], tmp['DATA_CLASS'] = idline[0].split(/ +/) tmp['SEQUENCE_VERSION'] = idline[1] tmp['MOLECULE_CLASS'] = idline[2] tmp['MOLECULE_TYPE'] = idline[3] tmp['DIVISION'] = idline[4] tmp['SEQUENCE_LENGTH'] = idline[5].strip.split(' ').first.to_i @data['ID'] = tmp end if key @data['ID'][key] else @data['ID'] end end # and for the sequence version def sv id_line('SEQUENCE_VERSION') end def version sv.split(" ")[1].to_i end From zagato.gekko at gmail.com Tue Mar 13 09:56:17 2007 From: zagato.gekko at gmail.com (Zagato) Date: Tue, 13 Mar 2007 08:56:17 -0500 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Message-ID: <98028b00703130656i6d702d2cj4fe3e04f50b00c31@mail.gmail.com> I need BioSQL thinking that in the future other software can access to the databse, and i belive that it's better use a Scheme Well-Defined. And the other hand, i need read ASN.1 because contains <> and i need this info to organize in a tree the genome of bacterias, by now i thinking in use a Regex to extract this. Thanks for the tips. Alan Jairo Acosta On 3/13/07, Moses M. Hohman wrote: > > Hi Zagato, > > Why do you need to populate a BioSQL database, is the database an > integration point with another BioSQL-compliant codebase? > > I have limited BioRuby expertise (what I know I know from writing > unit tests for BioRuby long ago, and reading over the codebase just > now), but AFAIK BioRuby does not support BioSQL, nor does it support > ASN.1. You can however parse that genome in the GenBank file format > as follows: > > genome = Bio::FlatFile.open(Bio::GenBank, "BA000002.gbk").entries[0] > > That returns you a Bio::GenBank object, which has the following > methods you can play around with: > > ["acc_version", "accession", "accessions", "basecount", "circular", > "comment", "common_name", "date", "definition", "division", > "each_cds", "each_gene", "entry_id", "exists?", "features", "fetch", > "get", "gi", "keywords", "length", "locus", "nalen", "naseq", > "natype", "nid", "organism", "origin", "references", "segment", > "seq", "seq_len", "source", "strand", "tags", "taxonomy", > "vernacular_name", "version", "versions"] > > Hope that helps, > > Moses > > On Mar 9, 2007, at 6:53 AM, Zagato wrote: > > > Thanks, it's a good start, for a newbie, but i still want to test, > > so i test > > BioRuby Vs BioJava, and BioRuby is more faster :D and less harder > > with the > > memory, i will try now with JRuby :-p, for enable JMS. > > In any case, i still want to know how to populate a BioSQL database > > with > > Ruby automatically and if i can read an ASN.1 file to extract the > > lineage. > > > > Lot of Thanks :D > > > > Alan Jairo Acosta > > > > On 3/8/07, Joel Dudley wrote: > >> > >> You may find this link useful: > >> > >> http://sciruby.codeforpeople.com/sr.cgi/BioProjects > >> > >> - Joel > >> > >> On Mar 8, 2007, at 3:02 PM, Zagato wrote: > >> > >>> Hello, i'm trying to decide between BioJava and BioRuby for a work, > >>> but i'm > >>> a newbie, and doesn't exists a "table" that explanis what is the > >>> better > >>> choice an what are the differences :'(. > >>> > >>> By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with > >>> BioRuby to get > >>> lineage to poulate a BioSQL database on Postgres, is this > >>> posibble?, how?. > >>> Exists a form to load the BioSQL database from a .gbk, and asn > >>> Files from a > >>> genome automagicaly :-p ? > >>> > >>> Thanks and any help it's aprecciate. > >>> > >>> Alan Jairo Acosta > >>> > >>> -- > >>> Farewell. > >>> http://www.youtube.com/zagatogekko > >>> ruby << __EOF__ > >>> puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > >>> __EOF__ > >>> _______________________________________________ > >>> BioRuby mailing list > >>> BioRuby at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> > > > > > > -- > > Farewell. > > http://www.youtube.com/zagatogekko > > ruby << __EOF__ > > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > > __EOF__ > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From n at bioruby.org Tue Mar 13 13:10:32 2007 From: n at bioruby.org (Mitsuteru Nakao) Date: Wed, 14 Mar 2007 02:10:32 +0900 Subject: [BioRuby] db/embl/embl.rb In-Reply-To: References: Message-ID: <90ca35f70703131010j26d6dc79k1157d64a73cde5d4@mail.gmail.com> Hi Michael Han, Thank you for your bug report and fixed code suggestion. I fixed this bug for parsing EBML id line in release 89. You can get the fixed version from the bioruby CVS. 2007/3/13, Michael Han : > Hi, > > I think the bioruby embl parser is slightly broken with the last EMBL > format. > I did some changes to the embl.rb that should fix it. Best Mitsuteru - Mitsuteru Nakao, Ph.D. on behalf of the BioRuby Project n at bioruby.org http://bioruby.org * b-Src - Bioinformatics Packages Source Code Search Engine by gonzui From johncumbers at gmail.com Sun Mar 18 22:54:44 2007 From: johncumbers at gmail.com (John Cumbers) Date: Sun, 18 Mar 2007 22:54:44 -0400 Subject: [BioRuby] ISMB ECCB Student Symposium - Call for abstracts Message-ID: Dear friends and colleagues, This year the ISMB and ECCB conference (Intelligent Systems For Molecular Biology and European conference on Computational Biology) is in Vienna Austria, and the student council is hosting the 3rd annual symposium offering you the chance to present your work and network with other students working in computational biology. When: Saturday, July 21st, 2007. 8.30am - 5pm, the day before the main conference starts. You can vote for the keynote speakers here: http://www.surveymonkey.com/s.asp?u=242703462636 You can register here: http://www.events.mondial.at/ei/2007/ismbeccb2007/default.html. The cost is 55 Euro. Submit an abstract here: http://www.iscbsc.org/scs3/#abstracts Or download the poster here: http://www.iscbsc.org/scs3/posters/scs-3_poster_01.pdf Best wishes, John -- John Cumbers, Brown University, Biology and Medicine Box G-W, Providence, Rhode Island, 02912, USA Tel USA: +1 401 523 8190, Fax: +1 401 863-2166 UK to USA: 0207 617 7824 From trevor at corevx.com Thu Mar 22 20:44:10 2007 From: trevor at corevx.com (Trevor Wennblom) Date: Thu, 22 Mar 2007 19:44:10 -0500 Subject: [BioRuby] Next release? Message-ID: Hello all, What do we need to do to make BioRuby v1.1 happen?[1] I'm extremely interested in seeing a release along with more frequent minor-version releases.[2] Would it be possible to include more of us in the main development process? Could we tag releases ourselves? Presently I'm in talks with Chris D. at OBF about the possibility of migrating from CVS to Subversion. Also I wouldn't mind seeing a repository browser such as svnweb, Trac, or possibly Dev'il if that shapes up well.[3] What are your opinions on this? [1]: http://lists.open-bio.org/pipermail/bioruby/2006-December/ 000272.html [2]: http://lists.open-bio.org/pipermail/bioruby/2007-February/ 000277.html [3]: http://redhanded.hobix.com/inspect/rubiniusAndItsHelpfulDevIl.html From trevor at corevx.com Sun Mar 25 02:26:37 2007 From: trevor at corevx.com (Trevor Wennblom) Date: Sun, 25 Mar 2007 01:26:37 -0500 Subject: [BioRuby] Fork In-Reply-To: <45E9F78E.8040406@campus.iztacala.unam.mx> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com> <45E9F78E.8040406@campus.iztacala.unam.mx> Message-ID: <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> Judging by the overwhelming response that I've received over the past year (2006-2007) compared to the previous year (2005-2006) does this mean that's it's time for a fork? If it's time let's do it. Wake. Up. Trevor From jan.aerts at bbsrc.ac.uk Mon Mar 26 08:59:06 2007 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Mon, 26 Mar 2007 13:59:06 +0100 Subject: [BioRuby] Fork => suggestions In-Reply-To: <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com><45E9F78E.8040406@campus.iztacala.unam.mx> <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB14C8@rie2ksrv1.ri.bbsrc.ac.uk> Trevor, I must admit that I stopped mailing the list months ago after not getting much response... I'm afraid that also included answering to other people's questions. Was thinking about some suggestions for a project like bioruby to keep people informed and make clear (or sure?) that it's very much alive. I believe I mentioned some/most of these in earlier posts way back, and many/most of these will be completely stupid (copyright: myself), but it might get people thinking a bit. Note that the _last_ thing I want to do is step on the toes of the real developers. Just read this as some thoughts during your coffee.... (1) bioruby board ----------------- As English is only my x-th language, I can't think of another word than 'board'. Wouldn't it be nice if there was a limited group of people (3 to 5) that would act as a central authority so to speak to represent bioruby. This 'board' would preferably consist of people from different continents. Some things that this group could do is: * make sure that questions on the mailing list get answered or at least directed to the right people for answering * make the end-decision on which new modules (from BiorubyExtensions, see below) should be added * discuss releases (2) BiorubyEdge aka BiorubyExtensions ------------------------------------- Purpose: to make clear what's in store for bioruby in the near future and to allow for preparing new classes for inclusion in bioruby. I suppose that more people will have ruby classes defined locally that are not really ready to be included in an 'official' repository like bioruby, but that could become candidates later on. I know I have. How about creating something like BiorubyExtensions, which would be like a waiting room for classes before they get into bioruby. If a class gets polished enough and ends up fitting into the official bioruby structure, it could be 'upgraded' to the main bioruby. On the other hand: it can also be removed from BiorubyExtensions instead if not supported or well-developed enough, of course. An example would be Bio::Graphics. Someone asked about that a while ago on the mailing list, and some people (including myself) might actually have a working class for this. It's just not polished enough and misses some functionality. And therefore a candidate for such an 'extensions' waiting room. (3) feature requests + bugs --------------------------- How about using the rubyforge system for bugs and feature requests? (This mainly means making it clear on the bioruby website to submit them on rubyforge...) (5) blog -------- I don't want to sound like trying to follow latest trends nilly-willy, but a bioruby blog by the board-thingy (see above) and/or developers (a) would make really clear to the community that people are working on bioruby, (b) give more background on the development and/or (c) could give additional examples on how to use it. (6) manuscript -------------- I believe bioruby needs a reference in a journal read by a large cross-section of bioinformaticians (Bioinformatics? BMC Bioinformatics?). I've actually worked on this about year ago with Toshiaki, but it kind-a got stranded in the end... Just to get some discussion started... Comments welcome. jan. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of > Trevor Wennblom > Sent: 25 March 2007 07:27 > To: bioruby at lists.open-bio.org > Subject: [BioRuby] Fork > > Judging by the overwhelming response that I've received over > the past year (2006-2007) compared to the previous year > (2005-2006) does this mean that's it's time for a fork? > > If it's time let's do it. > > Wake. Up. > > Trevor > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Tue Mar 27 01:24:14 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Tue, 27 Mar 2007 14:24:14 +0900 Subject: [BioRuby] Fork => suggestions In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB14C8@rie2ksrv1.ri.bbsrc.ac.uk> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com><45E9F78E.8040406@campus.iztacala.unam.mx> <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> <84DA9D8AC9B05F4B889E7C70238CB45104FB14C8@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Trevor, Jan, Thank you for all of your discussions to make our bioruby community better. And, Pj, thank you for your kind personal mail. I'm very sorry that I couldn't spare enough time for the release management, but I'll work on bioruby extensively starting from tomorrow until April 1 to make the next release. Trevor, could you suspend your fork plan until my attempt fails? One more thing, do you think your modules are ready for the next release? Jan, your board plan (1) sounds nice as I'm not good in release management. I think face-to-face meeting will accelerate to make it possible, so if we could have BoF meeting during the BOSC 2007, it would be great. Everyone who wish to involved in the bioruby development and future planning, please consider to gather there. These days, I slowly worked on brushing up the bioruby shell to use with rails. I wish to figure out how it can be integrated with rails smoothly. I hope to provide repository which stores bioinformatics related rails plug-ins, rake tasks, models etc. so that user can develop your-own databases, web services and workflows easily utilizing the functionality of bioruby. This might also serve as Jan's plan (2). But I still not sure how it should be shaped. Switching towards svn may solve the part of technical problems, but, personally I want to wait until OS X includes svn by default. Does anyone know whether Leopard includes svn? I'll respond to mails stacking in my mail box as much as possible during this week. (3) future reqests + bugs I agree with utilizing rubyforge. Last year, I added some todo list there. Trevor, do you think Trac is better? (4) missing? :) (5) blog Writing English blogs must be a burden for me, but I'm happy to create links to yours at bioruby.org (6) manuscript Your draft was excellent but I want to rewrite it to cover various aspects that bioruby offers, and want to include future plans which may stand out the difference with other Open Bio* projects. Regards, Toshiaki Katayama On 2007/03/26, at 21:59, jan aerts (RI) wrote: > Trevor, > > I must admit that I stopped mailing the list months ago after not > getting much response... I'm afraid that also included answering to > other people's questions. > > Was thinking about some suggestions for a project like bioruby to keep > people informed and make clear (or sure?) that it's very much alive. I > believe I mentioned some/most of these in earlier posts way back, and > many/most of these will be completely stupid (copyright: myself), but it > might get people thinking a bit. Note that the _last_ thing I want to do > is step on the toes of the real developers. > > Just read this as some thoughts during your coffee.... > > (1) bioruby board > ----------------- > As English is only my x-th language, I can't think of another word than > 'board'. Wouldn't it be nice if there was a limited group of people (3 > to 5) that would act as a central authority so to speak to represent > bioruby. This 'board' would preferably consist of people from different > continents. Some things that this group could do is: > * make sure that questions on the mailing list get answered or at least > directed to the right people for answering > * make the end-decision on which new modules (from BiorubyExtensions, > see below) should be added > * discuss releases > > (2) BiorubyEdge aka BiorubyExtensions > ------------------------------------- > Purpose: to make clear what's in store for bioruby in the near future > and to allow for preparing new classes for inclusion in bioruby. > > I suppose that more people will have ruby classes defined locally that > are not really ready to be included in an 'official' repository like > bioruby, but that could become candidates later on. I know I have. How > about creating something like BiorubyExtensions, which would be like a > waiting room for classes before they get into bioruby. If a class gets > polished enough and ends up fitting into the official bioruby structure, > it could be 'upgraded' to the main bioruby. On the other hand: it can > also be removed from BiorubyExtensions instead if not supported or > well-developed enough, of course. > An example would be Bio::Graphics. Someone asked about that a while ago > on the mailing list, and some people (including myself) might actually > have a working class for this. It's just not polished enough and misses > some functionality. And therefore a candidate for such an 'extensions' > waiting room. > > > (3) feature requests + bugs > --------------------------- > How about using the rubyforge system for bugs and feature requests? > (This mainly means making it clear on the bioruby website to submit them > on rubyforge...) > > > (5) blog > -------- > I don't want to sound like trying to follow latest trends nilly-willy, > but a bioruby blog by the board-thingy (see above) and/or developers (a) > would make really clear to the community that people are working on > bioruby, (b) give more background on the development and/or (c) could > give additional examples on how to use it. > > > (6) manuscript > -------------- > I believe bioruby needs a reference in a journal read by a large > cross-section of bioinformaticians (Bioinformatics? BMC > Bioinformatics?). I've actually worked on this about year ago with > Toshiaki, but it kind-a got stranded in the end... > > Just to get some discussion started... Comments welcome. > > jan. > > > >> -----Original Message----- >> From: bioruby-bounces at lists.open-bio.org >> [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of >> Trevor Wennblom >> Sent: 25 March 2007 07:27 >> To: bioruby at lists.open-bio.org >> Subject: [BioRuby] Fork >> >> Judging by the overwhelming response that I've received over >> the past year (2006-2007) compared to the previous year >> (2005-2006) does this mean that's it's time for a fork? >> >> If it's time let's do it. >> >> Wake. Up. >> >> Trevor >> _______________________________________________ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Tue Mar 27 01:48:49 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Tue, 27 Mar 2007 14:48:49 +0900 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Message-ID: On 2007/03/13, at 14:23, Moses M. Hohman wrote: > but AFAIK BioRuby does not support BioSQL, Currently it might be broken, but BioRuby supported BioSQL from the beginning of the BioSQL project which is developed during three BioHackathon meetings (2002, 2003). I wrote basic BioSQL module which support Cape Town schema (2002), but I was lazy to update it. However, AFAIK, RJP is working on ActiveRecord + BioSQL integration (2006, December) to replace my old one. Raoul, could you post your recent status on it? > nor does it support ASN.1. I think this is true. It seems that there is one project on ASN.1 at rubyforge. http://rubyforge.org/projects/net-asn1/ Toshiaki From n at bioruby.org Wed Mar 28 06:45:50 2007 From: n at bioruby.org (Mitsuteru Nakao) Date: Wed, 28 Mar 2007 19:45:50 +0900 Subject: [BioRuby] Errors from ruby test/runner.rb Message-ID: <90ca35f70703280345r2fec2a99rdaf93ec81ce16bf8@mail.gmail.com> Hi Trevor, I am going to check the unit tests for the next release. Please check error message below and attached errors from "% ruby -r lib/bio/util/restriction_enzyme/cut_symbol.rb test/runner.rb", and make sure test/runner.rb (and/or ruby install.rb test) to be "0 failures, 0 errors." ------ ruby test/runner.rb ------- % ruby test/runner.rb ./lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb:51: uninitialized constant Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation::CutSymbol (NameError) from ./lib/bio/util/restriction_enzyme/single_strand.rb:14:in `require' from ./lib/bio/util/restriction_enzyme/single_strand.rb:14 from ./lib/bio/util/restriction_enzyme/double_stranded.rb:19:in `require' from ./lib/bio/util/restriction_enzyme/double_stranded.rb:19 from ./lib/bio/util/restriction_enzyme.rb:12:in `require' from ./lib/bio/util/restriction_enzyme.rb:12 from ./lib/bio/util/restriction_enzyme/cut_symbol.rb:14 from ./lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb:15:in `require' ... 25 levels... from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:198:in `[]' from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:198:in `run' from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' from test/runner.rb:10 Best, Mitsuteru - Mitsuteru Nakao Ph.D n at bioruby.org Kazusa DNA Research Institute mn at kazusa.or.jp -------------- next part -------------- Loaded suite . Started ..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................EE.............................................................................................................................................................................................................................................................................................................................................................................................................................................EEEEEEEEEEEEEEEEEEEE..... Finished in 65.205477 seconds. 1) Error: test_dataset(Bio::TestSOFT): Errno::ENOENT: No such file or directory - ../../../data/soft/GSE3457_family_partial.soft ./test/unit/bio/db/test_soft.rb:22:in `readlines' ./test/unit/bio/db/test_soft.rb:22:in `setup' 2) Error: test_series(Bio::TestSOFT): Errno::ENOENT: No such file or directory - ../../../data/soft/GSE3457_family_partial.soft ./test/unit/bio/db/test_soft.rb:22:in `readlines' ./test/unit/bio/db/test_soft.rb:22:in `setup' 3) Error: test_argument_error(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 4) Error: test_complement(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 5) Error: test_contents(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 6) Error: test_primary(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 7) Error: test_argument_error(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 8) Error: test_complement(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 9) Error: test_contents(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 10) Error: test_primary(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 11) Error: test_complement(Bio::TestDoubleStrandedCutLocations): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup' 12) Error: test_contents(Bio::TestDoubleStrandedCutLocations): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup' 13) Error: test_primary(Bio::TestDoubleStrandedCutLocations): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup' 14) Error: test_complement(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 15) Error: test_complement_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 16) Error: test_complement_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 17) Error: test_contents(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 18) Error: test_primary(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 19) Error: test_primary_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 20) Error: test_primary_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 21) Error: test_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 22) Error: test_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 1282 tests, 2443 assertions, 0 failures, 22 errors From ngoto at gen-info.osaka-u.ac.jp Wed Mar 28 06:50:45 2007 From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa) Date: Wed, 28 Mar 2007 19:50:45 +0900 Subject: [BioRuby] Bug in writing PDB ATOM In-Reply-To: References: <45cd751d.28e949d0.4e3f.ffff9a4dSMTPIN_ADDED@mx.google.com> Message-ID: <20070328105022.9F2B71CBC54E@idnmail.gen-info.osaka-u.ac.jp> Hi, Yen-Ju, I changed pdb.rb in the CVS and the bug is fixed, although it may still fail in few exceptional ATOM/HETATM lines. http://code.open-bio.org/cgi/viewcvs.cgi/*checkout*/bioruby/lib/bio/db/pdb/pdb.rb?rev=HEAD&cvsroot=bioruby&content-type=text/plain Thank you, Naohisa Goto ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp On Sat, 10 Feb 2007 06:13:25 -0800 "Yen-Ju Chen" wrote: > On 2/9/07, GOTO Naohisa wrote: > > Hi, Yen-Ju, > > > > Which bioruby version do you use? > > By using CVS HEAD 'pdb.rb,v 1.16 2006/06/27 14:23:45', > > it seems fine. > > I tried both 1.0 and CVS. > And your example indeed works fine. > Here is the data and script I used: > > ATOM 1 CB TYR A 4 46.803 20.433 46.159 1.00130.00 > ATOM 2 CG TYR A 4 46.708 19.122 46.931 1.00130.00 > ATOM 3 CD1 TYR A 4 46.708 17.892 46.257 1.00130.00 > ATOM 4 CE1 TYR A 4 46.596 16.691 46.961 1.00130.00 > ATOM 5 CD2 TYR A 4 46.599 19.109 48.336 1.00130.00 > > ######### > require 'bio' > > file = File.new('a.pdb').gets(nil) > structure = Bio::PDB.new(file) > > structure.each do |model| > model.each do |chain| > chain.each do |residue| > residue.each do |atom| > atom.resSeq += 400 > end > end > end > end > > File.open('x.pdb', 'w') do |file| > file << structure.to_s > end > > Yen-Ju > > > > > #### sample script > > require 'bio' > > atom = Bio::PDB::Record::ATOM.new > > atom.serial = 61 > > atom.name = 'OD1' > > atom.altLoc = '' > > atom.resName = 'ASN' > > atom.chainID = 'A' > > atom.resSeq = 8 > > atom.iCode = '' > > atom.x = 102.025 > > atom.y = 27.929 > > atom.z = 144.984 > > atom.occupancy = 1.0 > > atom.tempFactor = 88.56 > > atom.segID = '' > > atom.element = 'O' > > atom.charge = '' > > print atom.to_s > > # "ATOM 61 OD1 ASN A 8 102.025 27.929 144.984 1.00 88.56 O \n" > > #### end of sample script > > > > However, it still fails in some rare cases. > > > > require 'bio' > > # record from PDB 1CX1 > > str = "ATOM 376 HH TYR A 25 " + > > "4.479 12.801 -3.919 1.00 1.72 H " > > atom = Bio::PDB::Record::ATOM.new.initialize_from_string(str) > > print atom.to_s > > # > > # "ATOM 376 HH TYR A 25 4.479 12.801 -3.919 1.00 1.72 H \n" > > # ^ an excess space!! > > > > I'll make changes in the CVS to give more accurate results, > > but it'll be still imperfect (becase of ambiguity, as Alex said). > > > > Thanks, > > > > Naohisa Goto > > ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp > > > > On Thu, 8 Feb 2007 14:54:09 -0800 > > "Yen-Ju Chen" wrote: > > > > > In bio/db/pdb/pdb.rb line 1019, > > > the ATOM entry is written as: > > > > > > sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s > > > > > > It results an ATOM entry as: > > > ATOM 61 OD1 ASN A 8 102.025 27.929 144.984 1.00 88.56 O > > > > > > But the right ATOM entry should be > > > ATOM 61 OD1 ASN A 8 102.025 27.929 144.984 1.00 88.56 O > > > > > > Note there are 2 spaces after '61' and one space before 'ASN' > > > I change this line to: > > > > > > sprintf("%-6s%5d %-3s%-1s%3s %-1s%4d%-1s > > > > > > and it works fine now. > > > But I am new to Ruby and not familiar with the format yet. > > > > > > Yen-Ju > > > _______________________________________________ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > From ktym at hgc.jp Wed Mar 28 07:42:30 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 28 Mar 2007 20:42:30 +0900 Subject: [BioRuby] License Message-ID: Dear BioRuby developers, Few months ago, we made decision to change the license of BioRuby library from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby is also able to use BioRuby not be bothered by legal restrictions. We are now working on the next release and this is the time to complete changes on every modules. * Alex, could you agree with us to change the license of your PDB modules? * Fujita-san, Suga-san, could you agree with us to change the license of your HMMER module? * Shigenobu-san, could you agree with us to change the license of your Fastacmd module? Thanks in advance. Regards, Toshiaki Katayama From angel at mail.med.upenn.edu Wed Mar 28 08:33:22 2007 From: angel at mail.med.upenn.edu (Angel Pizarro) Date: Wed, 28 Mar 2007 08:33:22 -0400 Subject: [BioRuby] License In-Reply-To: References: Message-ID: I believe that a consistent license is best, but let's not let that be a barrier to release. Strictly speaking, GPL is not as restrictive as it perceived to be by the general public. For more information look here: http://www.sitepoint.com/article/public-license-explained What this means for Ruby (and Rails applications) is that unless you extend the GPL module in some way (for instance wrapping a C library in SWIG to derive a Ruby C extension or adding methods to a module/class) it is not effected by the GPL and can be released along with other licensing terms. Simply calling the methods of a module does not constitute a "derived work". Passing data between modules is also not considered a derived work. Cheers! -angel On 3/28/07, Toshiaki Katayama wrote: > > Dear BioRuby developers, > > Few months ago, we made decision to change the license of BioRuby library > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > is also able to use BioRuby not be bothered by legal restrictions. > > We are now working on the next release and this is the time to complete > changes on every modules. > > * Alex, could you agree with us to change the license of your PDB modules? > > * Fujita-san, Suga-san, could you agree with us to change the license of > your HMMER module? > > * Shigenobu-san, could you agree with us to change the license of your > Fastacmd module? > > Thanks in advance. > > Regards, > Toshiaki Katayama > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Thu Mar 29 09:16:09 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu, 29 Mar 2007 22:16:09 +0900 Subject: [BioRuby] License In-Reply-To: References: Message-ID: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> Moses, We realized that your codes licensed under the LGPL exists in the test/ subdirectory. Could you agree with us to change the license to Ruby's on following files? test/unit/bio/test_alignment.rb test/unit/bio/test_location.rb test/unit/bio/test_pathway.rb test/unit/bio/test_sequence.rb As for the other modules, we got very quick response from most of license holders that permit us to change the license of their modules. We, core team, appreciate your understanding and cooperations! Regards, Toshiaki Katayama On 2007/03/28, at 20:42, Toshiaki Katayama wrote: > Dear BioRuby developers, > > Few months ago, we made decision to change the license of BioRuby library > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > is also able to use BioRuby not be bothered by legal restrictions. > > We are now working on the next release and this is the time to complete > changes on every modules. > > * Alex, could you agree with us to change the license of your PDB modules? > > * Fujita-san, Suga-san, could you agree with us to change the license of your HMMER module? > > * Shigenobu-san, could you agree with us to change the license of your Fastacmd module? > > Thanks in advance. > > Regards, > Toshiaki Katayama > From zagato.gekko at gmail.com Thu Mar 29 18:15:47 2007 From: zagato.gekko at gmail.com (Zagato) Date: Thu, 29 Mar 2007 17:15:47 -0500 Subject: [BioRuby] License In-Reply-To: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> Message-ID: <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Hello everybody... Just for curiosity I wondering: ?what are the advantages or disadvantages of using Ruby Vs LGPL?... thinking in final users like me ! ?Somebody can please give an explain of how affect this changes for good or bad to the users...? Lot of thanks :D Alan Jairo Acosta Cali - Colombia On 3/29/07, Toshiaki Katayama wrote: > > Moses, > > We realized that your codes licensed under the LGPL exists in the test/ > subdirectory. > Could you agree with us to change the license to Ruby's on following > files? > > test/unit/bio/test_alignment.rb > test/unit/bio/test_location.rb > test/unit/bio/test_pathway.rb > test/unit/bio/test_sequence.rb > > As for the other modules, we got very quick response from most of license > holders that permit us to change the license of their modules. > We, core team, appreciate your understanding and cooperations! > > Regards, > Toshiaki Katayama > > > On 2007/03/28, at 20:42, Toshiaki Katayama wrote: > > > Dear BioRuby developers, > > > > Few months ago, we made decision to change the license of BioRuby > library > > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > > is also able to use BioRuby not be bothered by legal restrictions. > > > > We are now working on the next release and this is the time to complete > > changes on every modules. > > > > * Alex, could you agree with us to change the license of your PDB > modules? > > > > * Fujita-san, Suga-san, could you agree with us to change the license of > your HMMER module? > > > > * Shigenobu-san, could you agree with us to change the license of your > Fastacmd module? > > > > Thanks in advance. > > > > Regards, > > Toshiaki Katayama > > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From ktym at hgc.jp Fri Mar 30 00:32:34 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 30 Mar 2007 13:32:34 +0900 Subject: [BioRuby] License In-Reply-To: <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Message-ID: Advantage: * we (developers and users) can be free from this kind of boring comparison. :) Disadvantage: * none. Note that, I thank and respect the GNU project and the spirit, although. Toshiaki On 2007/03/30, at 7:15, Zagato wrote: > Hello everybody... > > Just for curiosity I wondering: ?what are the advantages or disadvantages of using Ruby Vs LGPL?... thinking in final users like me ! > > ?Somebody can please give an explain of how affect this changes for good or bad to the users...? > > Lot of thanks :D > > Alan Jairo Acosta > Cali - Colombia > > On 3/29/07, Toshiaki Katayama wrote: Moses, > > We realized that your codes licensed under the LGPL exists in the test/ subdirectory. > Could you agree with us to change the license to Ruby's on following files? > > test/unit/bio/test_alignment.rb > test/unit/bio/test_location.rb > test/unit/bio/test_pathway.rb > test/unit/bio/test_sequence.rb > > As for the other modules, we got very quick response from most of license holders that permit us to change the license of their modules. > We, core team, appreciate your understanding and cooperations! > > Regards, > Toshiaki Katayama > > > On 2007/03/28, at 20:42, Toshiaki Katayama wrote: > > > Dear BioRuby developers, > > > > Few months ago, we made decision to change the license of BioRuby library > > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > > is also able to use BioRuby not be bothered by legal restrictions. > > > > We are now working on the next release and this is the time to complete > > changes on every modules. > > > > * Alex, could you agree with us to change the license of your PDB modules? > > > > * Fujita-san, Suga-san, could you agree with us to change the license of your HMMER module? > > > > * Shigenobu-san, could you agree with us to change the license of your Fastacmd module? > > > > Thanks in advance. > > > > Regards, > > Toshiaki Katayama > > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > Farewell. > http://www.youtube.com/zagatogekko > ruby << __EOF__ > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > __EOF__ From trevor at corevx.com Fri Mar 30 02:14:13 2007 From: trevor at corevx.com (Trevor Wennblom) Date: Fri, 30 Mar 2007 01:14:13 -0500 Subject: [BioRuby] License In-Reply-To: References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Message-ID: On Mar 29, 2007, at 11:32 PM, Toshiaki Katayama wrote: > Advantage: > * we (developers and users) can be free from this kind of boring > comparison. :) > > Disadvantage: > * none. Just about to go to bed so this will be brief. The biggest advantage to moving to the Ruby license, which is essentially the MIT license,[1] is that is compatible with Ruby itself. What an honor it would be - though not necessarily desired - to be included in the main Ruby package itself as a standard library. The least we can do is acknowledge the word "Ruby" is itself in the name of the project. Let us not forget that the Ruby license is completely compatible with the GPL according to the Free Software Foundation.[2] Trevor [1]: http://en.wikipedia.org/wiki/MIT_License [2]: http://en.wikipedia.org/wiki/Ruby_License From zagato.gekko at gmail.com Fri Mar 30 12:41:25 2007 From: zagato.gekko at gmail.com (Zagato) Date: Fri, 30 Mar 2007 11:41:25 -0500 Subject: [BioRuby] License In-Reply-To: References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Message-ID: <98028b00703300941p778e25a1n630e943d39fcb1aa@mail.gmail.com> Thanks for the comments about my question, i think now that Ruby's License it's a good choice :D!!! Bye Alan Jairo Acosta Cali - Colombia On 3/30/07, Trevor Wennblom wrote: > > > On Mar 29, 2007, at 11:32 PM, Toshiaki Katayama wrote: > > > Advantage: > > * we (developers and users) can be free from this kind of boring > > comparison. :) > > > > Disadvantage: > > * none. > > > Just about to go to bed so this will be brief. > > The biggest advantage to moving to the Ruby license, which is > essentially the MIT license,[1] is that is compatible with Ruby > itself. What an honor it would be - though not necessarily desired - > to be included in the main Ruby package itself as a standard > library. The least we can do is acknowledge the word "Ruby" is > itself in the name of the project. > > Let us not forget that the Ruby license is completely compatible with > the GPL according to the Free Software Foundation.[2] > > Trevor > > [1]: http://en.wikipedia.org/wiki/MIT_License > [2]: http://en.wikipedia.org/wiki/Ruby_License > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From arareko at campus.iztacala.unam.mx Sat Mar 3 22:32:46 2007 From: arareko at campus.iztacala.unam.mx (Mauricio Herrera Cuadra) Date: Sat, 03 Mar 2007 16:32:46 -0600 Subject: [BioRuby] [Bioperl-l] New Article on Approaches to Web Development for Bioinformatics In-Reply-To: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com> Message-ID: <45E9F78E.8040406@campus.iztacala.unam.mx> Hi Alex, I think you've put a very nice & concise introductory article. I'd like to comment a little on some sections I've read: * Introduction > "Given that you have an idea for analyzing or presenting data in a > particular was, a complete bioinformatics web application depends of > these basic pieces, which is what this article is all about: > > 1. A source of data... > 2. An application programming language... > 3. A web application platform... > 4. Optionally, a data store... > 5. Optionally, you would reuse software tools..." Even though you do a small mention about Web Services at the very end of the article (under Application Integration -> Programmatic Integration), I believe that Web Services can be another optional (or even basic) piece of a web application. In fact, many web applications consist only of Web Services without HTML user interfaces. * Application Development Languages > "There are many different programming platforms and tools available to > solve bioinformatics problems. It can be bewildering at first, but it > makes more sense to build on top of some of these tools rather than > build from scratch. Some the problems with using these tools for a > bioinformatics portal are > > 1. Many tools are written... > 2. Some tools have particular prerequisites... > 3. Many may not be in a form... > 4. The context that gives meaning... > > Standardization on a particular platform can help manageability but > for most organizations a compromise between standardization and > adoption of several different platforms will allow many people to > develop software in platforms that they are already comfortable with > and allow the reuse of a large amount of freely available software..." I would add to the problems list the fact that building web (or other kind of) applications on top of a platform whose codebase is evolving constantly, can make them very difficult to maintain. The case of EnsEMBL comes to my mind here: they opted to stick with BioPerl 1.2.3 as a core library and haven't moved onto a higher version of it because the EnsEMBL code is so vast, that a simple upgrade of BioPerl would break a lot of their code. AFAIK, it's because of this and the slowness at some parts of BioPerl that EnsEMBL is gradually saying goodbye to BioPerl. Also, I think that depending on the amount of available code you plan to import into your application, sometimes having a whole platform at the very bottom can add unnecessary extra weight to your application. More weight could be equal to less speed, this is critical in web development. * Application Integration -> Navigation > "The basic way that users will navigate into and around your > application should be using HTTP GET and POST requests with specific > URL's. Users bookmark these URL's and other applications will link to > them. Most applications developers did not realize it at first, but > these URL's are, in fact, an interface into your application that you > must maintain in a consistent way as you change and evolve your > software. Otherwise, they will find dead links..." Just as I clicked the bookmark button for your article :) The same principle could apply to its filenames. A URL of the form: http://medicalcomputing.net/tools_dna17.php is less indicative of the real content of the article and can mislead potential readers. Optimising the URL's will make them better to be indexed by search engines, something like: http://medicalcomputing.net/web-development-bioinformatics17.php would do the trick. To conclude my comments, I was surprised to see a section about BioPHP and not about other more-known toolkits like BioPython or BioRuby. What about their role in web development? Python is also a common language for web programming and with all the recent *hot* stuff like Ruby On Rails, it's very likely that both Bio* toolkits are more than ready for deploying web applications. I'm Cc'ing this to their respective mailing lists to see if someone wants to give you some feedback about them in order to complement your article. Other than that, I really liked your work :) Cheers, Mauricio. Alex Amies wrote: > I have written an article on Approaches to Web Development for > Bioinformatics at > > http://medicalcomputing.net/tools_dna1.php > > There is a fairly large section on BioPerl at > > http://medicalcomputing.net/tools_dna13.php > > I hope that someone gets something useful out of it. I also looking for > feedback on it and, in particular, please let me know about any mistakes in > it. > > The intent of the article is to give an overview of various approaches to > developing web based tools for bioinformatics. It describes the alternatives > at each layer of the system, including the data layer and sources of data, > the application programming layer, the web layer, and bioinformatics tools > and software libraries. > > Alex > _______________________________________________ > Bioperl-l mailing list > Bioperl-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioperl-l > -- MAURICIO HERRERA CUADRA arareko at campus.iztacala.unam.mx Laboratorio de Gen?tica Unidad de Morfofisiolog?a y Funci?n Facultad de Estudios Superiores Iztacala, UNAM From phidippus at yahoo.com Tue Mar 6 16:42:03 2007 From: phidippus at yahoo.com (TO) Date: Tue, 6 Mar 2007 08:42:03 -0800 (PST) Subject: [BioRuby] ka/ks computation Message-ID: <885190.43458.qm@web56102.mail.re3.yahoo.com> Hello, I just started using BioRuby and like to compute Ka/Ks for pairs of sequences. Is there a function that is equivalent to dnds() of Matlab in BioRuby? http://www.mathworks.com/access/helpdesk/help/toolbox/bioinfo/ or could you instruct me some alternative way? Thank you for your help! TO ____________________________________________________________________________________ TV dinner still cooling? Check out "Tonight's Picks" on Yahoo! TV. http://tv.yahoo.com/ From georgkam at gmail.com Wed Mar 7 07:50:05 2007 From: georgkam at gmail.com (george) Date: Tue, 06 Mar 2007 23:50:05 -0800 Subject: [BioRuby] Making Contributions Message-ID: <45EE6EAD.1010705@gmail.com> Hello Guys! I have been using ruby for 2 months now and i have loved its elegance. Previous i have been much of a perl guy and what i miss in ruby is the extensive bioinformatics library available in perl. However am grateful that ruby also has some bioinformatics library though the last release is over an year ago. Please is there any news of a major expected release for bioruby? How can i make some contributions? Am excited about rails and am developing on rails. i would be happy to contribute in a small way to the development of bioruby API on RoR framework. Thanks george From jdudley at stanford.edu Wed Mar 7 17:22:35 2007 From: jdudley at stanford.edu (Joel Dudley) Date: Wed, 7 Mar 2007 09:22:35 -0800 Subject: [BioRuby] Making Contributions In-Reply-To: <45EE6EAD.1010705@gmail.com> References: <45EE6EAD.1010705@gmail.com> Message-ID: Ditto for me as well. I'm using BioRuby and Ruby on Rails in translational genomics research. - Joel On Mar 6, 2007, at 11:50 PM, george wrote: > Hello Guys! > I have been using ruby for 2 months now and i have loved its elegance. > Previous i have been much of a perl guy and what i miss in ruby is the > extensive bioinformatics library available in perl. However am > grateful > that ruby also has some bioinformatics library though the last release > is over an year ago. > > Please is there any news of a major expected release for bioruby? How > can i make some contributions? Am excited about rails and am > developing > on rails. > i would be happy to contribute in a small way to the development of > bioruby API on RoR framework. > > Thanks > > george > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From s-merchant at northwestern.edu Thu Mar 8 15:42:06 2007 From: s-merchant at northwestern.edu (Sohel Merchant) Date: Thu, 8 Mar 2007 09:42:06 -0600 Subject: [BioRuby] Making Contributions In-Reply-To: References: <45EE6EAD.1010705@gmail.com> Message-ID: <000c01c76198$53f8dc50$c2987ca5@pc13> Hey Guys, It is very exciting to see a number of people using Ruby/Rails in the Bioinformatics community. Although, I have been primarily developing in Perl, I have started and am working on some new projects in Rails. I was wondering if any of you guys are planning to attend the Rails conference coming up in May 2007, we could have a BOF session. Cheers, Sohel Merchant. dictyBase -----Original Message----- From: bioruby-bounces at lists.open-bio.org [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Joel Dudley Sent: Wednesday, March 07, 2007 11:23 AM To: george Cc: bioruby at lists.open-bio.org Subject: Re: [BioRuby] Making Contributions Ditto for me as well. I'm using BioRuby and Ruby on Rails in translational genomics research. - Joel On Mar 6, 2007, at 11:50 PM, george wrote: > Hello Guys! > I have been using ruby for 2 months now and i have loved its elegance. > Previous i have been much of a perl guy and what i miss in ruby is the > extensive bioinformatics library available in perl. However am > grateful > that ruby also has some bioinformatics library though the last release > is over an year ago. > > Please is there any news of a major expected release for bioruby? How > can i make some contributions? Am excited about rails and am > developing > on rails. > i would be happy to contribute in a small way to the development of > bioruby API on RoR framework. > > Thanks > > george > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby _______________________________________________ BioRuby mailing list BioRuby at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/bioruby From angel at mail.med.upenn.edu Thu Mar 8 16:26:11 2007 From: angel at mail.med.upenn.edu (Angel Pizarro) Date: Thu, 8 Mar 2007 11:26:11 -0500 Subject: [BioRuby] Making Contributions In-Reply-To: <000c01c76198$53f8dc50$c2987ca5@pc13> References: <45EE6EAD.1010705@gmail.com> <000c01c76198$53f8dc50$c2987ca5@pc13> Message-ID: Looks like it is sold out, so no ;) I made a small bioinf web application, you can take a look at the unfinished (but close!) product here http://wasabi.itmat.upenn.edu/zebrafish The schema behind the app is a stripped down biosql that has been railed ( e.g. plural names) The originating schema was populated using bioperl and the SQL scripts to ETL into the rails schema and augment with data types missing from biosql. Keyword searching is basic MySQL on the full text records and some additional annotations (GO, Ingenuity, etc) Source code will be avail upon request or publication. Whichever comes first! Other Ruby RoR projects I amworking on: - pure ruby mzXML/mzData reader (finished, but slow 221 seconds to read peaks from mzXML file) - fast (e.g. C ext wrapper on RAMP) read libs for mzXML/mzData format (working but unpolished, adds minimal overhead to straight RAMP access (21 seconds vs. 31 seconds for equiv readmzXML performance test) - MS1 signal processing and quantification (based on C++ code from OpenMS group) If anyone is is interested in these drop a line. -angel On 3/8/07, Sohel Merchant wrote: > > Hey Guys, > It is very exciting to see a number of people using Ruby/Rails in the > Bioinformatics community. Although, I have been primarily developing in > Perl, I have started and am working on some new projects in Rails. I was > wondering if any of you guys are planning to attend the Rails conference > coming up in May 2007, we could have a BOF session. > > Cheers, > Sohel Merchant. > dictyBase > > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Joel Dudley > Sent: Wednesday, March 07, 2007 11:23 AM > To: george > Cc: bioruby at lists.open-bio.org > Subject: Re: [BioRuby] Making Contributions > > Ditto for me as well. I'm using BioRuby and Ruby on Rails in > translational genomics research. > > - Joel > > On Mar 6, 2007, at 11:50 PM, george wrote: > > > Hello Guys! > > I have been using ruby for 2 months now and i have loved its elegance. > > Previous i have been much of a perl guy and what i miss in ruby is the > > extensive bioinformatics library available in perl. However am > > grateful > > that ruby also has some bioinformatics library though the last release > > is over an year ago. > > > > Please is there any news of a major expected release for bioruby? How > > can i make some contributions? Am excited about rails and am > > developing > > on rails. > > i would be happy to contribute in a small way to the development of > > bioruby API on RoR framework. > > > > Thanks > > > > george > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 From jdudley at stanford.edu Thu Mar 8 18:09:49 2007 From: jdudley at stanford.edu (Joel Dudley) Date: Thu, 8 Mar 2007 10:09:49 -0800 Subject: [BioRuby] Making Contributions In-Reply-To: <000c01c76198$53f8dc50$c2987ca5@pc13> References: <45EE6EAD.1010705@gmail.com> <000c01c76198$53f8dc50$c2987ca5@pc13> Message-ID: <07A48B9E-C0F3-4077-88C3-511CCB5298B6@stanford.edu> I would love to attend RailsConf but it looks like it already sold out. Hopefully some tickets will free up right before the conference. - Joel On Mar 8, 2007, at 7:42 AM, Sohel Merchant wrote: > Hey Guys, > It is very exciting to see a number of people using Ruby/Rails in > the > Bioinformatics community. Although, I have been primarily > developing in > Perl, I have started and am working on some new projects in Rails. > I was > wondering if any of you guys are planning to attend the Rails > conference > coming up in May 2007, we could have a BOF session. > > Cheers, > Sohel Merchant. > dictyBase From zagato.gekko at gmail.com Thu Mar 8 23:02:26 2007 From: zagato.gekko at gmail.com (Zagato) Date: Thu, 8 Mar 2007 18:02:26 -0500 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! Message-ID: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> Hello, i'm trying to decide between BioJava and BioRuby for a work, but i'm a newbie, and doesn't exists a "table" that explanis what is the better choice an what are the differences :'(. By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with BioRuby to get lineage to poulate a BioSQL database on Postgres, is this posibble?, how?. Exists a form to load the BioSQL database from a .gbk, and asn Files from a genome automagicaly :-p ? Thanks and any help it's aprecciate. Alan Jairo Acosta -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From jdudley at stanford.edu Thu Mar 8 23:17:05 2007 From: jdudley at stanford.edu (Joel Dudley) Date: Thu, 8 Mar 2007 15:17:05 -0800 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> Message-ID: You may find this link useful: http://sciruby.codeforpeople.com/sr.cgi/BioProjects - Joel On Mar 8, 2007, at 3:02 PM, Zagato wrote: > Hello, i'm trying to decide between BioJava and BioRuby for a work, > but i'm > a newbie, and doesn't exists a "table" that explanis what is the > better > choice an what are the differences :'(. > > By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with > BioRuby to get > lineage to poulate a BioSQL database on Postgres, is this > posibble?, how?. > Exists a form to load the BioSQL database from a .gbk, and asn > Files from a > genome automagicaly :-p ? > > Thanks and any help it's aprecciate. > > Alan Jairo Acosta > > -- > Farewell. > http://www.youtube.com/zagatogekko > ruby << __EOF__ > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > __EOF__ > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From zagato.gekko at gmail.com Fri Mar 9 14:53:32 2007 From: zagato.gekko at gmail.com (Zagato) Date: Fri, 9 Mar 2007 09:53:32 -0500 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> Message-ID: <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Thanks, it's a good start, for a newbie, but i still want to test, so i test BioRuby Vs BioJava, and BioRuby is more faster :D and less harder with the memory, i will try now with JRuby :-p, for enable JMS. In any case, i still want to know how to populate a BioSQL database with Ruby automatically and if i can read an ASN.1 file to extract the lineage. Lot of Thanks :D Alan Jairo Acosta On 3/8/07, Joel Dudley wrote: > > You may find this link useful: > > http://sciruby.codeforpeople.com/sr.cgi/BioProjects > > - Joel > > On Mar 8, 2007, at 3:02 PM, Zagato wrote: > > > Hello, i'm trying to decide between BioJava and BioRuby for a work, > > but i'm > > a newbie, and doesn't exists a "table" that explanis what is the > > better > > choice an what are the differences :'(. > > > > By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with > > BioRuby to get > > lineage to poulate a BioSQL database on Postgres, is this > > posibble?, how?. > > Exists a form to load the BioSQL database from a .gbk, and asn > > Files from a > > genome automagicaly :-p ? > > > > Thanks and any help it's aprecciate. > > > > Alan Jairo Acosta > > > > -- > > Farewell. > > http://www.youtube.com/zagatogekko > > ruby << __EOF__ > > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > > __EOF__ > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From mmhohman at northwestern.edu Tue Mar 13 05:23:11 2007 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Mon, 12 Mar 2007 22:23:11 -0700 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Message-ID: Hi Zagato, Why do you need to populate a BioSQL database, is the database an integration point with another BioSQL-compliant codebase? I have limited BioRuby expertise (what I know I know from writing unit tests for BioRuby long ago, and reading over the codebase just now), but AFAIK BioRuby does not support BioSQL, nor does it support ASN.1. You can however parse that genome in the GenBank file format as follows: genome = Bio::FlatFile.open(Bio::GenBank, "BA000002.gbk").entries[0] That returns you a Bio::GenBank object, which has the following methods you can play around with: ["acc_version", "accession", "accessions", "basecount", "circular", "comment", "common_name", "date", "definition", "division", "each_cds", "each_gene", "entry_id", "exists?", "features", "fetch", "get", "gi", "keywords", "length", "locus", "nalen", "naseq", "natype", "nid", "organism", "origin", "references", "segment", "seq", "seq_len", "source", "strand", "tags", "taxonomy", "vernacular_name", "version", "versions"] Hope that helps, Moses On Mar 9, 2007, at 6:53 AM, Zagato wrote: > Thanks, it's a good start, for a newbie, but i still want to test, > so i test > BioRuby Vs BioJava, and BioRuby is more faster :D and less harder > with the > memory, i will try now with JRuby :-p, for enable JMS. > In any case, i still want to know how to populate a BioSQL database > with > Ruby automatically and if i can read an ASN.1 file to extract the > lineage. > > Lot of Thanks :D > > Alan Jairo Acosta > > On 3/8/07, Joel Dudley wrote: >> >> You may find this link useful: >> >> http://sciruby.codeforpeople.com/sr.cgi/BioProjects >> >> - Joel >> >> On Mar 8, 2007, at 3:02 PM, Zagato wrote: >> >>> Hello, i'm trying to decide between BioJava and BioRuby for a work, >>> but i'm >>> a newbie, and doesn't exists a "table" that explanis what is the >>> better >>> choice an what are the differences :'(. >>> >>> By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with >>> BioRuby to get >>> lineage to poulate a BioSQL database on Postgres, is this >>> posibble?, how?. >>> Exists a form to load the BioSQL database from a .gbk, and asn >>> Files from a >>> genome automagicaly :-p ? >>> >>> Thanks and any help it's aprecciate. >>> >>> Alan Jairo Acosta >>> >>> -- >>> Farewell. >>> http://www.youtube.com/zagatogekko >>> ruby << __EOF__ >>> puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse >>> __EOF__ >>> _______________________________________________ >>> BioRuby mailing list >>> BioRuby at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/bioruby >> >> > > > -- > Farewell. > http://www.youtube.com/zagatogekko > ruby << __EOF__ > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > __EOF__ > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From mh6 at sanger.ac.uk Tue Mar 13 12:57:21 2007 From: mh6 at sanger.ac.uk (Michael Han) Date: Tue, 13 Mar 2007 12:57:21 +0000 Subject: [BioRuby] db/embl/embl.rb Message-ID: Hi, I think the bioruby embl parser is slightly broken with the last EMBL format. I did some changes to the embl.rb that should fix it. Could someone have a look at the changes? thanks, Michael ---------------------- db/embl/embl.rb ---------- # added the new fields to the id_line parser def id_line(key=nil) unless @data['ID'] tmp = Hash.new idline = fetch('ID').split(/; +/) tmp['ENTRY_NAME'], tmp['DATA_CLASS'] = idline[0].split(/ +/) tmp['SEQUENCE_VERSION'] = idline[1] tmp['MOLECULE_CLASS'] = idline[2] tmp['MOLECULE_TYPE'] = idline[3] tmp['DIVISION'] = idline[4] tmp['SEQUENCE_LENGTH'] = idline[5].strip.split(' ').first.to_i @data['ID'] = tmp end if key @data['ID'][key] else @data['ID'] end end # and for the sequence version def sv id_line('SEQUENCE_VERSION') end def version sv.split(" ")[1].to_i end From zagato.gekko at gmail.com Tue Mar 13 13:56:17 2007 From: zagato.gekko at gmail.com (Zagato) Date: Tue, 13 Mar 2007 08:56:17 -0500 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Message-ID: <98028b00703130656i6d702d2cj4fe3e04f50b00c31@mail.gmail.com> I need BioSQL thinking that in the future other software can access to the databse, and i belive that it's better use a Scheme Well-Defined. And the other hand, i need read ASN.1 because contains <> and i need this info to organize in a tree the genome of bacterias, by now i thinking in use a Regex to extract this. Thanks for the tips. Alan Jairo Acosta On 3/13/07, Moses M. Hohman wrote: > > Hi Zagato, > > Why do you need to populate a BioSQL database, is the database an > integration point with another BioSQL-compliant codebase? > > I have limited BioRuby expertise (what I know I know from writing > unit tests for BioRuby long ago, and reading over the codebase just > now), but AFAIK BioRuby does not support BioSQL, nor does it support > ASN.1. You can however parse that genome in the GenBank file format > as follows: > > genome = Bio::FlatFile.open(Bio::GenBank, "BA000002.gbk").entries[0] > > That returns you a Bio::GenBank object, which has the following > methods you can play around with: > > ["acc_version", "accession", "accessions", "basecount", "circular", > "comment", "common_name", "date", "definition", "division", > "each_cds", "each_gene", "entry_id", "exists?", "features", "fetch", > "get", "gi", "keywords", "length", "locus", "nalen", "naseq", > "natype", "nid", "organism", "origin", "references", "segment", > "seq", "seq_len", "source", "strand", "tags", "taxonomy", > "vernacular_name", "version", "versions"] > > Hope that helps, > > Moses > > On Mar 9, 2007, at 6:53 AM, Zagato wrote: > > > Thanks, it's a good start, for a newbie, but i still want to test, > > so i test > > BioRuby Vs BioJava, and BioRuby is more faster :D and less harder > > with the > > memory, i will try now with JRuby :-p, for enable JMS. > > In any case, i still want to know how to populate a BioSQL database > > with > > Ruby automatically and if i can read an ASN.1 file to extract the > > lineage. > > > > Lot of Thanks :D > > > > Alan Jairo Acosta > > > > On 3/8/07, Joel Dudley wrote: > >> > >> You may find this link useful: > >> > >> http://sciruby.codeforpeople.com/sr.cgi/BioProjects > >> > >> - Joel > >> > >> On Mar 8, 2007, at 3:02 PM, Zagato wrote: > >> > >>> Hello, i'm trying to decide between BioJava and BioRuby for a work, > >>> but i'm > >>> a newbie, and doesn't exists a "table" that explanis what is the > >>> better > >>> choice an what are the differences :'(. > >>> > >>> By now, i'm trying to read Aeropyrum_pernix/BA000002.asn with > >>> BioRuby to get > >>> lineage to poulate a BioSQL database on Postgres, is this > >>> posibble?, how?. > >>> Exists a form to load the BioSQL database from a .gbk, and asn > >>> Files from a > >>> genome automagicaly :-p ? > >>> > >>> Thanks and any help it's aprecciate. > >>> > >>> Alan Jairo Acosta > >>> > >>> -- > >>> Farewell. > >>> http://www.youtube.com/zagatogekko > >>> ruby << __EOF__ > >>> puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > >>> __EOF__ > >>> _______________________________________________ > >>> BioRuby mailing list > >>> BioRuby at lists.open-bio.org > >>> http://lists.open-bio.org/mailman/listinfo/bioruby > >> > >> > > > > > > -- > > Farewell. > > http://www.youtube.com/zagatogekko > > ruby << __EOF__ > > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > > __EOF__ > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From n at bioruby.org Tue Mar 13 17:10:32 2007 From: n at bioruby.org (Mitsuteru Nakao) Date: Wed, 14 Mar 2007 02:10:32 +0900 Subject: [BioRuby] db/embl/embl.rb In-Reply-To: References: Message-ID: <90ca35f70703131010j26d6dc79k1157d64a73cde5d4@mail.gmail.com> Hi Michael Han, Thank you for your bug report and fixed code suggestion. I fixed this bug for parsing EBML id line in release 89. You can get the fixed version from the bioruby CVS. 2007/3/13, Michael Han : > Hi, > > I think the bioruby embl parser is slightly broken with the last EMBL > format. > I did some changes to the embl.rb that should fix it. Best Mitsuteru - Mitsuteru Nakao, Ph.D. on behalf of the BioRuby Project n at bioruby.org http://bioruby.org * b-Src - Bioinformatics Packages Source Code Search Engine by gonzui From johncumbers at gmail.com Mon Mar 19 02:54:44 2007 From: johncumbers at gmail.com (John Cumbers) Date: Sun, 18 Mar 2007 22:54:44 -0400 Subject: [BioRuby] ISMB ECCB Student Symposium - Call for abstracts Message-ID: Dear friends and colleagues, This year the ISMB and ECCB conference (Intelligent Systems For Molecular Biology and European conference on Computational Biology) is in Vienna Austria, and the student council is hosting the 3rd annual symposium offering you the chance to present your work and network with other students working in computational biology. When: Saturday, July 21st, 2007. 8.30am - 5pm, the day before the main conference starts. You can vote for the keynote speakers here: http://www.surveymonkey.com/s.asp?u=242703462636 You can register here: http://www.events.mondial.at/ei/2007/ismbeccb2007/default.html. The cost is 55 Euro. Submit an abstract here: http://www.iscbsc.org/scs3/#abstracts Or download the poster here: http://www.iscbsc.org/scs3/posters/scs-3_poster_01.pdf Best wishes, John -- John Cumbers, Brown University, Biology and Medicine Box G-W, Providence, Rhode Island, 02912, USA Tel USA: +1 401 523 8190, Fax: +1 401 863-2166 UK to USA: 0207 617 7824 From trevor at corevx.com Fri Mar 23 00:44:10 2007 From: trevor at corevx.com (Trevor Wennblom) Date: Thu, 22 Mar 2007 19:44:10 -0500 Subject: [BioRuby] Next release? Message-ID: Hello all, What do we need to do to make BioRuby v1.1 happen?[1] I'm extremely interested in seeing a release along with more frequent minor-version releases.[2] Would it be possible to include more of us in the main development process? Could we tag releases ourselves? Presently I'm in talks with Chris D. at OBF about the possibility of migrating from CVS to Subversion. Also I wouldn't mind seeing a repository browser such as svnweb, Trac, or possibly Dev'il if that shapes up well.[3] What are your opinions on this? [1]: http://lists.open-bio.org/pipermail/bioruby/2006-December/ 000272.html [2]: http://lists.open-bio.org/pipermail/bioruby/2007-February/ 000277.html [3]: http://redhanded.hobix.com/inspect/rubiniusAndItsHelpfulDevIl.html From trevor at corevx.com Sun Mar 25 06:26:37 2007 From: trevor at corevx.com (Trevor Wennblom) Date: Sun, 25 Mar 2007 01:26:37 -0500 Subject: [BioRuby] Fork In-Reply-To: <45E9F78E.8040406@campus.iztacala.unam.mx> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com> <45E9F78E.8040406@campus.iztacala.unam.mx> Message-ID: <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> Judging by the overwhelming response that I've received over the past year (2006-2007) compared to the previous year (2005-2006) does this mean that's it's time for a fork? If it's time let's do it. Wake. Up. Trevor From jan.aerts at bbsrc.ac.uk Mon Mar 26 12:59:06 2007 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Mon, 26 Mar 2007 13:59:06 +0100 Subject: [BioRuby] Fork => suggestions In-Reply-To: <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com><45E9F78E.8040406@campus.iztacala.unam.mx> <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45104FB14C8@rie2ksrv1.ri.bbsrc.ac.uk> Trevor, I must admit that I stopped mailing the list months ago after not getting much response... I'm afraid that also included answering to other people's questions. Was thinking about some suggestions for a project like bioruby to keep people informed and make clear (or sure?) that it's very much alive. I believe I mentioned some/most of these in earlier posts way back, and many/most of these will be completely stupid (copyright: myself), but it might get people thinking a bit. Note that the _last_ thing I want to do is step on the toes of the real developers. Just read this as some thoughts during your coffee.... (1) bioruby board ----------------- As English is only my x-th language, I can't think of another word than 'board'. Wouldn't it be nice if there was a limited group of people (3 to 5) that would act as a central authority so to speak to represent bioruby. This 'board' would preferably consist of people from different continents. Some things that this group could do is: * make sure that questions on the mailing list get answered or at least directed to the right people for answering * make the end-decision on which new modules (from BiorubyExtensions, see below) should be added * discuss releases (2) BiorubyEdge aka BiorubyExtensions ------------------------------------- Purpose: to make clear what's in store for bioruby in the near future and to allow for preparing new classes for inclusion in bioruby. I suppose that more people will have ruby classes defined locally that are not really ready to be included in an 'official' repository like bioruby, but that could become candidates later on. I know I have. How about creating something like BiorubyExtensions, which would be like a waiting room for classes before they get into bioruby. If a class gets polished enough and ends up fitting into the official bioruby structure, it could be 'upgraded' to the main bioruby. On the other hand: it can also be removed from BiorubyExtensions instead if not supported or well-developed enough, of course. An example would be Bio::Graphics. Someone asked about that a while ago on the mailing list, and some people (including myself) might actually have a working class for this. It's just not polished enough and misses some functionality. And therefore a candidate for such an 'extensions' waiting room. (3) feature requests + bugs --------------------------- How about using the rubyforge system for bugs and feature requests? (This mainly means making it clear on the bioruby website to submit them on rubyforge...) (5) blog -------- I don't want to sound like trying to follow latest trends nilly-willy, but a bioruby blog by the board-thingy (see above) and/or developers (a) would make really clear to the community that people are working on bioruby, (b) give more background on the development and/or (c) could give additional examples on how to use it. (6) manuscript -------------- I believe bioruby needs a reference in a journal read by a large cross-section of bioinformaticians (Bioinformatics? BMC Bioinformatics?). I've actually worked on this about year ago with Toshiaki, but it kind-a got stranded in the end... Just to get some discussion started... Comments welcome. jan. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of > Trevor Wennblom > Sent: 25 March 2007 07:27 > To: bioruby at lists.open-bio.org > Subject: [BioRuby] Fork > > Judging by the overwhelming response that I've received over > the past year (2006-2007) compared to the previous year > (2005-2006) does this mean that's it's time for a fork? > > If it's time let's do it. > > Wake. Up. > > Trevor > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Tue Mar 27 05:24:14 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Tue, 27 Mar 2007 14:24:14 +0900 Subject: [BioRuby] Fork => suggestions In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45104FB14C8@rie2ksrv1.ri.bbsrc.ac.uk> References: <1ad8057e0703021842y683853f5k1c97dbf362f20dda@mail.gmail.com><45E9F78E.8040406@campus.iztacala.unam.mx> <99E854A1-8FA3-4301-8CF0-5CAB1B7FEB09@corevx.com> <84DA9D8AC9B05F4B889E7C70238CB45104FB14C8@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Trevor, Jan, Thank you for all of your discussions to make our bioruby community better. And, Pj, thank you for your kind personal mail. I'm very sorry that I couldn't spare enough time for the release management, but I'll work on bioruby extensively starting from tomorrow until April 1 to make the next release. Trevor, could you suspend your fork plan until my attempt fails? One more thing, do you think your modules are ready for the next release? Jan, your board plan (1) sounds nice as I'm not good in release management. I think face-to-face meeting will accelerate to make it possible, so if we could have BoF meeting during the BOSC 2007, it would be great. Everyone who wish to involved in the bioruby development and future planning, please consider to gather there. These days, I slowly worked on brushing up the bioruby shell to use with rails. I wish to figure out how it can be integrated with rails smoothly. I hope to provide repository which stores bioinformatics related rails plug-ins, rake tasks, models etc. so that user can develop your-own databases, web services and workflows easily utilizing the functionality of bioruby. This might also serve as Jan's plan (2). But I still not sure how it should be shaped. Switching towards svn may solve the part of technical problems, but, personally I want to wait until OS X includes svn by default. Does anyone know whether Leopard includes svn? I'll respond to mails stacking in my mail box as much as possible during this week. (3) future reqests + bugs I agree with utilizing rubyforge. Last year, I added some todo list there. Trevor, do you think Trac is better? (4) missing? :) (5) blog Writing English blogs must be a burden for me, but I'm happy to create links to yours at bioruby.org (6) manuscript Your draft was excellent but I want to rewrite it to cover various aspects that bioruby offers, and want to include future plans which may stand out the difference with other Open Bio* projects. Regards, Toshiaki Katayama On 2007/03/26, at 21:59, jan aerts (RI) wrote: > Trevor, > > I must admit that I stopped mailing the list months ago after not > getting much response... I'm afraid that also included answering to > other people's questions. > > Was thinking about some suggestions for a project like bioruby to keep > people informed and make clear (or sure?) that it's very much alive. I > believe I mentioned some/most of these in earlier posts way back, and > many/most of these will be completely stupid (copyright: myself), but it > might get people thinking a bit. Note that the _last_ thing I want to do > is step on the toes of the real developers. > > Just read this as some thoughts during your coffee.... > > (1) bioruby board > ----------------- > As English is only my x-th language, I can't think of another word than > 'board'. Wouldn't it be nice if there was a limited group of people (3 > to 5) that would act as a central authority so to speak to represent > bioruby. This 'board' would preferably consist of people from different > continents. Some things that this group could do is: > * make sure that questions on the mailing list get answered or at least > directed to the right people for answering > * make the end-decision on which new modules (from BiorubyExtensions, > see below) should be added > * discuss releases > > (2) BiorubyEdge aka BiorubyExtensions > ------------------------------------- > Purpose: to make clear what's in store for bioruby in the near future > and to allow for preparing new classes for inclusion in bioruby. > > I suppose that more people will have ruby classes defined locally that > are not really ready to be included in an 'official' repository like > bioruby, but that could become candidates later on. I know I have. How > about creating something like BiorubyExtensions, which would be like a > waiting room for classes before they get into bioruby. If a class gets > polished enough and ends up fitting into the official bioruby structure, > it could be 'upgraded' to the main bioruby. On the other hand: it can > also be removed from BiorubyExtensions instead if not supported or > well-developed enough, of course. > An example would be Bio::Graphics. Someone asked about that a while ago > on the mailing list, and some people (including myself) might actually > have a working class for this. It's just not polished enough and misses > some functionality. And therefore a candidate for such an 'extensions' > waiting room. > > > (3) feature requests + bugs > --------------------------- > How about using the rubyforge system for bugs and feature requests? > (This mainly means making it clear on the bioruby website to submit them > on rubyforge...) > > > (5) blog > -------- > I don't want to sound like trying to follow latest trends nilly-willy, > but a bioruby blog by the board-thingy (see above) and/or developers (a) > would make really clear to the community that people are working on > bioruby, (b) give more background on the development and/or (c) could > give additional examples on how to use it. > > > (6) manuscript > -------------- > I believe bioruby needs a reference in a journal read by a large > cross-section of bioinformaticians (Bioinformatics? BMC > Bioinformatics?). I've actually worked on this about year ago with > Toshiaki, but it kind-a got stranded in the end... > > Just to get some discussion started... Comments welcome. > > jan. > > > >> -----Original Message----- >> From: bioruby-bounces at lists.open-bio.org >> [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of >> Trevor Wennblom >> Sent: 25 March 2007 07:27 >> To: bioruby at lists.open-bio.org >> Subject: [BioRuby] Fork >> >> Judging by the overwhelming response that I've received over >> the past year (2006-2007) compared to the previous year >> (2005-2006) does this mean that's it's time for a fork? >> >> If it's time let's do it. >> >> Wake. Up. >> >> Trevor >> _______________________________________________ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Tue Mar 27 05:48:49 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Tue, 27 Mar 2007 14:48:49 +0900 Subject: [BioRuby] "Read an ASN.1 file" and "Using a BioSQL database" !!! In-Reply-To: References: <98028b00703081502p6277cc4h5bae0e0908b0fe89@mail.gmail.com> <98028b00703090653x1fc3567eyddf1f135d217f668@mail.gmail.com> Message-ID: On 2007/03/13, at 14:23, Moses M. Hohman wrote: > but AFAIK BioRuby does not support BioSQL, Currently it might be broken, but BioRuby supported BioSQL from the beginning of the BioSQL project which is developed during three BioHackathon meetings (2002, 2003). I wrote basic BioSQL module which support Cape Town schema (2002), but I was lazy to update it. However, AFAIK, RJP is working on ActiveRecord + BioSQL integration (2006, December) to replace my old one. Raoul, could you post your recent status on it? > nor does it support ASN.1. I think this is true. It seems that there is one project on ASN.1 at rubyforge. http://rubyforge.org/projects/net-asn1/ Toshiaki From n at bioruby.org Wed Mar 28 10:45:50 2007 From: n at bioruby.org (Mitsuteru Nakao) Date: Wed, 28 Mar 2007 19:45:50 +0900 Subject: [BioRuby] Errors from ruby test/runner.rb Message-ID: <90ca35f70703280345r2fec2a99rdaf93ec81ce16bf8@mail.gmail.com> Hi Trevor, I am going to check the unit tests for the next release. Please check error message below and attached errors from "% ruby -r lib/bio/util/restriction_enzyme/cut_symbol.rb test/runner.rb", and make sure test/runner.rb (and/or ruby install.rb test) to be "0 failures, 0 errors." ------ ruby test/runner.rb ------- % ruby test/runner.rb ./lib/bio/util/restriction_enzyme/single_strand/cut_locations_in_enzyme_notation.rb:51: uninitialized constant Bio::RestrictionEnzyme::SingleStrand::CutLocationsInEnzymeNotation::CutSymbol (NameError) from ./lib/bio/util/restriction_enzyme/single_strand.rb:14:in `require' from ./lib/bio/util/restriction_enzyme/single_strand.rb:14 from ./lib/bio/util/restriction_enzyme/double_stranded.rb:19:in `require' from ./lib/bio/util/restriction_enzyme/double_stranded.rb:19 from ./lib/bio/util/restriction_enzyme.rb:12:in `require' from ./lib/bio/util/restriction_enzyme.rb:12 from ./lib/bio/util/restriction_enzyme/cut_symbol.rb:14 from ./lib/bio/util/restriction_enzyme/range/sequence_range/calculated_cuts.rb:15:in `require' ... 25 levels... from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:198:in `[]' from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:198:in `run' from /opt/local/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' from test/runner.rb:10 Best, Mitsuteru - Mitsuteru Nakao Ph.D n at bioruby.org Kazusa DNA Research Institute mn at kazusa.or.jp -------------- next part -------------- Loaded suite . Started ..........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................EE.............................................................................................................................................................................................................................................................................................................................................................................................................................................EEEEEEEEEEEEEEEEEEEE..... Finished in 65.205477 seconds. 1) Error: test_dataset(Bio::TestSOFT): Errno::ENOENT: No such file or directory - ../../../data/soft/GSE3457_family_partial.soft ./test/unit/bio/db/test_soft.rb:22:in `readlines' ./test/unit/bio/db/test_soft.rb:22:in `setup' 2) Error: test_series(Bio::TestSOFT): Errno::ENOENT: No such file or directory - ../../../data/soft/GSE3457_family_partial.soft ./test/unit/bio/db/test_soft.rb:22:in `readlines' ./test/unit/bio/db/test_soft.rb:22:in `setup' 3) Error: test_argument_error(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 4) Error: test_complement(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 5) Error: test_contents(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 6) Error: test_primary(Bio::TestDoubleStrandedCutLocationPair): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair.rb:27:in `setup' 7) Error: test_argument_error(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 8) Error: test_complement(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 9) Error: test_contents(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 10) Error: test_primary(Bio::TestDoubleStrandedCutLocationPairInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_location_pair_in_enzyme_notation.rb:27:in `setup' 11) Error: test_complement(Bio::TestDoubleStrandedCutLocations): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup' 12) Error: test_contents(Bio::TestDoubleStrandedCutLocations): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup' 13) Error: test_primary(Bio::TestDoubleStrandedCutLocations): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations.rb:29:in `setup' 14) Error: test_complement(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 15) Error: test_complement_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 16) Error: test_complement_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 17) Error: test_contents(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 18) Error: test_primary(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 19) Error: test_primary_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 20) Error: test_primary_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 21) Error: test_to_array_index(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 22) Error: test_to_array_index_class(Bio::TestDoubleStrandedCutLocationsInEnzymeNotation): ArgumentError: Range is an invalid class type to initalize CutLocationPair. ./lib/bio/util/restriction_enzyme/double_stranded/cut_location_pair.rb:72:in `initialize' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `new' ./test/unit/bio/util/restriction_enzyme/double_stranded/test_cut_locations_in_enzyme_notation.rb:28:in `setup' 1282 tests, 2443 assertions, 0 failures, 22 errors From ngoto at gen-info.osaka-u.ac.jp Wed Mar 28 10:50:45 2007 From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa) Date: Wed, 28 Mar 2007 19:50:45 +0900 Subject: [BioRuby] Bug in writing PDB ATOM In-Reply-To: References: <45cd751d.28e949d0.4e3f.ffff9a4dSMTPIN_ADDED@mx.google.com> Message-ID: <20070328105022.9F2B71CBC54E@idnmail.gen-info.osaka-u.ac.jp> Hi, Yen-Ju, I changed pdb.rb in the CVS and the bug is fixed, although it may still fail in few exceptional ATOM/HETATM lines. http://code.open-bio.org/cgi/viewcvs.cgi/*checkout*/bioruby/lib/bio/db/pdb/pdb.rb?rev=HEAD&cvsroot=bioruby&content-type=text/plain Thank you, Naohisa Goto ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp On Sat, 10 Feb 2007 06:13:25 -0800 "Yen-Ju Chen" wrote: > On 2/9/07, GOTO Naohisa wrote: > > Hi, Yen-Ju, > > > > Which bioruby version do you use? > > By using CVS HEAD 'pdb.rb,v 1.16 2006/06/27 14:23:45', > > it seems fine. > > I tried both 1.0 and CVS. > And your example indeed works fine. > Here is the data and script I used: > > ATOM 1 CB TYR A 4 46.803 20.433 46.159 1.00130.00 > ATOM 2 CG TYR A 4 46.708 19.122 46.931 1.00130.00 > ATOM 3 CD1 TYR A 4 46.708 17.892 46.257 1.00130.00 > ATOM 4 CE1 TYR A 4 46.596 16.691 46.961 1.00130.00 > ATOM 5 CD2 TYR A 4 46.599 19.109 48.336 1.00130.00 > > ######### > require 'bio' > > file = File.new('a.pdb').gets(nil) > structure = Bio::PDB.new(file) > > structure.each do |model| > model.each do |chain| > chain.each do |residue| > residue.each do |atom| > atom.resSeq += 400 > end > end > end > end > > File.open('x.pdb', 'w') do |file| > file << structure.to_s > end > > Yen-Ju > > > > > #### sample script > > require 'bio' > > atom = Bio::PDB::Record::ATOM.new > > atom.serial = 61 > > atom.name = 'OD1' > > atom.altLoc = '' > > atom.resName = 'ASN' > > atom.chainID = 'A' > > atom.resSeq = 8 > > atom.iCode = '' > > atom.x = 102.025 > > atom.y = 27.929 > > atom.z = 144.984 > > atom.occupancy = 1.0 > > atom.tempFactor = 88.56 > > atom.segID = '' > > atom.element = 'O' > > atom.charge = '' > > print atom.to_s > > # "ATOM 61 OD1 ASN A 8 102.025 27.929 144.984 1.00 88.56 O \n" > > #### end of sample script > > > > However, it still fails in some rare cases. > > > > require 'bio' > > # record from PDB 1CX1 > > str = "ATOM 376 HH TYR A 25 " + > > "4.479 12.801 -3.919 1.00 1.72 H " > > atom = Bio::PDB::Record::ATOM.new.initialize_from_string(str) > > print atom.to_s > > # > > # "ATOM 376 HH TYR A 25 4.479 12.801 -3.919 1.00 1.72 H \n" > > # ^ an excess space!! > > > > I'll make changes in the CVS to give more accurate results, > > but it'll be still imperfect (becase of ambiguity, as Alex said). > > > > Thanks, > > > > Naohisa Goto > > ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp > > > > On Thu, 8 Feb 2007 14:54:09 -0800 > > "Yen-Ju Chen" wrote: > > > > > In bio/db/pdb/pdb.rb line 1019, > > > the ATOM entry is written as: > > > > > > sprintf("%-6s%5d %-4s%-1s%3s %-1s%4d%-1s > > > > > > It results an ATOM entry as: > > > ATOM 61 OD1 ASN A 8 102.025 27.929 144.984 1.00 88.56 O > > > > > > But the right ATOM entry should be > > > ATOM 61 OD1 ASN A 8 102.025 27.929 144.984 1.00 88.56 O > > > > > > Note there are 2 spaces after '61' and one space before 'ASN' > > > I change this line to: > > > > > > sprintf("%-6s%5d %-3s%-1s%3s %-1s%4d%-1s > > > > > > and it works fine now. > > > But I am new to Ruby and not familiar with the format yet. > > > > > > Yen-Ju > > > _______________________________________________ > > > BioRuby mailing list > > > BioRuby at lists.open-bio.org > > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > > > From ktym at hgc.jp Wed Mar 28 11:42:30 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 28 Mar 2007 20:42:30 +0900 Subject: [BioRuby] License Message-ID: Dear BioRuby developers, Few months ago, we made decision to change the license of BioRuby library from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby is also able to use BioRuby not be bothered by legal restrictions. We are now working on the next release and this is the time to complete changes on every modules. * Alex, could you agree with us to change the license of your PDB modules? * Fujita-san, Suga-san, could you agree with us to change the license of your HMMER module? * Shigenobu-san, could you agree with us to change the license of your Fastacmd module? Thanks in advance. Regards, Toshiaki Katayama From angel at mail.med.upenn.edu Wed Mar 28 12:33:22 2007 From: angel at mail.med.upenn.edu (Angel Pizarro) Date: Wed, 28 Mar 2007 08:33:22 -0400 Subject: [BioRuby] License In-Reply-To: References: Message-ID: I believe that a consistent license is best, but let's not let that be a barrier to release. Strictly speaking, GPL is not as restrictive as it perceived to be by the general public. For more information look here: http://www.sitepoint.com/article/public-license-explained What this means for Ruby (and Rails applications) is that unless you extend the GPL module in some way (for instance wrapping a C library in SWIG to derive a Ruby C extension or adding methods to a module/class) it is not effected by the GPL and can be released along with other licensing terms. Simply calling the methods of a module does not constitute a "derived work". Passing data between modules is also not considered a derived work. Cheers! -angel On 3/28/07, Toshiaki Katayama wrote: > > Dear BioRuby developers, > > Few months ago, we made decision to change the license of BioRuby library > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > is also able to use BioRuby not be bothered by legal restrictions. > > We are now working on the next release and this is the time to complete > changes on every modules. > > * Alex, could you agree with us to change the license of your PDB modules? > > * Fujita-san, Suga-san, could you agree with us to change the license of > your HMMER module? > > * Shigenobu-san, could you agree with us to change the license of your > Fastacmd module? > > Thanks in advance. > > Regards, > Toshiaki Katayama > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Thu Mar 29 13:16:09 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Thu, 29 Mar 2007 22:16:09 +0900 Subject: [BioRuby] License In-Reply-To: References: Message-ID: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> Moses, We realized that your codes licensed under the LGPL exists in the test/ subdirectory. Could you agree with us to change the license to Ruby's on following files? test/unit/bio/test_alignment.rb test/unit/bio/test_location.rb test/unit/bio/test_pathway.rb test/unit/bio/test_sequence.rb As for the other modules, we got very quick response from most of license holders that permit us to change the license of their modules. We, core team, appreciate your understanding and cooperations! Regards, Toshiaki Katayama On 2007/03/28, at 20:42, Toshiaki Katayama wrote: > Dear BioRuby developers, > > Few months ago, we made decision to change the license of BioRuby library > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > is also able to use BioRuby not be bothered by legal restrictions. > > We are now working on the next release and this is the time to complete > changes on every modules. > > * Alex, could you agree with us to change the license of your PDB modules? > > * Fujita-san, Suga-san, could you agree with us to change the license of your HMMER module? > > * Shigenobu-san, could you agree with us to change the license of your Fastacmd module? > > Thanks in advance. > > Regards, > Toshiaki Katayama > From zagato.gekko at gmail.com Thu Mar 29 22:15:47 2007 From: zagato.gekko at gmail.com (Zagato) Date: Thu, 29 Mar 2007 17:15:47 -0500 Subject: [BioRuby] License In-Reply-To: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> Message-ID: <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Hello everybody... Just for curiosity I wondering: ?what are the advantages or disadvantages of using Ruby Vs LGPL?... thinking in final users like me ! ?Somebody can please give an explain of how affect this changes for good or bad to the users...? Lot of thanks :D Alan Jairo Acosta Cali - Colombia On 3/29/07, Toshiaki Katayama wrote: > > Moses, > > We realized that your codes licensed under the LGPL exists in the test/ > subdirectory. > Could you agree with us to change the license to Ruby's on following > files? > > test/unit/bio/test_alignment.rb > test/unit/bio/test_location.rb > test/unit/bio/test_pathway.rb > test/unit/bio/test_sequence.rb > > As for the other modules, we got very quick response from most of license > holders that permit us to change the license of their modules. > We, core team, appreciate your understanding and cooperations! > > Regards, > Toshiaki Katayama > > > On 2007/03/28, at 20:42, Toshiaki Katayama wrote: > > > Dear BioRuby developers, > > > > Few months ago, we made decision to change the license of BioRuby > library > > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > > is also able to use BioRuby not be bothered by legal restrictions. > > > > We are now working on the next release and this is the time to complete > > changes on every modules. > > > > * Alex, could you agree with us to change the license of your PDB > modules? > > > > * Fujita-san, Suga-san, could you agree with us to change the license of > your HMMER module? > > > > * Shigenobu-san, could you agree with us to change the license of your > Fastacmd module? > > > > Thanks in advance. > > > > Regards, > > Toshiaki Katayama > > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__ From ktym at hgc.jp Fri Mar 30 04:32:34 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 30 Mar 2007 13:32:34 +0900 Subject: [BioRuby] License In-Reply-To: <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Message-ID: Advantage: * we (developers and users) can be free from this kind of boring comparison. :) Disadvantage: * none. Note that, I thank and respect the GNU project and the spirit, although. Toshiaki On 2007/03/30, at 7:15, Zagato wrote: > Hello everybody... > > Just for curiosity I wondering: ?what are the advantages or disadvantages of using Ruby Vs LGPL?... thinking in final users like me ! > > ?Somebody can please give an explain of how affect this changes for good or bad to the users...? > > Lot of thanks :D > > Alan Jairo Acosta > Cali - Colombia > > On 3/29/07, Toshiaki Katayama wrote: Moses, > > We realized that your codes licensed under the LGPL exists in the test/ subdirectory. > Could you agree with us to change the license to Ruby's on following files? > > test/unit/bio/test_alignment.rb > test/unit/bio/test_location.rb > test/unit/bio/test_pathway.rb > test/unit/bio/test_sequence.rb > > As for the other modules, we got very quick response from most of license holders that permit us to change the license of their modules. > We, core team, appreciate your understanding and cooperations! > > Regards, > Toshiaki Katayama > > > On 2007/03/28, at 20:42, Toshiaki Katayama wrote: > > > Dear BioRuby developers, > > > > Few months ago, we made decision to change the license of BioRuby library > > from LGPL to Ruby's (same terms as Ruby) so that user who can use Ruby > > is also able to use BioRuby not be bothered by legal restrictions. > > > > We are now working on the next release and this is the time to complete > > changes on every modules. > > > > * Alex, could you agree with us to change the license of your PDB modules? > > > > * Fujita-san, Suga-san, could you agree with us to change the license of your HMMER module? > > > > * Shigenobu-san, could you agree with us to change the license of your Fastacmd module? > > > > Thanks in advance. > > > > Regards, > > Toshiaki Katayama > > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > -- > Farewell. > http://www.youtube.com/zagatogekko > ruby << __EOF__ > puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse > __EOF__ From trevor at corevx.com Fri Mar 30 06:14:13 2007 From: trevor at corevx.com (Trevor Wennblom) Date: Fri, 30 Mar 2007 01:14:13 -0500 Subject: [BioRuby] License In-Reply-To: References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Message-ID: On Mar 29, 2007, at 11:32 PM, Toshiaki Katayama wrote: > Advantage: > * we (developers and users) can be free from this kind of boring > comparison. :) > > Disadvantage: > * none. Just about to go to bed so this will be brief. The biggest advantage to moving to the Ruby license, which is essentially the MIT license,[1] is that is compatible with Ruby itself. What an honor it would be - though not necessarily desired - to be included in the main Ruby package itself as a standard library. The least we can do is acknowledge the word "Ruby" is itself in the name of the project. Let us not forget that the Ruby license is completely compatible with the GPL according to the Free Software Foundation.[2] Trevor [1]: http://en.wikipedia.org/wiki/MIT_License [2]: http://en.wikipedia.org/wiki/Ruby_License From zagato.gekko at gmail.com Fri Mar 30 16:41:25 2007 From: zagato.gekko at gmail.com (Zagato) Date: Fri, 30 Mar 2007 11:41:25 -0500 Subject: [BioRuby] License In-Reply-To: References: <9F213B54-524A-416A-8A77-6ADAC24632DF@hgc.jp> <98028b00703291515t3d191937h4cb6f869faafbe48@mail.gmail.com> Message-ID: <98028b00703300941p778e25a1n630e943d39fcb1aa@mail.gmail.com> Thanks for the comments about my question, i think now that Ruby's License it's a good choice :D!!! Bye Alan Jairo Acosta Cali - Colombia On 3/30/07, Trevor Wennblom wrote: > > > On Mar 29, 2007, at 11:32 PM, Toshiaki Katayama wrote: > > > Advantage: > > * we (developers and users) can be free from this kind of boring > > comparison. :) > > > > Disadvantage: > > * none. > > > Just about to go to bed so this will be brief. > > The biggest advantage to moving to the Ruby license, which is > essentially the MIT license,[1] is that is compatible with Ruby > itself. What an honor it would be - though not necessarily desired - > to be included in the main Ruby package itself as a standard > library. The least we can do is acknowledge the word "Ruby" is > itself in the name of the project. > > Let us not forget that the Ruby license is completely compatible with > the GPL according to the Free Software Foundation.[2] > > Trevor > > [1]: http://en.wikipedia.org/wiki/MIT_License > [2]: http://en.wikipedia.org/wiki/Ruby_License > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- Farewell. http://www.youtube.com/zagatogekko ruby << __EOF__ puts [ 111, 116, 97, 103, 97, 90 ].collect{|v| v.chr}.join.reverse __EOF__