From tomoakin at kenroku.kanazawa-u.ac.jp Fri Feb 6 00:27:10 2009 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Fri, 6 Feb 2009 14:27:10 +0900 Subject: [BioRuby] GFF3 status (possible bug?) In-Reply-To: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp> References: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <84B18E0F-3FF8-42E7-99F1-72DF2A96DFFE@kenroku.kanazawa-u.ac.jp> Hi, Today, I got the code from git and tried parsing a GFF3 file (from TAIR8). a code fragment open(transcriptgff,"r").each_line do |gffline| record=Bio::GFF::GFF3::Record.new(gffline) p record curid = record.id p curid ... results # /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in `[]': can't convert String into Integer (TypeError) from /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in `id' It seems that the @attributes is now not a hash, but an array of key, value pairs. On the otherhand, id expects it to be a hash. The code in gff.rb looks # Represents a single line of a GFF3-formatted file. # See Bio::GFF::GFF3 for more information. class Record < GFF2::Record include GFF3::Escape # shortcut to the ID attribute def id @attributes['ID'] end I suppose this is reminiscent of the GFF when attributes were a hash. The change from hash to array is presumably to because the key may not be unique in attributes. A way straighten may be create key to [array of values] hash when the same key are specified more than once. (when multiple values for each of key are given it should be represented as key to [array of arrays]. Otherwise, we may define id to scan the array as def id val = nil @attributes.each do |keyval| if(keyval[0] == 'ID') val = keyval[1] break end end val end It is also nice if a function to get the attribute value for a specific key is provided. This should be easier with key to array of values approach, although the order of attributes will not be conserved. Which way are you going? I hope this can be corrected before 1.3.0 release. Best wishes -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From missy at be.to Fri Feb 6 04:44:41 2009 From: missy at be.to (MISHIMA, Hiroyuki) Date: Fri, 06 Feb 2009 18:44:41 +0900 Subject: [BioRuby] biofetch server error on bioruby.org Message-ID: <498C0689.9060300@be.to> Dear list, Now http://bioruby.org/cgi-bin/biofetch.rb seems not to work (Internal Server Error). Is this service still maintained? If not, for BioRuby 1.3.0 release, etc/bioinformatics/seqdatabase.ini could be updated by replacing "http://bioruby.org/cgi-bin/biofetch.rb" with "http://www.ebi.ac.uk/cgi-bin/dbfetch". I am sorry if this questions is a FAQ. Thanks, Hiro -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From ktym at hgc.jp Fri Feb 6 05:10:14 2009 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 6 Feb 2009 19:10:14 +0900 Subject: [BioRuby] biofetch server error on bioruby.org In-Reply-To: <498C0689.9060300@be.to> References: <498C0689.9060300@be.to> Message-ID: Dear Hiro, I'm sorry about this problem. I'll fix the server within a week. Migration of bioruby.org, bioruby.open-bio.org and the wiki sites are also scheduled. Sorry for any inconveniences it may have caused. Regards, Toshiaki Katayama On 2009/02/06, at 18:44, MISHIMA, Hiroyuki wrote: > Dear list, > > Now http://bioruby.org/cgi-bin/biofetch.rb seems not to work (Internal > Server Error). Is this service still maintained? > > If not, for BioRuby 1.3.0 release, etc/bioinformatics/seqdatabase.ini > could be updated by replacing "http://bioruby.org/cgi-bin/biofetch.rb" > with "http://www.ebi.ac.uk/cgi-bin/dbfetch". > > I am sorry if this questions is a FAQ. > > Thanks, > > Hiro > > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ngoto at gen-info.osaka-u.ac.jp Fri Feb 6 06:29:40 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Fri, 6 Feb 2009 20:29:40 +0900 Subject: [BioRuby] GFF3 status (possible bug?) In-Reply-To: <84B18E0F-3FF8-42E7-99F1-72DF2A96DFFE@kenroku.kanazawa-u.ac.jp> References: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp> <84B18E0F-3FF8-42E7-99F1-72DF2A96DFFE@kenroku.kanazawa-u.ac.jp> Message-ID: <20090206112940.B83121CBC3AB@idnmail.gen-info.osaka-u.ac.jp> Hi, Thank you for reporting bugs. On Fri, 6 Feb 2009 14:27:10 +0900 Tomoaki NISHIYAMA wrote: > Hi, > > Today, I got the code from git and tried parsing a GFF3 file (from > TAIR8). > > a code fragment > > open(transcriptgff,"r").each_line do |gffline| > record=Bio::GFF::GFF3::Record.new(gffline) > p record > curid = record.id > p curid > ... > > results > > # @strand="+", @feature="gene", @score=nil, @source="TAIR8", > @attributes=[["ID", "AT1G01010"], ["Note", "protein_coding_gene"], > ["Name", "AT1G01010"]], @end=5899, @seqname="Chr1"> > /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in `[]': can't > convert String into Integer (TypeError) > from /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in > `id' > > It seems that the @attributes is now not a hash, but an array of key, > value pairs. @attributes is now an array of [ key, value ] pairs. See doc/Changes-1.3.rdoc about the changes. > On the otherhand, id expects it to be a hash. > > The code in gff.rb looks > > # Represents a single line of a GFF3-formatted file. > # See Bio::GFF::GFF3 for more information. > class Record < GFF2::Record > > include GFF3::Escape > > # shortcut to the ID attribute > def id > @attributes['ID'] > end > > I suppose this is reminiscent of the GFF when attributes were a hash. You are right. This is apparently a bug. I've just fixed. http://github.com/bioruby/bioruby/commit/5258d88ef98a12fd7829eb86aa8664a18a672a43 > The change from hash to array is presumably to because > the key may not be unique in attributes. That's a reason why the @attributes is changed. > A way straighten may be create key to [array of values] hash when the > same key are > specified more than once. (when multiple values for each of key are > given it should be > represented as key to [array of arrays]. > > Otherwise, we may define id to scan the array as > def id > val = nil > @attributes.each do |keyval| > if(keyval[0] == 'ID') > val = keyval[1] > break > end > end > val > end Ruby has a support for an array of [ key, value ] pairs. See Ruby reference manual for Array#assoc. For example, key, val = @attributes.assoc('ID') This is almost the same as key, val = @attributes.find { |a| a[0] == 'ID' } > It is also nice if a function to get the attribute value for > a specific key is provided. New methods to set/get/replace attributes have been added. See doc/Changes-1.3.rdoc and RDoc of Bio::GFF::GFF2 and Bio::GFF::GFF3 for details. > This should be easier with key to > array of values approach, although the order of attributes > will not be conserved. I think it is better keeping the order of attributes, and I determined to use an array containing [ key, value ] pairs. > > Which way are you going? > > I hope this can be corrected before 1.3.0 release. > > Best wishes > > -- > Tomoaki NISHIYAMA > > Advanced Science Research Center, > Kanazawa University, > 13-1 Takara-machi, > Kanazawa, 920-0934, Japan > Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Sun Feb 15 08:36:16 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 15 Feb 2009 14:36:16 +0100 Subject: [BioRuby] Added Staden io_lib support for Ruby Message-ID: <20090215133616.GA6278@thebird.nl> Hi, For Ruby I have added support for reading and writing trace files, using the Staden io_lib libraries (part of the Staden package). Now you can easily parse those files: See the API at http://thebird.nl/apidoc/biolib/index.html I hope it is useful to someone. Pj. From georgkam at gmail.com Tue Feb 17 10:39:28 2009 From: georgkam at gmail.com (George Githinji) Date: Tue, 17 Feb 2009 18:39:28 +0300 Subject: [BioRuby] google summer of code Message-ID: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> Just wondering.... Are the bioruby developers keen on Google summer of code and is there anyone who can avail themselves as a mentor? Are there some projects objectives that can be met through a summer of code opening? Thanks -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ From adamnkraut at gmail.com Tue Feb 17 11:01:36 2009 From: adamnkraut at gmail.com (Adam) Date: Tue, 17 Feb 2009 11:01:36 -0500 Subject: [BioRuby] google summer of code In-Reply-To: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> Message-ID: <134ede0b0902170801m8974dc4m2c22ef3210ab3643@mail.gmail.com> Off of the top of my head here are some things in BioRuby that might be nice SoC projects: - JRuby/Ruby1.9 compatibility - Optionally allow libxml to override REXML for Blast parsing and other places XML is used - Port some existing BioPerl modules that people deem useful - Docs, docs, and more docs! I'm sure others can thing of some nice student projects as well. Let's hear them! -Adam On Tue, Feb 17, 2009 at 10:39 AM, George Githinji wrote: > Just wondering.... Are the bioruby developers keen on Google summer of code > and is there anyone who can avail themselves as a mentor? > > Are there some projects objectives that can be met through a summer of code > opening? > > Thanks > > > > > -- > --------------- > Sincerely > George > > Skype: george_g2 > Blog: http://biorelated.wordpress.com/ > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at gmail.com Tue Feb 17 11:06:51 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Tue, 17 Feb 2009 16:06:51 +0000 Subject: [BioRuby] google summer of code In-Reply-To: <134ede0b0902170801m8974dc4m2c22ef3210ab3643@mail.gmail.com> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> <134ede0b0902170801m8974dc4m2c22ef3210ab3643@mail.gmail.com> Message-ID: <4c7507a70902170806h1adf5b78j521054be8811f8b@mail.gmail.com> Although probably not for summer of code: tutorials! Not documentation of the classes in bioruby, but tutorials on how to do certain bioinformatics analyses using bioruby (and likely to cover more than just one class). Similar to the bioperl HOWTOs at http://www.bioperl.org/wiki/HOWTOs Having some walkthroughs for certain types of analysis can really draw in the crowds, I think. jan. 2009/2/17 Adam > Off of the top of my head here are some things in BioRuby that might > be nice SoC projects: > > - JRuby/Ruby1.9 compatibility > - Optionally allow libxml to override REXML for Blast parsing and > other places XML is used > - Port some existing BioPerl modules that people deem useful > - Docs, docs, and more docs! > > I'm sure others can thing of some nice student projects as well. > Let's hear them! > > -Adam > > On Tue, Feb 17, 2009 at 10:39 AM, George Githinji > wrote: > > Just wondering.... Are the bioruby developers keen on Google summer of > code > > and is there anyone who can avail themselves as a mentor? > > > > Are there some projects objectives that can be met through a summer of > code > > opening? > > > > Thanks > > > > > > > > > > -- > > --------------- > > Sincerely > > George > > > > Skype: george_g2 > > Blog: http://biorelated.wordpress.com/ > > _______________________________________________ > > 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 czmasek at burnham.org Tue Feb 17 13:37:12 2009 From: czmasek at burnham.org (Christian M Zmasek) Date: Tue, 17 Feb 2009 10:37:12 -0800 Subject: [BioRuby] google summer of code In-Reply-To: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> Message-ID: <499B03D8.7000309@burnham.org> Hi, Yes, I am intending to propose/(co-)mentor an implementation of phyloXML (http://www.phyloxml.org/) in BioRuby (similar to the BioPerl version [http://www.bioperl.org/wiki/Phyloxml_Project_Demo] which was a SoC project in 2008 sponsored by Nescent [http://www.nescent.org/index.php]). I hope to realize this either under Nescent's SoC 2009 or a Bio* SoC (if there is to be one). Christian George Githinji wrote: > Just wondering.... Are the bioruby developers keen on Google summer of code > and is there anyone who can avail themselves as a mentor? > > Are there some projects objectives that can be met through a summer of code > opening? > > Thanks > > > > > From czmasek at burnham.org Wed Feb 18 22:41:13 2009 From: czmasek at burnham.org (Christian M Zmasek) Date: Wed, 18 Feb 2009 19:41:13 -0800 Subject: [BioRuby] google summer of code In-Reply-To: <20090217212754.GA23447@thebird.nl> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> <499B03D8.7000309@burnham.org> <20090217212754.GA23447@thebird.nl> Message-ID: <499CD4D9.2070203@burnham.org> Hi, Pjotr: Unfortunately, I am not going to Japan. Actually, last year, a phyloXML implementation in BioPerl was sponsored by Nescent. So, it might have a chance (even though, last year, the corresponding BioRuby project was indeed rejected). Christian Pjotr Prins wrote: > Hi Christian, > > I think we need a Bio* SoC - the Nescent's one is focussed on > phylogenetics. Not sure who would be the best to drive this. Are you > going to Japan, could you champion this idea? > > Pj. > > On Tue, Feb 17, 2009 at 10:37:12AM -0800, Christian M Zmasek wrote: > >> Hi, >> >> Yes, I am intending to propose/(co-)mentor an implementation of >> phyloXML (http://www.phyloxml.org/) in BioRuby (similar to the BioPerl >> version [http://www.bioperl.org/wiki/Phyloxml_Project_Demo] which was a >> SoC project in 2008 sponsored by Nescent >> [http://www.nescent.org/index.php]). >> I hope to realize this either under Nescent's SoC 2009 or a Bio* SoC (if >> there is to be one). >> >> Christian >> >> >> >> George Githinji wrote: >> >>> Just wondering.... Are the bioruby developers keen on Google summer of code >>> and is there anyone who can avail themselves as a mentor? >>> >>> Are there some projects objectives that can be met through a summer of code >>> opening? >>> >>> Thanks >>> >>> >>> >>> >>> >>> >> _______________________________________________ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> From pjotr.public14 at thebird.nl Thu Feb 19 02:25:52 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 19 Feb 2009 08:25:52 +0100 Subject: [BioRuby] google summer of code In-Reply-To: <499CD4D9.2070203@burnham.org> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> <499B03D8.7000309@burnham.org> <20090217212754.GA23447@thebird.nl> <499CD4D9.2070203@burnham.org> Message-ID: <20090219072552.GA5177@thebird.nl> The latest is that Hilmar is going to organise a Bio* initiative for the combined Bio* languages under the OBF! That is good news, it means we have a high chance of getting a Bio* Google of Summer Code project with one or more slots for BioRuby initiatives. Examples of templates are here: http://hackathon.nescent.org/ The SoC is about coding - not documentation. And the project has to be interesting from a coding point of view. Real impact helps too. Pj. From ngoto at gen-info.osaka-u.ac.jp Tue Feb 24 11:39:48 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Wed, 25 Feb 2009 01:39:48 +0900 Subject: [BioRuby] BioRuby 1.3.0 is released Message-ID: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> Hi all, We are pleased to announce the release of BioRuby 1.3.0. The archive is available at: http://bioruby.org/archive/bioruby-1.3.0.tar.gz Web page: http://bioruby.org/ http://bioruby.open-bio.org/ API documentation: http://bioruby.org/rdoc/ Bug report: http://rubyforge.org/projects/bioruby/ (Updating of http://bioruby.rubyforge.org/ is still in progress. Please wait for a moment.) We also put RubyGems pacakge at RubyForge as always. You can easily install by using RubyGems. % sudo gem install bio You can also obtain bioruby gem file from bioruby.org. http://bioruby.org/archive/gems/bio-1.3.0.gem Here is a brief summary of changes. * Support for GenBank/EMBL formatted sequence output with improvements of Bio::Sequence. * BioSQL support is completely rewritten by using ActiveRecord. * Bio::Blast bug fixes and improvements. * Bio::GFF::GFF2 and Bio::GFF::GFF3 improvements. * Bio::Locations improvements. * New classes and modules. * Bio::Hinv * Bio::NCBI::REST * Bio::PAML::Codeml * Bio::TogoWS::REST In addition, many changes have been made, including incompatible changes. For more information, you can see summary of changes at http://github.com/bioruby/bioruby/blob/e04da7a1e709195d0b3e957491e76e50af32e96d/doc/Changes-1.3.rdoc and ChangeLog at http://github.com/ngoto/bioruby/blob/27a31e1fa7e916ee2af09eeba992eea5a3ca6fbd/ChangeLog In ChangeLog, the release date is described as 20 Feb 2009, which indicates frozen date of the archive. I'm sorry I took much time for the final check of the archive contents. Hope you enjoy. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From jan.aerts at gmail.com Tue Feb 24 12:02:08 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Tue, 24 Feb 2009 17:02:08 +0000 Subject: [BioRuby] BioRuby 1.3.0 is released In-Reply-To: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <4c7507a70902240902t426073e2mdc2c4618c7c7e918@mail.gmail.com> Congratulations! Thanks Goto-san and others for all the effort you've put in! jan. 2009/2/24 Naohisa Goto > Hi all, > > We are pleased to announce the release of BioRuby 1.3.0. > > The archive is available at: > http://bioruby.org/archive/bioruby-1.3.0.tar.gz > > Web page: > http://bioruby.org/ > http://bioruby.open-bio.org/ > API documentation: > http://bioruby.org/rdoc/ > Bug report: > http://rubyforge.org/projects/bioruby/ > > (Updating of http://bioruby.rubyforge.org/ is still > in progress. Please wait for a moment.) > > We also put RubyGems pacakge at RubyForge as always. > You can easily install by using RubyGems. > % sudo gem install bio > > You can also obtain bioruby gem file from bioruby.org. > http://bioruby.org/archive/gems/bio-1.3.0.gem > > Here is a brief summary of changes. > > * Support for GenBank/EMBL formatted sequence output with > improvements of Bio::Sequence. > * BioSQL support is completely rewritten by using ActiveRecord. > * Bio::Blast bug fixes and improvements. > * Bio::GFF::GFF2 and Bio::GFF::GFF3 improvements. > * Bio::Locations improvements. > * New classes and modules. > * Bio::Hinv > * Bio::NCBI::REST > * Bio::PAML::Codeml > * Bio::TogoWS::REST > > In addition, many changes have been made, including incompatible changes. > For more information, you can see summary of changes at > > http://github.com/bioruby/bioruby/blob/e04da7a1e709195d0b3e957491e76e50af32e96d/doc/Changes-1.3.rdoc > > and ChangeLog at > > > http://github.com/ngoto/bioruby/blob/27a31e1fa7e916ee2af09eeba992eea5a3ca6fbd/ChangeLog > > In ChangeLog, the release date is described as 20 Feb 2009, which > indicates frozen date of the archive. I'm sorry I took much time > for the final check of the archive contents. > > Hope you enjoy. > > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Tue Feb 24 13:52:17 2009 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 25 Feb 2009 03:52:17 +0900 Subject: [BioRuby] BioRuby 1.3.0 is released In-Reply-To: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> Goto-san, Thank you for your wonderful works on this release. Just note that we've updated the BioRuby web sites: > Web page: > http://bioruby.org/ This site is our project top page as in the past. > http://bioruby.open-bio.org/ This remains as our mirror site. The new site design had actually been at the mirror site for one year and we finally bring it to the main site (beautiful icons are courtesy of Okamoto-san). Additionally, I have edited the structure of our Wiki site at http://bioruby.open-bio.org/wiki/ extensively to clarify the contents in it. I've also added a new page for BioRuby on Rails. Regards, Toshiaki Katayama On 2009/02/25, at 1:39, Naohisa Goto wrote: > Hi all, > > We are pleased to announce the release of BioRuby 1.3.0. > > The archive is available at: > http://bioruby.org/archive/bioruby-1.3.0.tar.gz > > Web page: > http://bioruby.org/ > http://bioruby.open-bio.org/ > API documentation: > http://bioruby.org/rdoc/ > Bug report: > http://rubyforge.org/projects/bioruby/ > > (Updating of http://bioruby.rubyforge.org/ is still > in progress. Please wait for a moment.) > > We also put RubyGems pacakge at RubyForge as always. > You can easily install by using RubyGems. > % sudo gem install bio > > You can also obtain bioruby gem file from bioruby.org. > http://bioruby.org/archive/gems/bio-1.3.0.gem > > Here is a brief summary of changes. > > * Support for GenBank/EMBL formatted sequence output with > improvements of Bio::Sequence. > * BioSQL support is completely rewritten by using ActiveRecord. > * Bio::Blast bug fixes and improvements. > * Bio::GFF::GFF2 and Bio::GFF::GFF3 improvements. > * Bio::Locations improvements. > * New classes and modules. > * Bio::Hinv > * Bio::NCBI::REST > * Bio::PAML::Codeml > * Bio::TogoWS::REST > > In addition, many changes have been made, including incompatible changes. > For more information, you can see summary of changes at > http://github.com/bioruby/bioruby/blob/e04da7a1e709195d0b3e957491e76e50af32e96d/doc/Changes-1.3.rdoc > > and ChangeLog at > > http://github.com/ngoto/bioruby/blob/27a31e1fa7e916ee2af09eeba992eea5a3ca6fbd/ChangeLog > > In ChangeLog, the release date is described as 20 Feb 2009, which > indicates frozen date of the archive. I'm sorry I took much time > for the final check of the archive contents. > > Hope you enjoy. > > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From marc.hoeppner at molbio.su.se Wed Feb 25 02:14:40 2009 From: marc.hoeppner at molbio.su.se (Marc Hoeppner) Date: Wed, 25 Feb 2009 08:14:40 +0100 Subject: [BioRuby] Problem with PAML wrapper In-Reply-To: <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> Message-ID: <49A4EFE0.8030908@molbio.su.se> Hi, now with vers. 1.3 released (congrats on that by the way!), I was hoping to speed up some analyses by using the Bio::PAML module. However, I can't get it to work... Ruby info: ruby 1.8.6 (2007-03-13 patchlevel 0) [universal-darwin8.0] on a Macbook, Os X 10.5 This is what I tried: 1) read in a fasta file -> to Bio::Alignment::OriginalAlignment Verified the object (i.e. alingment.each_pair produces what it should, so I am assuming that step was successful) 2) read in a newick-type tree (with branch lengths.. ) and converted it to Bio::Tree - again, printed it out to see if it worked, and it did. 3) Verified that taxon labels in both files/objects were identical 4) Verified that all the sequences in the alignment were in fact of equal lengths I then tried to use the module as described: baseml = Bio::PAML::Baseml.new report = baseml.query(alignment,tree) -> nothing happens, i.e. program just exists normally, report.to_yaml shows an empty object. In order to confirm that PAML was working and that the data is, in principle, compatible with Baseml, I created a normal ctl file and ran the whole analysis from command line. And that worked. So I then tried to do it the less sophisticated way: baseml = Bio::PAML::Baseml.new baseml.run(my_local_ctl_file) Again, nothing happened (should print out the results to the screen, as I understand it). Any suggestions on what I am doing wrong here? I suspect a problem with the creation of the temporary folder/files, but frankly don't know enough about the details to follow up on that. Also, I would guess that such issues were addressed when developing the module (?). Cheers, Marc From ngoto at gen-info.osaka-u.ac.jp Wed Feb 25 05:24:27 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Wed, 25 Feb 2009 19:24:27 +0900 Subject: [BioRuby] Problem with PAML wrapper In-Reply-To: <49A4EFE0.8030908@molbio.su.se> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> <49A4EFE0.8030908@molbio.su.se> Message-ID: <20090225102427.DAB051CBC3DA@idnmail.gen-info.osaka-u.ac.jp> Hi, On Wed, 25 Feb 2009 08:14:40 +0100 Marc Hoeppner wrote: > Hi, > > now with vers. 1.3 released (congrats on that by the way!), I was hoping > to speed up some analyses by using the Bio::PAML module. However, I > can't get it to work... > > Ruby info: > ruby 1.8.6 (2007-03-13 patchlevel 0) [universal-darwin8.0] > on a Macbook, Os X 10.5 > > This is what I tried: > > 1) read in a fasta file -> to Bio::Alignment::OriginalAlignment > Verified the object (i.e. alingment.each_pair produces what it should, > so I am assuming that step was successful) > 2) read in a newick-type tree (with branch lengths.. ) and converted it > to Bio::Tree - again, printed it out to see if it worked, and it did. > 3) Verified that taxon labels in both files/objects were identical > 4) Verified that all the sequences in the alignment were in fact of > equal lengths First, please check that the command "baseml" exists in the PATH directory. If not, you must specify the location of "baseml" binary. For example, baseml = Bio::PAML::Baseml.new("/home/ngoto/paml/bin/baseml") > I then tried to use the module as described: > > baseml = Bio::PAML::Baseml.new > report = baseml.query(alignment,tree) > > -> nothing happens, i.e. program just exists normally, report.to_yaml > shows an empty object. Unfortunately, Bio::PAML::Baseml::Report is still under construction, and it always returns an empty object now. Because PAML results are too complex to parse, I could not write parsing routine yet. In the future, above should work. Currently, you can only get raw results as strings by using Bio::Baseml#report and Bio::Baseml#supplemental_outputs. baseml = Bio::PAML::Baseml.new report = baseml.query(alignment,tree) # Now, the above "report" is only a dummy object. # Shows the output of baseml p baseml.output # Shows supplemental outputs of baseml p baseml.supplemental_ouputs > In order to confirm that PAML was working and that the data is, in > principle, compatible with Baseml, I created a normal ctl file and ran > the whole analysis from command line. And that worked. > > So I then tried to do it the less sophisticated way: > > baseml = Bio::PAML::Baseml.new > baseml.run(my_local_ctl_file) > > Again, nothing happened (should print out the results to the screen, as > I understand it). Bio::Baseml#run returns the contents normally printed out to the screen as a string. If you want screen output, just print the string. baseml = Bio::PAML::Baseml.new str = baseml.run("baseml.ctl") print str Note that the results of baseml are written to the file which is described in the specified control file. > Any suggestions on what I am doing wrong here? I suspect a problem with > the creation of the temporary folder/files, but frankly don't know > enough about the details to follow up on that. Also, I would guess that > such issues were addressed when developing the module (?). > > Cheers, > > Marc The PAML documentation says that PAML programs do not work with filenames containing spaces. In addition, it might not work with filenames containing non-ASCII characters. So, If the temporary file location contain spaces or non-ASCII characters, baseml could not work correctly. Cheers, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Wed Feb 25 07:16:57 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 25 Feb 2009 13:16:57 +0100 Subject: [BioRuby] Tutorial situation Message-ID: <20090225121657.GA4934@thebird.nl> Thanks everyone, and Naohisa in particular, for the new release! I would like discuss the Tutorial situation. Currently we have a wiki, which is updated by people, and a Tutorial.rd in the source tree. They are not in sync. I like the .rd version as it is a generator and I can use it for automated testing of the embedded source code - so we know the docs are up-to-date. On the other hand, the wiki is nice since it is proven to get updates from occasional users. The tutorial is a much used resource for introducing BioRuby. I think we need a solution to synchronize them. One option is to generate .rd from mediawiki - that would allow quick diffing. But there is no such tool. One we have one source I am happy to update the tutorial again. Any ideas for a resolution? Pj. From mail at michaelbarton.me.uk Wed Feb 25 12:24:38 2009 From: mail at michaelbarton.me.uk (Michael Barton) Date: Wed, 25 Feb 2009 17:24:38 +0000 Subject: [BioRuby] Tutorial situation In-Reply-To: <20090225121657.GA4934@thebird.nl> References: <20090225121657.GA4934@thebird.nl> Message-ID: GitHub pages is one option. The documentation is kept in an empty branch of the git source code; Github automatically converts the code into HTML which is which would be hosted at bioruby.github.com. The CNAME can be updated though, which means any url could be used. More info at: http://github.com/blog/272-github-pages Cheers Mike 2009/2/25 Pjotr Prins > Thanks everyone, and Naohisa in particular, for the new release! > > I would like discuss the Tutorial situation. Currently we have a > wiki, which is updated by people, and a Tutorial.rd in the source > tree. They are not in sync. > > I like the .rd version as it is a generator and I can use it for > automated testing of the embedded source code - so we know the docs > are up-to-date. On the other hand, the wiki is nice since it is proven > to get updates from occasional users. > > The tutorial is a much used resource for introducing BioRuby. I > think we need a solution to synchronize them. > > One option is to generate .rd from mediawiki - that would allow quick > diffing. But there is no such tool. > > One we have one source I am happy to update the tutorial again. > > Any ideas for a resolution? > > Pj. > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at gmail.com Wed Feb 25 12:35:04 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Wed, 25 Feb 2009 17:35:04 +0000 Subject: [BioRuby] Tutorial situation In-Reply-To: References: <20090225121657.GA4934@thebird.nl> Message-ID: <4c7507a70902250935o7fb808akfe4e31a2cb96a81e@mail.gmail.com> GitHub is not a bad option, but I'm afraid a github-page would be yet another "homepage for bioruby", which is something we really should avoid. How about we (let someone) write the tutorials in a "tutorials" subdirectory of bioruby (so it's kept under version control) but actually show those tutorials on the existing bioruby homepage (http://bioruby.open-bio.org). I don't care what formatting would be used for the tutorials, but my vote goes for Textile. jan. 2009/2/25 Michael Barton > GitHub pages is one option. > The documentation is kept in an empty branch of the git source code; Github > automatically converts the code into HTML which is which would be hosted at > bioruby.github.com. The CNAME can be updated though, which means any url > could be used. > > More info at: > http://github.com/blog/272-github-pages > > Cheers > > Mike > > 2009/2/25 Pjotr Prins > > > Thanks everyone, and Naohisa in particular, for the new release! > > > > I would like discuss the Tutorial situation. Currently we have a > > wiki, which is updated by people, and a Tutorial.rd in the source > > tree. They are not in sync. > > > > I like the .rd version as it is a generator and I can use it for > > automated testing of the embedded source code - so we know the docs > > are up-to-date. On the other hand, the wiki is nice since it is proven > > to get updates from occasional users. > > > > The tutorial is a much used resource for introducing BioRuby. I > > think we need a solution to synchronize them. > > > > One option is to generate .rd from mediawiki - that would allow quick > > diffing. But there is no such tool. > > > > One we have one source I am happy to update the tutorial again. > > > > Any ideas for a resolution? > > > > Pj. > > > > > > _______________________________________________ > > 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 pjotr.public14 at thebird.nl Thu Feb 26 06:31:10 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 26 Feb 2009 12:31:10 +0100 Subject: [BioRuby] Tutorial situation In-Reply-To: <4c7507a70902250935o7fb808akfe4e31a2cb96a81e@mail.gmail.com> References: <20090225121657.GA4934@thebird.nl> <4c7507a70902250935o7fb808akfe4e31a2cb96a81e@mail.gmail.com> Message-ID: <20090226113109.GA22852@thebird.nl> On Wed, Feb 25, 2009 at 05:35:04PM +0000, Jan Aerts wrote: > How about we (let someone) write the tutorials in a "tutorials" subdirectory > of bioruby (so it's kept under version control) but actually show those > tutorials on the existing bioruby homepage (http://bioruby.open-bio.org). Probably the best idea. I think most contributors will be developers anyway. This means we should remove the tutorial from Mediawiki and use a generated version (somewhere). Any objections? And where do we generate it? I can do it on one of my machines, for now. > I don't care what formatting would be used for the tutorials, but my vote > goes for Textile. That is (yet) another wiki formatter. There is a Ruby implementation here: http://redcloth.org/. We would also have to look at colored code output, I think. The current Tutorial.rd has multiple outputs. Where do we want to go with this? The same holds for RubyInAnger. Comments, decisions, please. Pj. From kemerson at uoregon.edu Thu Feb 26 21:13:29 2009 From: kemerson at uoregon.edu (Kevin Emerson) Date: Thu, 26 Feb 2009 18:13:29 -0800 (PST) Subject: [BioRuby] Bio::GO details Message-ID: Greetings RUBY gurus, I am relatively new to using Bioruby and am hoping that someone might be able to point me to some documentation on using the GO class. I have a bunch of sequences from a mosquito cDNA microarray and have a large number of them with strong homology to Drosophila sequences. This I have taken care of using Bio::Blast. Now I want to see if I can find the GO information for the Drosophila homologs to see if I can gain some insight into my dataset. I know enough programming to get myself into trouble, and would like to work on some scripts to get the GO information, but haven't been able to find any documentation that I could even use to get started. Any links or citations that come to mind - I would appreciate it. Cheers, Kevin From marc.hoeppner at molbio.su.se Fri Feb 27 01:54:05 2009 From: marc.hoeppner at molbio.su.se (Marc Hoeppner) Date: Fri, 27 Feb 2009 07:54:05 +0100 Subject: [BioRuby] Bio::GO details In-Reply-To: References: Message-ID: <49A78E0D.9070900@molbio.su.se> Hi Kevin, if you have a mapping of your mosquito genes to FlyBase accession numbers, the fastest way to get this information would probably be the Ensembl api (http://wiki.github.com/jandot/ruby-ensembl-api). The code would look something like this, given you have this mapping in say a csv-type file (comma separated) require 'ensembl' Ensembl::Core::DBConnection.connect('drosophila_melanogaster') infile = IO.readlines(ARGV.shift) # reading your comma-separated accession mapping file (one line per mapping) infile.each do |line| accs = line.split(",") # Split the comma-sep. entries into an array drosphila_acc = accs.shift # the first entry is the Drosophila acc mosq_acc = accs.shift # the second entry is you Mosq. acc gene = Ensembl::Core::Gene.find_by_stable_id(drosophila_acc) print "#{mosq_acc}" gene.go_terms.each do |go| print ",#{go}" end print "\n" end That would print each mosq. accession/uniq identifier and all the GO terms from the Drosphila homologue (orthologue, I assume) into one line, comma separated - which can then be opened in Excel as a spread sheet. Now, if you need to get information on what is behind these terms, the geneontology.org website should be a good starting point for finding analysis-tools. Hope that helped, Marc > Greetings RUBY gurus, > > I am relatively new to using Bioruby and am hoping that someone might > be able to point me to some documentation on using the GO class. I > have a bunch of sequences from a mosquito cDNA microarray and have a > large number of them with strong homology to Drosophila sequences. > This I have taken care of using Bio::Blast. > > Now I want to see if I can find the GO information for the Drosophila > homologs to see if I can gain some insight into my dataset. I know > enough programming to get myself into trouble, and would like to work > on some scripts to get the GO information, but haven't been able to > find any documentation that I could even use to get started. > > Any links or citations that come to mind - I would appreciate it. > > Cheers, > Kevin > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Marc P. Hoeppner PhD student Department of Molecular Biology and Functional Genomics Stockholm University, 10691 Stockholm, Sweden marc.hoeppner at molbio.su.se Tel: +46 (0)8 - 164195 From tomoakin at kenroku.kanazawa-u.ac.jp Fri Feb 6 05:27:10 2009 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Fri, 6 Feb 2009 14:27:10 +0900 Subject: [BioRuby] GFF3 status (possible bug?) In-Reply-To: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp> References: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp> Message-ID: <84B18E0F-3FF8-42E7-99F1-72DF2A96DFFE@kenroku.kanazawa-u.ac.jp> Hi, Today, I got the code from git and tried parsing a GFF3 file (from TAIR8). a code fragment open(transcriptgff,"r").each_line do |gffline| record=Bio::GFF::GFF3::Record.new(gffline) p record curid = record.id p curid ... results # /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in `[]': can't convert String into Integer (TypeError) from /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in `id' It seems that the @attributes is now not a hash, but an array of key, value pairs. On the otherhand, id expects it to be a hash. The code in gff.rb looks # Represents a single line of a GFF3-formatted file. # See Bio::GFF::GFF3 for more information. class Record < GFF2::Record include GFF3::Escape # shortcut to the ID attribute def id @attributes['ID'] end I suppose this is reminiscent of the GFF when attributes were a hash. The change from hash to array is presumably to because the key may not be unique in attributes. A way straighten may be create key to [array of values] hash when the same key are specified more than once. (when multiple values for each of key are given it should be represented as key to [array of arrays]. Otherwise, we may define id to scan the array as def id val = nil @attributes.each do |keyval| if(keyval[0] == 'ID') val = keyval[1] break end end val end It is also nice if a function to get the attribute value for a specific key is provided. This should be easier with key to array of values approach, although the order of attributes will not be conserved. Which way are you going? I hope this can be corrected before 1.3.0 release. Best wishes -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From missy at be.to Fri Feb 6 09:44:41 2009 From: missy at be.to (MISHIMA, Hiroyuki) Date: Fri, 06 Feb 2009 18:44:41 +0900 Subject: [BioRuby] biofetch server error on bioruby.org Message-ID: <498C0689.9060300@be.to> Dear list, Now http://bioruby.org/cgi-bin/biofetch.rb seems not to work (Internal Server Error). Is this service still maintained? If not, for BioRuby 1.3.0 release, etc/bioinformatics/seqdatabase.ini could be updated by replacing "http://bioruby.org/cgi-bin/biofetch.rb" with "http://www.ebi.ac.uk/cgi-bin/dbfetch". I am sorry if this questions is a FAQ. Thanks, Hiro -- MISHIMA, Hiroyuki, DDS, Ph.D. COE Research Fellow Department of Human Genetics Nagasaki University Graduate School of Biomedical Sciences From ktym at hgc.jp Fri Feb 6 10:10:14 2009 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 6 Feb 2009 19:10:14 +0900 Subject: [BioRuby] biofetch server error on bioruby.org In-Reply-To: <498C0689.9060300@be.to> References: <498C0689.9060300@be.to> Message-ID: Dear Hiro, I'm sorry about this problem. I'll fix the server within a week. Migration of bioruby.org, bioruby.open-bio.org and the wiki sites are also scheduled. Sorry for any inconveniences it may have caused. Regards, Toshiaki Katayama On 2009/02/06, at 18:44, MISHIMA, Hiroyuki wrote: > Dear list, > > Now http://bioruby.org/cgi-bin/biofetch.rb seems not to work (Internal > Server Error). Is this service still maintained? > > If not, for BioRuby 1.3.0 release, etc/bioinformatics/seqdatabase.ini > could be updated by replacing "http://bioruby.org/cgi-bin/biofetch.rb" > with "http://www.ebi.ac.uk/cgi-bin/dbfetch". > > I am sorry if this questions is a FAQ. > > Thanks, > > Hiro > > -- > MISHIMA, Hiroyuki, DDS, Ph.D. > COE Research Fellow > Department of Human Genetics > Nagasaki University Graduate School of Biomedical Sciences > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ngoto at gen-info.osaka-u.ac.jp Fri Feb 6 11:29:40 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Fri, 6 Feb 2009 20:29:40 +0900 Subject: [BioRuby] GFF3 status (possible bug?) In-Reply-To: <84B18E0F-3FF8-42E7-99F1-72DF2A96DFFE@kenroku.kanazawa-u.ac.jp> References: <20090130160016.739601CBC443@idnmail.gen-info.osaka-u.ac.jp> <84B18E0F-3FF8-42E7-99F1-72DF2A96DFFE@kenroku.kanazawa-u.ac.jp> Message-ID: <20090206112940.B83121CBC3AB@idnmail.gen-info.osaka-u.ac.jp> Hi, Thank you for reporting bugs. On Fri, 6 Feb 2009 14:27:10 +0900 Tomoaki NISHIYAMA wrote: > Hi, > > Today, I got the code from git and tried parsing a GFF3 file (from > TAIR8). > > a code fragment > > open(transcriptgff,"r").each_line do |gffline| > record=Bio::GFF::GFF3::Record.new(gffline) > p record > curid = record.id > p curid > ... > > results > > # @strand="+", @feature="gene", @score=nil, @source="TAIR8", > @attributes=[["ID", "AT1G01010"], ["Note", "protein_coding_gene"], > ["Name", "AT1G01010"]], @end=5899, @seqname="Chr1"> > /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in `[]': can't > convert String into Integer (TypeError) > from /usr/local/lib/ruby/site_ruby/1.8/bio/db/gff.rb:1084:in > `id' > > It seems that the @attributes is now not a hash, but an array of key, > value pairs. @attributes is now an array of [ key, value ] pairs. See doc/Changes-1.3.rdoc about the changes. > On the otherhand, id expects it to be a hash. > > The code in gff.rb looks > > # Represents a single line of a GFF3-formatted file. > # See Bio::GFF::GFF3 for more information. > class Record < GFF2::Record > > include GFF3::Escape > > # shortcut to the ID attribute > def id > @attributes['ID'] > end > > I suppose this is reminiscent of the GFF when attributes were a hash. You are right. This is apparently a bug. I've just fixed. http://github.com/bioruby/bioruby/commit/5258d88ef98a12fd7829eb86aa8664a18a672a43 > The change from hash to array is presumably to because > the key may not be unique in attributes. That's a reason why the @attributes is changed. > A way straighten may be create key to [array of values] hash when the > same key are > specified more than once. (when multiple values for each of key are > given it should be > represented as key to [array of arrays]. > > Otherwise, we may define id to scan the array as > def id > val = nil > @attributes.each do |keyval| > if(keyval[0] == 'ID') > val = keyval[1] > break > end > end > val > end Ruby has a support for an array of [ key, value ] pairs. See Ruby reference manual for Array#assoc. For example, key, val = @attributes.assoc('ID') This is almost the same as key, val = @attributes.find { |a| a[0] == 'ID' } > It is also nice if a function to get the attribute value for > a specific key is provided. New methods to set/get/replace attributes have been added. See doc/Changes-1.3.rdoc and RDoc of Bio::GFF::GFF2 and Bio::GFF::GFF3 for details. > This should be easier with key to > array of values approach, although the order of attributes > will not be conserved. I think it is better keeping the order of attributes, and I determined to use an array containing [ key, value ] pairs. > > Which way are you going? > > I hope this can be corrected before 1.3.0 release. > > Best wishes > > -- > Tomoaki NISHIYAMA > > Advanced Science Research Center, > Kanazawa University, > 13-1 Takara-machi, > Kanazawa, 920-0934, Japan > Thanks, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Sun Feb 15 13:36:16 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 15 Feb 2009 14:36:16 +0100 Subject: [BioRuby] Added Staden io_lib support for Ruby Message-ID: <20090215133616.GA6278@thebird.nl> Hi, For Ruby I have added support for reading and writing trace files, using the Staden io_lib libraries (part of the Staden package). Now you can easily parse those files: See the API at http://thebird.nl/apidoc/biolib/index.html I hope it is useful to someone. Pj. From georgkam at gmail.com Tue Feb 17 15:39:28 2009 From: georgkam at gmail.com (George Githinji) Date: Tue, 17 Feb 2009 18:39:28 +0300 Subject: [BioRuby] google summer of code Message-ID: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> Just wondering.... Are the bioruby developers keen on Google summer of code and is there anyone who can avail themselves as a mentor? Are there some projects objectives that can be met through a summer of code opening? Thanks -- --------------- Sincerely George Skype: george_g2 Blog: http://biorelated.wordpress.com/ From adamnkraut at gmail.com Tue Feb 17 16:01:36 2009 From: adamnkraut at gmail.com (Adam) Date: Tue, 17 Feb 2009 11:01:36 -0500 Subject: [BioRuby] google summer of code In-Reply-To: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> Message-ID: <134ede0b0902170801m8974dc4m2c22ef3210ab3643@mail.gmail.com> Off of the top of my head here are some things in BioRuby that might be nice SoC projects: - JRuby/Ruby1.9 compatibility - Optionally allow libxml to override REXML for Blast parsing and other places XML is used - Port some existing BioPerl modules that people deem useful - Docs, docs, and more docs! I'm sure others can thing of some nice student projects as well. Let's hear them! -Adam On Tue, Feb 17, 2009 at 10:39 AM, George Githinji wrote: > Just wondering.... Are the bioruby developers keen on Google summer of code > and is there anyone who can avail themselves as a mentor? > > Are there some projects objectives that can be met through a summer of code > opening? > > Thanks > > > > > -- > --------------- > Sincerely > George > > Skype: george_g2 > Blog: http://biorelated.wordpress.com/ > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at gmail.com Tue Feb 17 16:06:51 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Tue, 17 Feb 2009 16:06:51 +0000 Subject: [BioRuby] google summer of code In-Reply-To: <134ede0b0902170801m8974dc4m2c22ef3210ab3643@mail.gmail.com> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> <134ede0b0902170801m8974dc4m2c22ef3210ab3643@mail.gmail.com> Message-ID: <4c7507a70902170806h1adf5b78j521054be8811f8b@mail.gmail.com> Although probably not for summer of code: tutorials! Not documentation of the classes in bioruby, but tutorials on how to do certain bioinformatics analyses using bioruby (and likely to cover more than just one class). Similar to the bioperl HOWTOs at http://www.bioperl.org/wiki/HOWTOs Having some walkthroughs for certain types of analysis can really draw in the crowds, I think. jan. 2009/2/17 Adam > Off of the top of my head here are some things in BioRuby that might > be nice SoC projects: > > - JRuby/Ruby1.9 compatibility > - Optionally allow libxml to override REXML for Blast parsing and > other places XML is used > - Port some existing BioPerl modules that people deem useful > - Docs, docs, and more docs! > > I'm sure others can thing of some nice student projects as well. > Let's hear them! > > -Adam > > On Tue, Feb 17, 2009 at 10:39 AM, George Githinji > wrote: > > Just wondering.... Are the bioruby developers keen on Google summer of > code > > and is there anyone who can avail themselves as a mentor? > > > > Are there some projects objectives that can be met through a summer of > code > > opening? > > > > Thanks > > > > > > > > > > -- > > --------------- > > Sincerely > > George > > > > Skype: george_g2 > > Blog: http://biorelated.wordpress.com/ > > _______________________________________________ > > 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 czmasek at burnham.org Tue Feb 17 18:37:12 2009 From: czmasek at burnham.org (Christian M Zmasek) Date: Tue, 17 Feb 2009 10:37:12 -0800 Subject: [BioRuby] google summer of code In-Reply-To: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> Message-ID: <499B03D8.7000309@burnham.org> Hi, Yes, I am intending to propose/(co-)mentor an implementation of phyloXML (http://www.phyloxml.org/) in BioRuby (similar to the BioPerl version [http://www.bioperl.org/wiki/Phyloxml_Project_Demo] which was a SoC project in 2008 sponsored by Nescent [http://www.nescent.org/index.php]). I hope to realize this either under Nescent's SoC 2009 or a Bio* SoC (if there is to be one). Christian George Githinji wrote: > Just wondering.... Are the bioruby developers keen on Google summer of code > and is there anyone who can avail themselves as a mentor? > > Are there some projects objectives that can be met through a summer of code > opening? > > Thanks > > > > > From czmasek at burnham.org Thu Feb 19 03:41:13 2009 From: czmasek at burnham.org (Christian M Zmasek) Date: Wed, 18 Feb 2009 19:41:13 -0800 Subject: [BioRuby] google summer of code In-Reply-To: <20090217212754.GA23447@thebird.nl> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> <499B03D8.7000309@burnham.org> <20090217212754.GA23447@thebird.nl> Message-ID: <499CD4D9.2070203@burnham.org> Hi, Pjotr: Unfortunately, I am not going to Japan. Actually, last year, a phyloXML implementation in BioPerl was sponsored by Nescent. So, it might have a chance (even though, last year, the corresponding BioRuby project was indeed rejected). Christian Pjotr Prins wrote: > Hi Christian, > > I think we need a Bio* SoC - the Nescent's one is focussed on > phylogenetics. Not sure who would be the best to drive this. Are you > going to Japan, could you champion this idea? > > Pj. > > On Tue, Feb 17, 2009 at 10:37:12AM -0800, Christian M Zmasek wrote: > >> Hi, >> >> Yes, I am intending to propose/(co-)mentor an implementation of >> phyloXML (http://www.phyloxml.org/) in BioRuby (similar to the BioPerl >> version [http://www.bioperl.org/wiki/Phyloxml_Project_Demo] which was a >> SoC project in 2008 sponsored by Nescent >> [http://www.nescent.org/index.php]). >> I hope to realize this either under Nescent's SoC 2009 or a Bio* SoC (if >> there is to be one). >> >> Christian >> >> >> >> George Githinji wrote: >> >>> Just wondering.... Are the bioruby developers keen on Google summer of code >>> and is there anyone who can avail themselves as a mentor? >>> >>> Are there some projects objectives that can be met through a summer of code >>> opening? >>> >>> Thanks >>> >>> >>> >>> >>> >>> >> _______________________________________________ >> BioRuby mailing list >> BioRuby at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/bioruby >> From pjotr.public14 at thebird.nl Thu Feb 19 07:25:52 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 19 Feb 2009 08:25:52 +0100 Subject: [BioRuby] google summer of code In-Reply-To: <499CD4D9.2070203@burnham.org> References: <55915f820902170739x2b662028la80777e28fedd7ea@mail.gmail.com> <499B03D8.7000309@burnham.org> <20090217212754.GA23447@thebird.nl> <499CD4D9.2070203@burnham.org> Message-ID: <20090219072552.GA5177@thebird.nl> The latest is that Hilmar is going to organise a Bio* initiative for the combined Bio* languages under the OBF! That is good news, it means we have a high chance of getting a Bio* Google of Summer Code project with one or more slots for BioRuby initiatives. Examples of templates are here: http://hackathon.nescent.org/ The SoC is about coding - not documentation. And the project has to be interesting from a coding point of view. Real impact helps too. Pj. From ngoto at gen-info.osaka-u.ac.jp Tue Feb 24 16:39:48 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Wed, 25 Feb 2009 01:39:48 +0900 Subject: [BioRuby] BioRuby 1.3.0 is released Message-ID: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> Hi all, We are pleased to announce the release of BioRuby 1.3.0. The archive is available at: http://bioruby.org/archive/bioruby-1.3.0.tar.gz Web page: http://bioruby.org/ http://bioruby.open-bio.org/ API documentation: http://bioruby.org/rdoc/ Bug report: http://rubyforge.org/projects/bioruby/ (Updating of http://bioruby.rubyforge.org/ is still in progress. Please wait for a moment.) We also put RubyGems pacakge at RubyForge as always. You can easily install by using RubyGems. % sudo gem install bio You can also obtain bioruby gem file from bioruby.org. http://bioruby.org/archive/gems/bio-1.3.0.gem Here is a brief summary of changes. * Support for GenBank/EMBL formatted sequence output with improvements of Bio::Sequence. * BioSQL support is completely rewritten by using ActiveRecord. * Bio::Blast bug fixes and improvements. * Bio::GFF::GFF2 and Bio::GFF::GFF3 improvements. * Bio::Locations improvements. * New classes and modules. * Bio::Hinv * Bio::NCBI::REST * Bio::PAML::Codeml * Bio::TogoWS::REST In addition, many changes have been made, including incompatible changes. For more information, you can see summary of changes at http://github.com/bioruby/bioruby/blob/e04da7a1e709195d0b3e957491e76e50af32e96d/doc/Changes-1.3.rdoc and ChangeLog at http://github.com/ngoto/bioruby/blob/27a31e1fa7e916ee2af09eeba992eea5a3ca6fbd/ChangeLog In ChangeLog, the release date is described as 20 Feb 2009, which indicates frozen date of the archive. I'm sorry I took much time for the final check of the archive contents. Hope you enjoy. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From jan.aerts at gmail.com Tue Feb 24 17:02:08 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Tue, 24 Feb 2009 17:02:08 +0000 Subject: [BioRuby] BioRuby 1.3.0 is released In-Reply-To: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <4c7507a70902240902t426073e2mdc2c4618c7c7e918@mail.gmail.com> Congratulations! Thanks Goto-san and others for all the effort you've put in! jan. 2009/2/24 Naohisa Goto > Hi all, > > We are pleased to announce the release of BioRuby 1.3.0. > > The archive is available at: > http://bioruby.org/archive/bioruby-1.3.0.tar.gz > > Web page: > http://bioruby.org/ > http://bioruby.open-bio.org/ > API documentation: > http://bioruby.org/rdoc/ > Bug report: > http://rubyforge.org/projects/bioruby/ > > (Updating of http://bioruby.rubyforge.org/ is still > in progress. Please wait for a moment.) > > We also put RubyGems pacakge at RubyForge as always. > You can easily install by using RubyGems. > % sudo gem install bio > > You can also obtain bioruby gem file from bioruby.org. > http://bioruby.org/archive/gems/bio-1.3.0.gem > > Here is a brief summary of changes. > > * Support for GenBank/EMBL formatted sequence output with > improvements of Bio::Sequence. > * BioSQL support is completely rewritten by using ActiveRecord. > * Bio::Blast bug fixes and improvements. > * Bio::GFF::GFF2 and Bio::GFF::GFF3 improvements. > * Bio::Locations improvements. > * New classes and modules. > * Bio::Hinv > * Bio::NCBI::REST > * Bio::PAML::Codeml > * Bio::TogoWS::REST > > In addition, many changes have been made, including incompatible changes. > For more information, you can see summary of changes at > > http://github.com/bioruby/bioruby/blob/e04da7a1e709195d0b3e957491e76e50af32e96d/doc/Changes-1.3.rdoc > > and ChangeLog at > > > http://github.com/ngoto/bioruby/blob/27a31e1fa7e916ee2af09eeba992eea5a3ca6fbd/ChangeLog > > In ChangeLog, the release date is described as 20 Feb 2009, which > indicates frozen date of the archive. I'm sorry I took much time > for the final check of the archive contents. > > Hope you enjoy. > > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Tue Feb 24 18:52:17 2009 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 25 Feb 2009 03:52:17 +0900 Subject: [BioRuby] BioRuby 1.3.0 is released In-Reply-To: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> Message-ID: <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> Goto-san, Thank you for your wonderful works on this release. Just note that we've updated the BioRuby web sites: > Web page: > http://bioruby.org/ This site is our project top page as in the past. > http://bioruby.open-bio.org/ This remains as our mirror site. The new site design had actually been at the mirror site for one year and we finally bring it to the main site (beautiful icons are courtesy of Okamoto-san). Additionally, I have edited the structure of our Wiki site at http://bioruby.open-bio.org/wiki/ extensively to clarify the contents in it. I've also added a new page for BioRuby on Rails. Regards, Toshiaki Katayama On 2009/02/25, at 1:39, Naohisa Goto wrote: > Hi all, > > We are pleased to announce the release of BioRuby 1.3.0. > > The archive is available at: > http://bioruby.org/archive/bioruby-1.3.0.tar.gz > > Web page: > http://bioruby.org/ > http://bioruby.open-bio.org/ > API documentation: > http://bioruby.org/rdoc/ > Bug report: > http://rubyforge.org/projects/bioruby/ > > (Updating of http://bioruby.rubyforge.org/ is still > in progress. Please wait for a moment.) > > We also put RubyGems pacakge at RubyForge as always. > You can easily install by using RubyGems. > % sudo gem install bio > > You can also obtain bioruby gem file from bioruby.org. > http://bioruby.org/archive/gems/bio-1.3.0.gem > > Here is a brief summary of changes. > > * Support for GenBank/EMBL formatted sequence output with > improvements of Bio::Sequence. > * BioSQL support is completely rewritten by using ActiveRecord. > * Bio::Blast bug fixes and improvements. > * Bio::GFF::GFF2 and Bio::GFF::GFF3 improvements. > * Bio::Locations improvements. > * New classes and modules. > * Bio::Hinv > * Bio::NCBI::REST > * Bio::PAML::Codeml > * Bio::TogoWS::REST > > In addition, many changes have been made, including incompatible changes. > For more information, you can see summary of changes at > http://github.com/bioruby/bioruby/blob/e04da7a1e709195d0b3e957491e76e50af32e96d/doc/Changes-1.3.rdoc > > and ChangeLog at > > http://github.com/ngoto/bioruby/blob/27a31e1fa7e916ee2af09eeba992eea5a3ca6fbd/ChangeLog > > In ChangeLog, the release date is described as 20 Feb 2009, which > indicates frozen date of the archive. I'm sorry I took much time > for the final check of the archive contents. > > Hope you enjoy. > > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From marc.hoeppner at molbio.su.se Wed Feb 25 07:14:40 2009 From: marc.hoeppner at molbio.su.se (Marc Hoeppner) Date: Wed, 25 Feb 2009 08:14:40 +0100 Subject: [BioRuby] Problem with PAML wrapper In-Reply-To: <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> Message-ID: <49A4EFE0.8030908@molbio.su.se> Hi, now with vers. 1.3 released (congrats on that by the way!), I was hoping to speed up some analyses by using the Bio::PAML module. However, I can't get it to work... Ruby info: ruby 1.8.6 (2007-03-13 patchlevel 0) [universal-darwin8.0] on a Macbook, Os X 10.5 This is what I tried: 1) read in a fasta file -> to Bio::Alignment::OriginalAlignment Verified the object (i.e. alingment.each_pair produces what it should, so I am assuming that step was successful) 2) read in a newick-type tree (with branch lengths.. ) and converted it to Bio::Tree - again, printed it out to see if it worked, and it did. 3) Verified that taxon labels in both files/objects were identical 4) Verified that all the sequences in the alignment were in fact of equal lengths I then tried to use the module as described: baseml = Bio::PAML::Baseml.new report = baseml.query(alignment,tree) -> nothing happens, i.e. program just exists normally, report.to_yaml shows an empty object. In order to confirm that PAML was working and that the data is, in principle, compatible with Baseml, I created a normal ctl file and ran the whole analysis from command line. And that worked. So I then tried to do it the less sophisticated way: baseml = Bio::PAML::Baseml.new baseml.run(my_local_ctl_file) Again, nothing happened (should print out the results to the screen, as I understand it). Any suggestions on what I am doing wrong here? I suspect a problem with the creation of the temporary folder/files, but frankly don't know enough about the details to follow up on that. Also, I would guess that such issues were addressed when developing the module (?). Cheers, Marc From ngoto at gen-info.osaka-u.ac.jp Wed Feb 25 10:24:27 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Wed, 25 Feb 2009 19:24:27 +0900 Subject: [BioRuby] Problem with PAML wrapper In-Reply-To: <49A4EFE0.8030908@molbio.su.se> References: <20090225013049.650B.EEF6E030@gen-info.osaka-u.ac.jp> <185DEF56-A1BA-4752-9E58-B0C3E0C4DFA5@hgc.jp> <49A4EFE0.8030908@molbio.su.se> Message-ID: <20090225102427.DAB051CBC3DA@idnmail.gen-info.osaka-u.ac.jp> Hi, On Wed, 25 Feb 2009 08:14:40 +0100 Marc Hoeppner wrote: > Hi, > > now with vers. 1.3 released (congrats on that by the way!), I was hoping > to speed up some analyses by using the Bio::PAML module. However, I > can't get it to work... > > Ruby info: > ruby 1.8.6 (2007-03-13 patchlevel 0) [universal-darwin8.0] > on a Macbook, Os X 10.5 > > This is what I tried: > > 1) read in a fasta file -> to Bio::Alignment::OriginalAlignment > Verified the object (i.e. alingment.each_pair produces what it should, > so I am assuming that step was successful) > 2) read in a newick-type tree (with branch lengths.. ) and converted it > to Bio::Tree - again, printed it out to see if it worked, and it did. > 3) Verified that taxon labels in both files/objects were identical > 4) Verified that all the sequences in the alignment were in fact of > equal lengths First, please check that the command "baseml" exists in the PATH directory. If not, you must specify the location of "baseml" binary. For example, baseml = Bio::PAML::Baseml.new("/home/ngoto/paml/bin/baseml") > I then tried to use the module as described: > > baseml = Bio::PAML::Baseml.new > report = baseml.query(alignment,tree) > > -> nothing happens, i.e. program just exists normally, report.to_yaml > shows an empty object. Unfortunately, Bio::PAML::Baseml::Report is still under construction, and it always returns an empty object now. Because PAML results are too complex to parse, I could not write parsing routine yet. In the future, above should work. Currently, you can only get raw results as strings by using Bio::Baseml#report and Bio::Baseml#supplemental_outputs. baseml = Bio::PAML::Baseml.new report = baseml.query(alignment,tree) # Now, the above "report" is only a dummy object. # Shows the output of baseml p baseml.output # Shows supplemental outputs of baseml p baseml.supplemental_ouputs > In order to confirm that PAML was working and that the data is, in > principle, compatible with Baseml, I created a normal ctl file and ran > the whole analysis from command line. And that worked. > > So I then tried to do it the less sophisticated way: > > baseml = Bio::PAML::Baseml.new > baseml.run(my_local_ctl_file) > > Again, nothing happened (should print out the results to the screen, as > I understand it). Bio::Baseml#run returns the contents normally printed out to the screen as a string. If you want screen output, just print the string. baseml = Bio::PAML::Baseml.new str = baseml.run("baseml.ctl") print str Note that the results of baseml are written to the file which is described in the specified control file. > Any suggestions on what I am doing wrong here? I suspect a problem with > the creation of the temporary folder/files, but frankly don't know > enough about the details to follow up on that. Also, I would guess that > such issues were addressed when developing the module (?). > > Cheers, > > Marc The PAML documentation says that PAML programs do not work with filenames containing spaces. In addition, it might not work with filenames containing non-ASCII characters. So, If the temporary file location contain spaces or non-ASCII characters, baseml could not work correctly. Cheers, Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From pjotr.public14 at thebird.nl Wed Feb 25 12:16:57 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 25 Feb 2009 13:16:57 +0100 Subject: [BioRuby] Tutorial situation Message-ID: <20090225121657.GA4934@thebird.nl> Thanks everyone, and Naohisa in particular, for the new release! I would like discuss the Tutorial situation. Currently we have a wiki, which is updated by people, and a Tutorial.rd in the source tree. They are not in sync. I like the .rd version as it is a generator and I can use it for automated testing of the embedded source code - so we know the docs are up-to-date. On the other hand, the wiki is nice since it is proven to get updates from occasional users. The tutorial is a much used resource for introducing BioRuby. I think we need a solution to synchronize them. One option is to generate .rd from mediawiki - that would allow quick diffing. But there is no such tool. One we have one source I am happy to update the tutorial again. Any ideas for a resolution? Pj. From mail at michaelbarton.me.uk Wed Feb 25 17:24:38 2009 From: mail at michaelbarton.me.uk (Michael Barton) Date: Wed, 25 Feb 2009 17:24:38 +0000 Subject: [BioRuby] Tutorial situation In-Reply-To: <20090225121657.GA4934@thebird.nl> References: <20090225121657.GA4934@thebird.nl> Message-ID: GitHub pages is one option. The documentation is kept in an empty branch of the git source code; Github automatically converts the code into HTML which is which would be hosted at bioruby.github.com. The CNAME can be updated though, which means any url could be used. More info at: http://github.com/blog/272-github-pages Cheers Mike 2009/2/25 Pjotr Prins > Thanks everyone, and Naohisa in particular, for the new release! > > I would like discuss the Tutorial situation. Currently we have a > wiki, which is updated by people, and a Tutorial.rd in the source > tree. They are not in sync. > > I like the .rd version as it is a generator and I can use it for > automated testing of the embedded source code - so we know the docs > are up-to-date. On the other hand, the wiki is nice since it is proven > to get updates from occasional users. > > The tutorial is a much used resource for introducing BioRuby. I > think we need a solution to synchronize them. > > One option is to generate .rd from mediawiki - that would allow quick > diffing. But there is no such tool. > > One we have one source I am happy to update the tutorial again. > > Any ideas for a resolution? > > Pj. > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at gmail.com Wed Feb 25 17:35:04 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Wed, 25 Feb 2009 17:35:04 +0000 Subject: [BioRuby] Tutorial situation In-Reply-To: References: <20090225121657.GA4934@thebird.nl> Message-ID: <4c7507a70902250935o7fb808akfe4e31a2cb96a81e@mail.gmail.com> GitHub is not a bad option, but I'm afraid a github-page would be yet another "homepage for bioruby", which is something we really should avoid. How about we (let someone) write the tutorials in a "tutorials" subdirectory of bioruby (so it's kept under version control) but actually show those tutorials on the existing bioruby homepage (http://bioruby.open-bio.org). I don't care what formatting would be used for the tutorials, but my vote goes for Textile. jan. 2009/2/25 Michael Barton > GitHub pages is one option. > The documentation is kept in an empty branch of the git source code; Github > automatically converts the code into HTML which is which would be hosted at > bioruby.github.com. The CNAME can be updated though, which means any url > could be used. > > More info at: > http://github.com/blog/272-github-pages > > Cheers > > Mike > > 2009/2/25 Pjotr Prins > > > Thanks everyone, and Naohisa in particular, for the new release! > > > > I would like discuss the Tutorial situation. Currently we have a > > wiki, which is updated by people, and a Tutorial.rd in the source > > tree. They are not in sync. > > > > I like the .rd version as it is a generator and I can use it for > > automated testing of the embedded source code - so we know the docs > > are up-to-date. On the other hand, the wiki is nice since it is proven > > to get updates from occasional users. > > > > The tutorial is a much used resource for introducing BioRuby. I > > think we need a solution to synchronize them. > > > > One option is to generate .rd from mediawiki - that would allow quick > > diffing. But there is no such tool. > > > > One we have one source I am happy to update the tutorial again. > > > > Any ideas for a resolution? > > > > Pj. > > > > > > _______________________________________________ > > 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 pjotr.public14 at thebird.nl Thu Feb 26 11:31:10 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Thu, 26 Feb 2009 12:31:10 +0100 Subject: [BioRuby] Tutorial situation In-Reply-To: <4c7507a70902250935o7fb808akfe4e31a2cb96a81e@mail.gmail.com> References: <20090225121657.GA4934@thebird.nl> <4c7507a70902250935o7fb808akfe4e31a2cb96a81e@mail.gmail.com> Message-ID: <20090226113109.GA22852@thebird.nl> On Wed, Feb 25, 2009 at 05:35:04PM +0000, Jan Aerts wrote: > How about we (let someone) write the tutorials in a "tutorials" subdirectory > of bioruby (so it's kept under version control) but actually show those > tutorials on the existing bioruby homepage (http://bioruby.open-bio.org). Probably the best idea. I think most contributors will be developers anyway. This means we should remove the tutorial from Mediawiki and use a generated version (somewhere). Any objections? And where do we generate it? I can do it on one of my machines, for now. > I don't care what formatting would be used for the tutorials, but my vote > goes for Textile. That is (yet) another wiki formatter. There is a Ruby implementation here: http://redcloth.org/. We would also have to look at colored code output, I think. The current Tutorial.rd has multiple outputs. Where do we want to go with this? The same holds for RubyInAnger. Comments, decisions, please. Pj. From kemerson at uoregon.edu Fri Feb 27 02:13:29 2009 From: kemerson at uoregon.edu (Kevin Emerson) Date: Thu, 26 Feb 2009 18:13:29 -0800 (PST) Subject: [BioRuby] Bio::GO details Message-ID: Greetings RUBY gurus, I am relatively new to using Bioruby and am hoping that someone might be able to point me to some documentation on using the GO class. I have a bunch of sequences from a mosquito cDNA microarray and have a large number of them with strong homology to Drosophila sequences. This I have taken care of using Bio::Blast. Now I want to see if I can find the GO information for the Drosophila homologs to see if I can gain some insight into my dataset. I know enough programming to get myself into trouble, and would like to work on some scripts to get the GO information, but haven't been able to find any documentation that I could even use to get started. Any links or citations that come to mind - I would appreciate it. Cheers, Kevin From marc.hoeppner at molbio.su.se Fri Feb 27 06:54:05 2009 From: marc.hoeppner at molbio.su.se (Marc Hoeppner) Date: Fri, 27 Feb 2009 07:54:05 +0100 Subject: [BioRuby] Bio::GO details In-Reply-To: References: Message-ID: <49A78E0D.9070900@molbio.su.se> Hi Kevin, if you have a mapping of your mosquito genes to FlyBase accession numbers, the fastest way to get this information would probably be the Ensembl api (http://wiki.github.com/jandot/ruby-ensembl-api). The code would look something like this, given you have this mapping in say a csv-type file (comma separated) require 'ensembl' Ensembl::Core::DBConnection.connect('drosophila_melanogaster') infile = IO.readlines(ARGV.shift) # reading your comma-separated accession mapping file (one line per mapping) infile.each do |line| accs = line.split(",") # Split the comma-sep. entries into an array drosphila_acc = accs.shift # the first entry is the Drosophila acc mosq_acc = accs.shift # the second entry is you Mosq. acc gene = Ensembl::Core::Gene.find_by_stable_id(drosophila_acc) print "#{mosq_acc}" gene.go_terms.each do |go| print ",#{go}" end print "\n" end That would print each mosq. accession/uniq identifier and all the GO terms from the Drosphila homologue (orthologue, I assume) into one line, comma separated - which can then be opened in Excel as a spread sheet. Now, if you need to get information on what is behind these terms, the geneontology.org website should be a good starting point for finding analysis-tools. Hope that helped, Marc > Greetings RUBY gurus, > > I am relatively new to using Bioruby and am hoping that someone might > be able to point me to some documentation on using the GO class. I > have a bunch of sequences from a mosquito cDNA microarray and have a > large number of them with strong homology to Drosophila sequences. > This I have taken care of using Bio::Blast. > > Now I want to see if I can find the GO information for the Drosophila > homologs to see if I can gain some insight into my dataset. I know > enough programming to get myself into trouble, and would like to work > on some scripts to get the GO information, but haven't been able to > find any documentation that I could even use to get started. > > Any links or citations that come to mind - I would appreciate it. > > Cheers, > Kevin > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby -- Marc P. Hoeppner PhD student Department of Molecular Biology and Functional Genomics Stockholm University, 10691 Stockholm, Sweden marc.hoeppner at molbio.su.se Tel: +46 (0)8 - 164195