From jan.aerts at gmail.com Thu Mar 5 04:40:44 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Thu, 5 Mar 2009 09:40:44 +0000 Subject: [BioRuby] bioruby tutorials Message-ID: <4c7507a70903050140y77a46c8bs2b09cd1cc9fc3d96@mail.gmail.com> Had another frustrated comment from someone about missing tutorials for bioruby. It'd be nice if we had tutorials similar to the HOWTOs in BioPerl at http://www.bioperl.org/wiki/HOWTOs. Apart from the fact that we could try and finish the sample code at http://bioruby.open-bio.org/wiki/SampleCodes (although congratulations to the authors of what's already there!), we can try to think of use cases that go beyond just one class and actually reflect the bigger picture of a bioinformatics analysis. Something like "How to find conserved non-coding regions in a genome" which would be using bioruby's BLAST parser, Bio::Feature and maybe other classes as well. jan. From craigknox at gmail.com Thu Mar 5 14:16:23 2009 From: craigknox at gmail.com (craigknox) Date: Thu, 5 Mar 2009 12:16:23 -0700 Subject: [BioRuby] efetch/esearch broken Message-ID: Hi Everyone, I am using the latest bioruby gem (1.3.0) and I am having trouble running efetch. The following is copied directly from the tutorial on "http://bioruby.open-bio.org/wiki/BiorubyTutorial". When I run it, "Bio::PubMed.efetch(entries)" returns a string instead of an array of strings. Additionally, the "retmax" parameter for esearch is not working - it is only returning the default of 100 entries. Is the tutorial just out of date or is this a bug? Thanks, Craig Knox #!/usr/bin/env ruby require 'bio' keywords = ARGV.join(' ') # I am using "histamine" here options = { 'maxdate' => '2003/05/31', 'retmax' => 1000, } entries = Bio::PubMed.esearch(keywords, options) Bio::PubMed.efetch(entries).each do |entry| medline = Bio::MEDLINE.new(entry) reference = medline.reference puts reference.bibtex end From fredjoha at bioreg.kyushu-u.ac.jp Mon Mar 9 02:19:22 2009 From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson) Date: Mon, 09 Mar 2009 15:19:22 +0900 Subject: [BioRuby] Made a change in format10.rb Message-ID: <49B4B4EA.6060401@bioreg.kyushu-u.ac.jp> I found that Bioruby can't handle large amounts of output from Fasta. So I made this change to /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/fasta/format10.rb : 6,7c6,8 < data.sub!(/(.*)\n\n>>>/m, '') < @list = "The best scores are" + $1 --- > border = data.index("\n\n>>>") > @list = "The best scores are" + data[0...border] > data = data[border+5..-1] The old code reported an error when the output was huge: RegexpError: Stack overflow in regexp matcher: /(.*)\n\n>>>/m So I thought that maybe these lines of code should be changed in Bioruby. Regards, Fredrik Johansson From pjotr.public14 at thebird.nl Thu Mar 12 19:21:16 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Mar 2009 00:21:16 +0100 Subject: [BioRuby] bioruby tutorials In-Reply-To: <4c7507a70903050140y77a46c8bs2b09cd1cc9fc3d96@mail.gmail.com> References: <4c7507a70903050140y77a46c8bs2b09cd1cc9fc3d96@mail.gmail.com> Message-ID: <20090312232116.GA14834@thebird.nl> On Thu, Mar 05, 2009 at 09:40:44AM +0000, Jan Aerts wrote: > Apart from the fact that we could try and finish the sample code at > http://bioruby.open-bio.org/wiki/SampleCodes (although congratulations to > the authors of what's already there!), we can try to think of use cases that > go beyond just one class and actually reflect the bigger picture of a > bioinformatics analysis. Something like "How to find conserved non-coding > regions in a genome" which would be using bioruby's BLAST parser, > Bio::Feature and maybe other classes as well. Today I fixed the Tutorial to run with rubydoctest. This is a good way of making sure the examples still work. Not everything is in there yet, but I'll continue that work. I just had a look at github gists - they are interesting as you can embed them as syntax coloured code in web documents - while they are single files in a git directory. I.e. we can create 'live' documentation that can also run as tests, or example, code. This has good potential for material that lives in the git repository. One example: http://gist.github.com/13874 See the 'embed' link in the top right corner. Now we still need to decide on a way of doing it for BioRuby. Jan, maybe you can have a discussion in Japan. Personally I don't like wikis for documentation - though they can make it easier for people to contribute. But I have seen some real wild growth in other projects. That is a crucial point. Are we willing to drop the wiki? Or will we keep a wiki presence and I'll have to find a way to keep the docs in sync? Maybe I am the only one who feels the need for a resolution. Pj. From pjotr.public14 at thebird.nl Fri Mar 13 06:37:00 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Mar 2009 11:37:00 +0100 Subject: [BioRuby] Google summer of code... Message-ID: <20090313103700.GA20887@thebird.nl> Hilmar Lapp writes: You may recall my message to the developer lists of several O|B|F projects in February about the idea of O|B|F applying to Google Summer of Code as a mentoring organization [1]. I felt that the response to this was very positive and encouraging. Although late (sorry, been swamped too much), I've now put up the skeleton of an ideas page at http://open-bio.org/wiki/Google_Summer_Code_2009 I basically modeled (in fact, largely copied) this page after the NESCent Phyloinformatics Summer of Code ideas pages, which I think worked pretty well. We can completely rework this, though - any feedback and suggestions are very much welcome. In the meantime, I need all developers to double check the information under 'Contact'. Would the open-bio-l mailing list indeed reach the prospective mentors and other devs? Will be you be fine with students asking for feedback to their applications on the developers (i.e., this) list? Is there a blessed IRC where at least some of the prospective mentors hang out for students to ask questions during the time they apply? I also need space for the reference information for all projects that will participate with at least one project idea (I would hope that that's all projects) to be added in the 'Open-Bio projects involved' section. ***** Most important of all, if you can volunteer to mentor a project, please post a project idea to the page in the respective section, using the idea template that's there already (copy, paste, and edit). ***** The deadline for organization applications is Friday this week, Mar 13, which is very soon. The ideas page is a major factor and component in how Google scores new mentoring organizations - the more we can show the resourcefulness and diversity of our member projects the more competitive I think we'll be. So all those who responded with ideas or willingness to help out as primary or secondary mentores earlier, I need you to think about and put up your idea(s) now. Cheers, -hilmar [1] http://tinyurl.com/ck7tqe -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== _______________________________________________ BioLib-dev mailing list BioLib-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biolib-dev From bonnalraoul at ingm.it Fri Mar 13 06:57:38 2009 From: bonnalraoul at ingm.it (Raoul JP Bonnal) Date: Fri, 13 Mar 2009 11:57:38 +0100 Subject: [BioRuby] Ruby & R Message-ID: <49BA3C22.2090505@ingm.it> Hi guys, I have always worked on sequences and bioruby gave me everything I need to work with that kind of data. Now I moved to Illumina gene expression and rtpcr data, I think there is a lack of support in this kind of data. Isn't it ? I found that usually this data are handled by R, but which are the pro/cons of this lang ? And as "lang/syntax"... it's not very confortable I think :-( Pjotr is providing support for biolib to Ruby. Could Ruby do it better ? I mean, Python/Ruby/Perl seems that depends on the end user, they can do the same things but for R ? -- Ra From bonnalraoul at ingm.it Fri Mar 13 08:00:21 2009 From: bonnalraoul at ingm.it (Raoul JP Bonnal) Date: Fri, 13 Mar 2009 13:00:21 +0100 Subject: [BioRuby] Google summer of code... In-Reply-To: <20090313103700.GA20887@thebird.nl> References: <20090313103700.GA20887@thebird.nl> Message-ID: <49BA4AD5.1020501@ingm.it> Related to BioSQL idea I was reading this link: http://code.google.com/intl/en/apis/gdata/articles/gdata_on_rails.html#Introduction Pjotr Prins ha scritto: > Hilmar Lapp writes: > > You may recall my message to the developer lists of several O|B|F > projects in February about the idea of O|B|F applying to Google Summer > of Code as a mentoring organization [1]. > > I felt that the response to this was very positive and encouraging. > Although late (sorry, been swamped too much), I've now put up the > skeleton of an ideas page at > > http://open-bio.org/wiki/Google_Summer_Code_2009 > > I basically modeled (in fact, largely copied) this page after the > NESCent Phyloinformatics Summer of Code ideas pages, which I think > worked pretty well. We can completely rework this, though - any > feedback and suggestions are very much welcome. > > In the meantime, I need all developers to double check the information > under 'Contact'. Would the open-bio-l mailing list indeed reach the > prospective mentors and other devs? Will be you be fine with students > asking for feedback to their applications on the developers (i.e., > this) list? Is there a blessed IRC where at least some of the > prospective mentors hang out for students to ask questions during the > time they apply? > > I also need space for the reference information for all projects that > will participate with at least one project idea (I would hope that > that's all projects) to be added in the 'Open-Bio projects involved' > section. > > ***** > Most important of all, if you can volunteer to mentor a project, > please post a project idea to the page in the respective section, > using the idea template that's there already (copy, paste, and edit). > ***** > > The deadline for organization applications is Friday this week, Mar > 13, which is very soon. The ideas page is a major factor and component > in how Google scores new mentoring organizations - the more we can > show the resourcefulness and diversity of our member projects the more > competitive I think we'll be. So all those who responded with ideas or > willingness to help out as primary or secondary mentores earlier, I > need you to think about and put up your idea(s) now. > > Cheers, > > -hilmar > > [1] http://tinyurl.com/ck7tqe > > From jdudley at stanford.edu Fri Mar 13 11:09:01 2009 From: jdudley at stanford.edu (Joel Dudley) Date: Fri, 13 Mar 2009 08:09:01 -0700 Subject: [BioRuby] Ruby & R In-Reply-To: <49BA3C22.2090505@ingm.it> References: <49BA3C22.2090505@ingm.it> Message-ID: <2567FB6B-9965-4705-AE11-72114D23C61E@stanford.edu> Ra, I work mainly with expression data, and what I do is use Ruby for as much as I can, then use RSRuby to call the key R functions I need. You are right, it is not comfortable to work in R at all, but it's hard to deny the wealth of packages it has for working with expression and genotyping data. Of course it is up to people like you and me to add this kind of functionality to BioRuby if we can manage it. Unfortunately I can't seem to find the time. -- Joel On Mar 13, 2009, at 3:57 AM, Raoul JP Bonnal wrote: > Hi guys, > I have always worked on sequences and bioruby gave me everything I > need to work with that kind of data. > Now I moved to Illumina gene expression and rtpcr data, I think > there is a lack of support in this kind of data. Isn't it ? > I found that usually this data are handled by R, but which are the > pro/cons of this lang ? And as "lang/syntax"... it's not very > confortable I think :-( > > Pjotr is providing support for biolib to Ruby. > > Could Ruby do it better ? > > I mean, Python/Ruby/Perl seems that depends on the end user, they > can do the same things but for R ? > > -- > Ra > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby =============Email Policy============= I now only check mail at the following times: - 8 a.m., Noon, 5 p.m. Mon-Fri - 8 a.m. Sat-Sun If this is a true emergency, or you require an immediate response from me, please contact me via my mobile phone: (408) 464-8258 ==================================== From pjotr.public14 at thebird.nl Fri Mar 13 15:17:37 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Mar 2009 20:17:37 +0100 Subject: [BioRuby] Ruby & R In-Reply-To: <49BA3C22.2090505@ingm.it> References: <49BA3C22.2090505@ingm.it> Message-ID: <20090313191737.GA21375@thebird.nl> Hi Raoul, On Fri, Mar 13, 2009 at 11:57:38AM +0100, Raoul JP Bonnal wrote: > Hi guys, > I have always worked on sequences and bioruby gave me everything I need > to work with that kind of data. > Now I moved to Illumina gene expression and rtpcr data, I think there is > a lack of support in this kind of data. Isn't it ? > I found that usually this data are handled by R, but which are the > pro/cons of this lang ? And as "lang/syntax"... it's not very > confortable I think :-( R is the language of choice for most statisticians. So it is natural that where statistics count R gets the functionality. R as a language is not a good bargain. I see it more as as succesfull 'glue' language of C libraries (rather slow glue too). I think the only place it shines is with matrix manipulations. And then there are the libraries - which, as it happens, are mostly written in C. > Pjotr is providing support for biolib to Ruby. As these are C libraries I can easily provide Ruby mappings with biolib. If you point me at specific R functionality you want I can see if I can map it. > Could Ruby do it better ? I don't think so. We are with too few. In fact I have become truely multilingual. I use R for most statistical stuff, microarrays and (soon) deep sequencing. That is why I am driven to map to Ruby. To be honest, these days I am also using BioPerl stuff. BioRuby has quite a bit of functionality, but the BioPerl people are ahead and still moving faster. We have a problem in bioinformatics. Too few people, too many language domains. > I mean, Python/Ruby/Perl seems that depends on the end user, they can do > the same things but for R ? We can map the R C libraries using biolib. I have done the fundamentals. Tell me what functions you require. I think mapping is the way forward. Pj. From hlapp at gmx.net Sat Mar 14 18:59:39 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 14 Mar 2009 18:59:39 -0400 Subject: [BioRuby] Google Summer of Code: application submitted, action needed In-Reply-To: <37C2E759-7D01-4333-A949-70465D453D9C@gmx.net> References: <8E3950DE-6B8C-450F-9780-1BB77A193C46@gmx.net> <37C2E759-7D01-4333-A949-70465D453D9C@gmx.net> Message-ID: <0D94A4F0-FAF2-4E9F-838B-159F7DBA8AA4@gmx.net> Hi all, I have submitted the application yesterday for O|B|F participating in the 2009 Google Summer of Code as a mentoring organization. The application is at http://docs.google.com/Doc?id=dhs98hzv_7zn8bxqjm and is also linked to from the ideas page at http://open-bio.org/wiki/Google_Summer_of_Code_2009 Now keep your fingers crossed, Google is slated to announce acceptances on March 18. This is the last cross-project message re: Summer of Code that addresses mentors and our projects; future messages that I'll post across projects will be primarily for students such as announcing whether we are accepted or not and issuing calls for application. **What we need most and right now is action from our projects' developers and from possible mentors.** Google admins will start reviewing organization applications on Monday. The ideas page has 6 project ideas right now - though the ideas are good ones, the quantity won't be particularly impressive to Google. Therefore, if you have an idea for a summer project for a student please use the C& template (it is commented out now but you'll see it when you pull the Ideas section into the editor) and put it up there ASAP. If you're not sure yet who'll mentor, put tentative names there. We don't need a full commitment from mentors until the student application period starts (March 23). Next, for all projects, the leads and/or volunteers should check the reference information for their project: http://open-bio.org/wiki/Google_Summer_of_Code_2009#Open-Bio_projects_involved I just culled these links from the various project websites - it'd be much appreciated if going forward everyone can lend a hand in this. Please review what's there and add or fix as you see fit. *These links must be correct and complete - otherwise potential students may not find you.* Finally, all prospective mentors, primary or secondary, committed or not, and anyone else who would like to volunteer to help out, should subscribe themselves ASAP to the mailing list for communicating GSoC- related administrivia: http://lists.open-bio.org/mailman/listinfo/gsoc I will *not* cross-post all administrative announcements or requests for information, and so you *will* miss information if you don't subscribe yourself there. (Note: students will be subscribed there only *after* acceptance). Those who are considering to mentor, primary or helping out, please also add yourselves to the Mentors section on the Ideas page (and check your link if you're already there): http://open-bio.org/wiki/Google_Summer_of_Code_2009#Mentors Cheers everyone, and fingers crossed! -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From ktym at hgc.jp Tue Mar 17 21:34:50 2009 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 18 Mar 2009 10:34:50 +0900 Subject: [BioRuby] efetch/esearch broken In-Reply-To: References: Message-ID: <1C957035-3095-483C-BE30-CF06FE8FF422@hgc.jp> Hi Craig, Thank you for pointing this out. It was a bug. --- /usr/local/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/ncbirest.rb.orig 2009-03-18 10:33:14.000000000 +0900 +++ /usr/local/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/ncbirest.rb 2009-03-18 10:24:25.000000000 +0900 @@ -147,7 +147,7 @@ class REST list = [] 0.step(limit, step) do |i| - retmax = [step, limit - i].min + retmax = hash["retmax"] || [step, limit - i].min opts.update("retmax" => retmax, "retstart" => i) ncbi_access_wait response = Bio::Command.post_form(serv, opts) Regards, Toshiaki Katayama On 2009/03/06, at 4:16, craigknox wrote: > Hi Everyone, > > I am using the latest bioruby gem (1.3.0) and I am having trouble running efetch. The following is copied directly from the tutorial on "http://bioruby.open-bio.org/wiki/BiorubyTutorial". When I run it, "Bio::PubMed.efetch(entries)" returns a string instead of an array of strings. Additionally, the "retmax" parameter for esearch is not working - it is only returning the default of 100 entries. > > Is the tutorial just out of date or is this a bug? > > Thanks, > Craig Knox > > #!/usr/bin/env ruby > require 'bio' > > keywords = ARGV.join(' ') # I am using "histamine" here > > options = { > 'maxdate' => '2003/05/31', > 'retmax' => 1000, > } > > entries = Bio::PubMed.esearch(keywords, options) > > Bio::PubMed.efetch(entries).each do |entry| > medline = Bio::MEDLINE.new(entry) > reference = medline.reference > puts reference.bibtex > end > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From hlapp at gmx.net Wed Mar 18 14:45:50 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 18 Mar 2009 14:45:50 -0400 Subject: [BioRuby] OBF application for Summer of Code has been rejected Message-ID: <44D1FAFD-B5D7-418B-9FDA-6945219A5481@gmx.net> I hope to find out later why, but our Google Summer of Code application as an umbrella org has been rejected. However, NESCent has been accepted. If you can give your project idea a phylogenetics/phyloinformatics focus, go and put it up on the NESCent ideas page at http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 Do so pretty much **now** - we will start broadcasting and reaching out to students tonight and tomorrow. If someone comes to the site and they don't see a Bio* project that they would have been interested in, they may not check back for updates. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Mar 19 18:50:58 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 19 Mar 2009 18:50:58 -0400 Subject: [BioRuby] Summer of Code 2009 Message-ID: PHYLOINFORMATICS SUMMER OF CODE 2009 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from hardware accerelation for phylogenetic inference, to tree visualization within a wiki, to alignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/ ), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 23rd and runs through Friday, April 3rd, 2009. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org From flashdog at gmx.net Fri Mar 20 06:53:03 2009 From: flashdog at gmx.net (Flash Dog) Date: Fri, 20 Mar 2009 20:53:03 +1000 Subject: [BioRuby] rotation of protein Message-ID: <49C3758F.6060100@gmx.net> Hello, I have a translation vector and a rotation matrix how can I used it for a protein in a PDB? Best regards, From bonnalraoul at ingm.it Sun Mar 22 07:34:45 2009 From: bonnalraoul at ingm.it (Raoul JP Bonnal) Date: Sun, 22 Mar 2009 12:34:45 +0100 Subject: [BioRuby] euruko 09 but Message-ID: <49C62255.9090909@ingm.it> seems sold out :-( http://app.euruko2009.org/calendar -- Ra From kenglish at gmail.com Mon Mar 23 01:55:26 2009 From: kenglish at gmail.com (Kevin English) Date: Sun, 22 Mar 2009 19:55:26 -1000 Subject: [BioRuby] Error running standalone blast Message-ID: Hello all, New to bioRuby. Following the example I found here: http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1, I wrote the following program to run a standalone blast. I am getting an exception related to rexml... Does anyone know if there is a fix for this? #!/usr/bin/ruby require 'rubygems' require 'bio' factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') ff = Bio::FlatFile.open(Bio::FastaFormat, '/home/kenglish/Data/EST_A.fasta') ff.each do |entry| puts "Searching..." + entry.definition report = factory.query(entry) report.each do |hit| hit.each do |hsp| puts hsp.query_from end end end /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method `record_entity_expansion' for nil:NilClass (NoMethodError) from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' from /usr/lib/ruby/1.8/rexml/element.rb:384:in `each_element_with_text' from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' from /usr/lib/ruby/1.8/rexml/element.rb:388:in `each_element_with_text' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in `rexml_parse_program' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in `rexml_parse' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in `auto_parse' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in `initialize' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in `new' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in `parse_result' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in `query' from blast1.rb:11 from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in `each' from blast1.rb:9 Thanks in advance for any help... Kevin English From donttrustben at gmail.com Mon Mar 23 03:07:47 2009 From: donttrustben at gmail.com (Ben Woodcroft) Date: Mon, 23 Mar 2009 18:07:47 +1100 Subject: [BioRuby] Error running standalone blast In-Reply-To: References: Message-ID: Hi, I've run into this bug as well and managed to fix it - it is related to a problematic security fix for Debian and Ubuntu. See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502535 or https://bugs.launchpad.net/ubuntu/+source/ruby1.8/+bug/291893 Thanks, ben 2009/3/23 Kevin English > Hello all, > New to bioRuby. > Following the example I found here: > > http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1 > , > I wrote the following program to run a standalone blast. I am getting an > exception related to rexml... Does anyone know if there is a fix for this? > > > #!/usr/bin/ruby > > require 'rubygems' > require 'bio' > > factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') > ff = Bio::FlatFile.open(Bio::FastaFormat, > '/home/kenglish/Data/EST_A.fasta') > > ff.each do |entry| > puts "Searching..." + entry.definition > report = factory.query(entry) > report.each do |hit| > hit.each do |hsp| > puts hsp.query_from > end > end > end > > > /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method > `record_entity_expansion' for nil:NilClass (NoMethodError) > from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' > from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' > from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' > from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' > from /usr/lib/ruby/1.8/rexml/element.rb:384:in `each_element_with_text' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:388:in `each_element_with_text' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in > `rexml_parse_program' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in > `rexml_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in > `auto_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in > `initialize' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `new' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `parse_result' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in > `query' > from blast1.rb:11 > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in > `each' > from blast1.rb:9 > > Thanks in advance for any help... > > Kevin English > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- FYI: My email addresses at unimelb, uq and gmail all redirect to the same place. From ngoto at gen-info.osaka-u.ac.jp Mon Mar 23 02:46:24 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 23 Mar 2009 15:46:24 +0900 Subject: [BioRuby] Error running standalone blast In-Reply-To: References: Message-ID: <20090323064626.A98601CBC423@idnmail.gen-info.osaka-u.ac.jp> Hi, This is not a BioRuby's problem, but REXML DoS vulnerability fix patch's bug. See below for the deital of the REXML DoS fix's bug. http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502535 The issue have already been reported in KNOWN_ISSUES.rdoc bundled within BioRuby 1.3.0. See the section "Problem with REXML DoS vulnerability patch before 09-Nov-2008" http://github.com/bioruby/bioruby/blob/51c3223e033b2992a7bd95da282f88164406ff92/KNOWN_ISSUES.rdoc (quoted from KNOWN_ISSUES.rdoc) > If you have applied a patch taken from > www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/ > before 09 Nov 2008 12:40 +0900, because of the bug in the patch, > parsing of Blast XML results with REXML parser may fail. The bug > is already fixed and new patch is available on the above URL. > Note that some Linux distributions would have incorporated the > patch in their manners, and may have the same problem. To solve the problem, install the new patch, or upgrade to the newest Ruby 1.8.7. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Sun, 22 Mar 2009 19:55:26 -1000 Kevin English wrote: > Hello all, > New to bioRuby. > Following the example I found here: > http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1, > I wrote the following program to run a standalone blast. I am getting an > exception related to rexml... Does anyone know if there is a fix for this? > > > #!/usr/bin/ruby > > require 'rubygems' > require 'bio' > > factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') > ff = Bio::FlatFile.open(Bio::FastaFormat, '/home/kenglish/Data/EST_A.fasta') > > ff.each do |entry| > puts "Searching..." + entry.definition > report = factory.query(entry) > report.each do |hit| > hit.each do |hsp| > puts hsp.query_from > end > end > end > > > /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method > `record_entity_expansion' for nil:NilClass (NoMethodError) > from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' > from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' > from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' > from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' > from /usr/lib/ruby/1.8/rexml/element.rb:384:in `each_element_with_text' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:388:in `each_element_with_text' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in > `rexml_parse_program' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in > `rexml_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in > `auto_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in > `initialize' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `new' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `parse_result' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in > `query' > from blast1.rb:11 > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in > `each' > from blast1.rb:9 > > Thanks in advance for any help... > > Kevin English > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From kenglish at gmail.com Mon Mar 23 04:23:56 2009 From: kenglish at gmail.com (Kevin English) Date: Sun, 22 Mar 2009 22:23:56 -1000 Subject: [BioRuby] Error running standalone blast In-Reply-To: <20090323064626.A98601CBC423@idnmail.gen-info.osaka-u.ac.jp> References: <20090323064626.A98601CBC423@idnmail.gen-info.osaka-u.ac.jp> Message-ID: I edited line 76 in /usr/lib/ruby/1.8/rexml/entity.rb and changed: document.record_entity_expansion to document.record_entity_expansion unless document.nil? Seems to work now. Thanks for the quick response. Kevin document.record_entity_expansion unless document.nil? On Sun, Mar 22, 2009 at 8:46 PM, Naohisa GOTO wrote: > Hi, > > This is not a BioRuby's problem, but REXML DoS vulnerability > fix patch's bug. > > See below for the deital of the REXML DoS fix's bug. > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502535 > > The issue have already been reported in KNOWN_ISSUES.rdoc > bundled within BioRuby 1.3.0. See the section > "Problem with REXML DoS vulnerability patch before 09-Nov-2008" > > > http://github.com/bioruby/bioruby/blob/51c3223e033b2992a7bd95da282f88164406ff92/KNOWN_ISSUES.rdoc > > (quoted from KNOWN_ISSUES.rdoc) > > If you have applied a patch taken from > > www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/ > > before 09 Nov 2008 12:40 +0900, because of the bug in the patch, > > parsing of Blast XML results with REXML parser may fail. The bug > > is already fixed and new patch is available on the above URL. > > Note that some Linux distributions would have incorporated the > > patch in their manners, and may have the same problem. > > To solve the problem, install the new patch, or upgrade > to the newest Ruby 1.8.7. > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > > On Sun, 22 Mar 2009 19:55:26 -1000 > Kevin English wrote: > > > Hello all, > > New to bioRuby. > > Following the example I found here: > > > http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1 > , > > I wrote the following program to run a standalone blast. I am getting an > > exception related to rexml... Does anyone know if there is a fix for > this? > > > > > > #!/usr/bin/ruby > > > > require 'rubygems' > > require 'bio' > > > > factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') > > ff = Bio::FlatFile.open(Bio::FastaFormat, > '/home/kenglish/Data/EST_A.fasta') > > > > ff.each do |entry| > > puts "Searching..." + entry.definition > > report = factory.query(entry) > > report.each do |hit| > > hit.each do |hsp| > > puts hsp.query_from > > end > > end > > end > > > > > > /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method > > `record_entity_expansion' for nil:NilClass (NoMethodError) > > from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' > > from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' > > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' > > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' > > from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' > > from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' > > from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' > > from /usr/lib/ruby/1.8/rexml/element.rb:384:in > `each_element_with_text' > > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' > > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' > > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > > from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' > > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > > from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' > > from /usr/lib/ruby/1.8/rexml/element.rb:388:in > `each_element_with_text' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in > > `rexml_parse_program' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in > > `rexml_parse' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in > > `auto_parse' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in > > `initialize' > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > > `new' > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > > `parse_result' > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in > > `query' > > from blast1.rb:11 > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in > > `each' > > from blast1.rb:9 > > > > Thanks in advance for any help... > > > > Kevin English > > _______________________________________________ > > 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 mkikkawa at gmail.com Mon Mar 23 04:57:33 2009 From: mkikkawa at gmail.com (Masahide Kikkawa) Date: Mon, 23 Mar 2009 17:57:33 +0900 Subject: [BioRuby] rotation of protein In-Reply-To: <49C3758F.6060100@gmx.net> References: <49C3758F.6060100@gmx.net> Message-ID: <093A69F5-7DF2-42A3-B77D-7D69880F0050@gmail.com> Hi, Seems the ruby code in bioruby dealing with PDB does not have specific functions for translation or rotation. Since the ATOM coordinate is stored as Vector, you might be able to use the matrix library.. I would recommend to use moleman2 (written by Gerard J. Kleywegt) to get the job done. > Hello, > I have a translation vector and a rotation matrix how can I used it > for a protein in a PDB? > > Best regards, > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From flashdog at gmx.net Mon Mar 23 08:31:09 2009 From: flashdog at gmx.net (Flash Dog) Date: Mon, 23 Mar 2009 22:31:09 +1000 Subject: [BioRuby] rotation of protein In-Reply-To: <093A69F5-7DF2-42A3-B77D-7D69880F0050@gmail.com> References: <49C3758F.6060100@gmx.net> <093A69F5-7DF2-42A3-B77D-7D69880F0050@gmail.com> Message-ID: <49C7810D.8030000@gmx.net> Hello, Thank you for your email. Unfortunately I can only find a manual, but not the download link. Do you know where can I download moleman2? Thank you in advance. > Hi, > > Seems the ruby code in bioruby dealing with PDB does not have specific > functions for translation or rotation. Since the ATOM coordinate is > stored as Vector, you might be able to use the matrix library.. > > I would recommend to use moleman2 (written by Gerard J. Kleywegt) to > get the job done. > >> Hello, >> I have a translation vector and a rotation matrix how can I used it >> for a protein in a PDB? >> >> Best regards, >> _______________________________________________ >> 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 hlapp at gmx.net Sun Mar 29 14:41:12 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 29 Mar 2009 14:41:12 -0400 Subject: [BioRuby] Reminder: Student application deadline for Summer of Code 2009 Message-ID: *** Please disseminate widely to students at your institution. *** *** Note: Among the ideas and mentors are BioPerl, BioRuby, and BioLib *** PHYLOINFORMATICS SUMMER OF CODE 2009 - STUDENT APPLICATION DEADLINE IS APRIL 3 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and a T- shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Project ideas are listed on the website and range from hardware acceleration for phylogenetic inference, to support for phyloinformatics standards within the BioPerl and BioRuby toolkits, to alignment of next-gen sequencing data, to ontology term markup for biocuration, to semantic interoperability of web-services, to 3D-printing of phylogenies. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Instructions are at the website (see "When you apply"). You can find GSoC program rules and eligibility requirements at http://socghop.appspot.com . ***The 12-day application period for students ends on Friday, April 3rd, 2009, at 19:00 UTC (3pm EDT, 12pm PDT).*** INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org From czmasek at burnham.org Tue Mar 31 21:16:01 2009 From: czmasek at burnham.org (Christian M Zmasek) Date: Tue, 31 Mar 2009 18:16:01 -0700 Subject: [BioRuby] Google Summer of Code BioRuby project: Looking for co-mentors Message-ID: <49D2C051.9090002@burnham.org> Hi: As you probably read on previous messages, NESCent is again having a Google Summer of Code program (http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009). I am serving as the mentor of a project entitled "phyloXML support in BioRuby" (see: https://www.nescent.org/wg/phyloinformatics/index.php?title=Phyloinformatics_Summer_of_Code_2009#phyloXML_support_in_BioRuby). In order to ensure a successful outcome (should the project be accepted), as well as to improve the chances of being accepted, I am looking for people willing to serve as co-mentors. Christian PS: Here is the full description of the project: phyloXML support in BioRuby Rationale Evolutionary trees are central to comparative genomics studies. Trees used in this context are usually annotated with a variety of data elements, such as taxonomic information, genome-related data (gene names, functional annotations) and gene duplication events, as well as information related to the evolutionary tree itself (branch lengths, support values). phyloXML is an XML data exchange standard that can represent this data. Trees in phyloXML format can be displayed and analyzed with Archaeopteryx (the successor to ATV ), which also allows manipulation and navigation of the tree. While tools exist to convert other formats (such as the widely used Newick and Nexus formats) to phyloXML, there is currently support for phyloXML in only one of the open source Bio* projects (in BioPerl , as a result of Google's Summer of Code 2008). Approach Build phyloXML support in the increasingly popular, dynamic, and fully objected oriented language Ruby. More specifically, extend the open source BioRuby project to support phyloXML (BioRuby 1.3.0 has just been released). This will entail (i) the development of objects to represent all the elements of phyloXML (sequences, taxonomic data, annotations, etc), (ii) the development of a parser to read in phyloXML, and (iii) a phyloXML writer. Challenges Relating the data elements specific to phyloXML to the tree classes already in BioRuby while maintaining the standards of the BioRuby project. Development of a time and memory efficient phyloXML parser (the parser has to be able to process trees with thousands of external nodes, at least). Involved toolkits or projects BioRuby , phyloXML Degree of difficulty and needed skills Medium. Requires experience in an object oriented programming language (such as C++, Java, or, ideally, Ruby). Experience in genomics or a related biological field is also critical. Knowledge of BioRuby will obviously help, as well as familiarity with XML. Mentors Christian Zmasek From jan.aerts at gmail.com Thu Mar 5 09:40:44 2009 From: jan.aerts at gmail.com (Jan Aerts) Date: Thu, 5 Mar 2009 09:40:44 +0000 Subject: [BioRuby] bioruby tutorials Message-ID: <4c7507a70903050140y77a46c8bs2b09cd1cc9fc3d96@mail.gmail.com> Had another frustrated comment from someone about missing tutorials for bioruby. It'd be nice if we had tutorials similar to the HOWTOs in BioPerl at http://www.bioperl.org/wiki/HOWTOs. Apart from the fact that we could try and finish the sample code at http://bioruby.open-bio.org/wiki/SampleCodes (although congratulations to the authors of what's already there!), we can try to think of use cases that go beyond just one class and actually reflect the bigger picture of a bioinformatics analysis. Something like "How to find conserved non-coding regions in a genome" which would be using bioruby's BLAST parser, Bio::Feature and maybe other classes as well. jan. From craigknox at gmail.com Thu Mar 5 19:16:23 2009 From: craigknox at gmail.com (craigknox) Date: Thu, 5 Mar 2009 12:16:23 -0700 Subject: [BioRuby] efetch/esearch broken Message-ID: Hi Everyone, I am using the latest bioruby gem (1.3.0) and I am having trouble running efetch. The following is copied directly from the tutorial on "http://bioruby.open-bio.org/wiki/BiorubyTutorial". When I run it, "Bio::PubMed.efetch(entries)" returns a string instead of an array of strings. Additionally, the "retmax" parameter for esearch is not working - it is only returning the default of 100 entries. Is the tutorial just out of date or is this a bug? Thanks, Craig Knox #!/usr/bin/env ruby require 'bio' keywords = ARGV.join(' ') # I am using "histamine" here options = { 'maxdate' => '2003/05/31', 'retmax' => 1000, } entries = Bio::PubMed.esearch(keywords, options) Bio::PubMed.efetch(entries).each do |entry| medline = Bio::MEDLINE.new(entry) reference = medline.reference puts reference.bibtex end From fredjoha at bioreg.kyushu-u.ac.jp Mon Mar 9 06:19:22 2009 From: fredjoha at bioreg.kyushu-u.ac.jp (Fredrik Johansson) Date: Mon, 09 Mar 2009 15:19:22 +0900 Subject: [BioRuby] Made a change in format10.rb Message-ID: <49B4B4EA.6060401@bioreg.kyushu-u.ac.jp> I found that Bioruby can't handle large amounts of output from Fasta. So I made this change to /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/fasta/format10.rb : 6,7c6,8 < data.sub!(/(.*)\n\n>>>/m, '') < @list = "The best scores are" + $1 --- > border = data.index("\n\n>>>") > @list = "The best scores are" + data[0...border] > data = data[border+5..-1] The old code reported an error when the output was huge: RegexpError: Stack overflow in regexp matcher: /(.*)\n\n>>>/m So I thought that maybe these lines of code should be changed in Bioruby. Regards, Fredrik Johansson From pjotr.public14 at thebird.nl Thu Mar 12 23:21:16 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Mar 2009 00:21:16 +0100 Subject: [BioRuby] bioruby tutorials In-Reply-To: <4c7507a70903050140y77a46c8bs2b09cd1cc9fc3d96@mail.gmail.com> References: <4c7507a70903050140y77a46c8bs2b09cd1cc9fc3d96@mail.gmail.com> Message-ID: <20090312232116.GA14834@thebird.nl> On Thu, Mar 05, 2009 at 09:40:44AM +0000, Jan Aerts wrote: > Apart from the fact that we could try and finish the sample code at > http://bioruby.open-bio.org/wiki/SampleCodes (although congratulations to > the authors of what's already there!), we can try to think of use cases that > go beyond just one class and actually reflect the bigger picture of a > bioinformatics analysis. Something like "How to find conserved non-coding > regions in a genome" which would be using bioruby's BLAST parser, > Bio::Feature and maybe other classes as well. Today I fixed the Tutorial to run with rubydoctest. This is a good way of making sure the examples still work. Not everything is in there yet, but I'll continue that work. I just had a look at github gists - they are interesting as you can embed them as syntax coloured code in web documents - while they are single files in a git directory. I.e. we can create 'live' documentation that can also run as tests, or example, code. This has good potential for material that lives in the git repository. One example: http://gist.github.com/13874 See the 'embed' link in the top right corner. Now we still need to decide on a way of doing it for BioRuby. Jan, maybe you can have a discussion in Japan. Personally I don't like wikis for documentation - though they can make it easier for people to contribute. But I have seen some real wild growth in other projects. That is a crucial point. Are we willing to drop the wiki? Or will we keep a wiki presence and I'll have to find a way to keep the docs in sync? Maybe I am the only one who feels the need for a resolution. Pj. From pjotr.public14 at thebird.nl Fri Mar 13 10:37:00 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Mar 2009 11:37:00 +0100 Subject: [BioRuby] Google summer of code... Message-ID: <20090313103700.GA20887@thebird.nl> Hilmar Lapp writes: You may recall my message to the developer lists of several O|B|F projects in February about the idea of O|B|F applying to Google Summer of Code as a mentoring organization [1]. I felt that the response to this was very positive and encouraging. Although late (sorry, been swamped too much), I've now put up the skeleton of an ideas page at http://open-bio.org/wiki/Google_Summer_Code_2009 I basically modeled (in fact, largely copied) this page after the NESCent Phyloinformatics Summer of Code ideas pages, which I think worked pretty well. We can completely rework this, though - any feedback and suggestions are very much welcome. In the meantime, I need all developers to double check the information under 'Contact'. Would the open-bio-l mailing list indeed reach the prospective mentors and other devs? Will be you be fine with students asking for feedback to their applications on the developers (i.e., this) list? Is there a blessed IRC where at least some of the prospective mentors hang out for students to ask questions during the time they apply? I also need space for the reference information for all projects that will participate with at least one project idea (I would hope that that's all projects) to be added in the 'Open-Bio projects involved' section. ***** Most important of all, if you can volunteer to mentor a project, please post a project idea to the page in the respective section, using the idea template that's there already (copy, paste, and edit). ***** The deadline for organization applications is Friday this week, Mar 13, which is very soon. The ideas page is a major factor and component in how Google scores new mentoring organizations - the more we can show the resourcefulness and diversity of our member projects the more competitive I think we'll be. So all those who responded with ideas or willingness to help out as primary or secondary mentores earlier, I need you to think about and put up your idea(s) now. Cheers, -hilmar [1] http://tinyurl.com/ck7tqe -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== _______________________________________________ BioLib-dev mailing list BioLib-dev at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biolib-dev From bonnalraoul at ingm.it Fri Mar 13 10:57:38 2009 From: bonnalraoul at ingm.it (Raoul JP Bonnal) Date: Fri, 13 Mar 2009 11:57:38 +0100 Subject: [BioRuby] Ruby & R Message-ID: <49BA3C22.2090505@ingm.it> Hi guys, I have always worked on sequences and bioruby gave me everything I need to work with that kind of data. Now I moved to Illumina gene expression and rtpcr data, I think there is a lack of support in this kind of data. Isn't it ? I found that usually this data are handled by R, but which are the pro/cons of this lang ? And as "lang/syntax"... it's not very confortable I think :-( Pjotr is providing support for biolib to Ruby. Could Ruby do it better ? I mean, Python/Ruby/Perl seems that depends on the end user, they can do the same things but for R ? -- Ra From bonnalraoul at ingm.it Fri Mar 13 12:00:21 2009 From: bonnalraoul at ingm.it (Raoul JP Bonnal) Date: Fri, 13 Mar 2009 13:00:21 +0100 Subject: [BioRuby] Google summer of code... In-Reply-To: <20090313103700.GA20887@thebird.nl> References: <20090313103700.GA20887@thebird.nl> Message-ID: <49BA4AD5.1020501@ingm.it> Related to BioSQL idea I was reading this link: http://code.google.com/intl/en/apis/gdata/articles/gdata_on_rails.html#Introduction Pjotr Prins ha scritto: > Hilmar Lapp writes: > > You may recall my message to the developer lists of several O|B|F > projects in February about the idea of O|B|F applying to Google Summer > of Code as a mentoring organization [1]. > > I felt that the response to this was very positive and encouraging. > Although late (sorry, been swamped too much), I've now put up the > skeleton of an ideas page at > > http://open-bio.org/wiki/Google_Summer_Code_2009 > > I basically modeled (in fact, largely copied) this page after the > NESCent Phyloinformatics Summer of Code ideas pages, which I think > worked pretty well. We can completely rework this, though - any > feedback and suggestions are very much welcome. > > In the meantime, I need all developers to double check the information > under 'Contact'. Would the open-bio-l mailing list indeed reach the > prospective mentors and other devs? Will be you be fine with students > asking for feedback to their applications on the developers (i.e., > this) list? Is there a blessed IRC where at least some of the > prospective mentors hang out for students to ask questions during the > time they apply? > > I also need space for the reference information for all projects that > will participate with at least one project idea (I would hope that > that's all projects) to be added in the 'Open-Bio projects involved' > section. > > ***** > Most important of all, if you can volunteer to mentor a project, > please post a project idea to the page in the respective section, > using the idea template that's there already (copy, paste, and edit). > ***** > > The deadline for organization applications is Friday this week, Mar > 13, which is very soon. The ideas page is a major factor and component > in how Google scores new mentoring organizations - the more we can > show the resourcefulness and diversity of our member projects the more > competitive I think we'll be. So all those who responded with ideas or > willingness to help out as primary or secondary mentores earlier, I > need you to think about and put up your idea(s) now. > > Cheers, > > -hilmar > > [1] http://tinyurl.com/ck7tqe > > From jdudley at stanford.edu Fri Mar 13 15:09:01 2009 From: jdudley at stanford.edu (Joel Dudley) Date: Fri, 13 Mar 2009 08:09:01 -0700 Subject: [BioRuby] Ruby & R In-Reply-To: <49BA3C22.2090505@ingm.it> References: <49BA3C22.2090505@ingm.it> Message-ID: <2567FB6B-9965-4705-AE11-72114D23C61E@stanford.edu> Ra, I work mainly with expression data, and what I do is use Ruby for as much as I can, then use RSRuby to call the key R functions I need. You are right, it is not comfortable to work in R at all, but it's hard to deny the wealth of packages it has for working with expression and genotyping data. Of course it is up to people like you and me to add this kind of functionality to BioRuby if we can manage it. Unfortunately I can't seem to find the time. -- Joel On Mar 13, 2009, at 3:57 AM, Raoul JP Bonnal wrote: > Hi guys, > I have always worked on sequences and bioruby gave me everything I > need to work with that kind of data. > Now I moved to Illumina gene expression and rtpcr data, I think > there is a lack of support in this kind of data. Isn't it ? > I found that usually this data are handled by R, but which are the > pro/cons of this lang ? And as "lang/syntax"... it's not very > confortable I think :-( > > Pjotr is providing support for biolib to Ruby. > > Could Ruby do it better ? > > I mean, Python/Ruby/Perl seems that depends on the end user, they > can do the same things but for R ? > > -- > Ra > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby =============Email Policy============= I now only check mail at the following times: - 8 a.m., Noon, 5 p.m. Mon-Fri - 8 a.m. Sat-Sun If this is a true emergency, or you require an immediate response from me, please contact me via my mobile phone: (408) 464-8258 ==================================== From pjotr.public14 at thebird.nl Fri Mar 13 19:17:37 2009 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Fri, 13 Mar 2009 20:17:37 +0100 Subject: [BioRuby] Ruby & R In-Reply-To: <49BA3C22.2090505@ingm.it> References: <49BA3C22.2090505@ingm.it> Message-ID: <20090313191737.GA21375@thebird.nl> Hi Raoul, On Fri, Mar 13, 2009 at 11:57:38AM +0100, Raoul JP Bonnal wrote: > Hi guys, > I have always worked on sequences and bioruby gave me everything I need > to work with that kind of data. > Now I moved to Illumina gene expression and rtpcr data, I think there is > a lack of support in this kind of data. Isn't it ? > I found that usually this data are handled by R, but which are the > pro/cons of this lang ? And as "lang/syntax"... it's not very > confortable I think :-( R is the language of choice for most statisticians. So it is natural that where statistics count R gets the functionality. R as a language is not a good bargain. I see it more as as succesfull 'glue' language of C libraries (rather slow glue too). I think the only place it shines is with matrix manipulations. And then there are the libraries - which, as it happens, are mostly written in C. > Pjotr is providing support for biolib to Ruby. As these are C libraries I can easily provide Ruby mappings with biolib. If you point me at specific R functionality you want I can see if I can map it. > Could Ruby do it better ? I don't think so. We are with too few. In fact I have become truely multilingual. I use R for most statistical stuff, microarrays and (soon) deep sequencing. That is why I am driven to map to Ruby. To be honest, these days I am also using BioPerl stuff. BioRuby has quite a bit of functionality, but the BioPerl people are ahead and still moving faster. We have a problem in bioinformatics. Too few people, too many language domains. > I mean, Python/Ruby/Perl seems that depends on the end user, they can do > the same things but for R ? We can map the R C libraries using biolib. I have done the fundamentals. Tell me what functions you require. I think mapping is the way forward. Pj. From hlapp at gmx.net Sat Mar 14 22:59:39 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sat, 14 Mar 2009 18:59:39 -0400 Subject: [BioRuby] Google Summer of Code: application submitted, action needed In-Reply-To: <37C2E759-7D01-4333-A949-70465D453D9C@gmx.net> References: <8E3950DE-6B8C-450F-9780-1BB77A193C46@gmx.net> <37C2E759-7D01-4333-A949-70465D453D9C@gmx.net> Message-ID: <0D94A4F0-FAF2-4E9F-838B-159F7DBA8AA4@gmx.net> Hi all, I have submitted the application yesterday for O|B|F participating in the 2009 Google Summer of Code as a mentoring organization. The application is at http://docs.google.com/Doc?id=dhs98hzv_7zn8bxqjm and is also linked to from the ideas page at http://open-bio.org/wiki/Google_Summer_of_Code_2009 Now keep your fingers crossed, Google is slated to announce acceptances on March 18. This is the last cross-project message re: Summer of Code that addresses mentors and our projects; future messages that I'll post across projects will be primarily for students such as announcing whether we are accepted or not and issuing calls for application. **What we need most and right now is action from our projects' developers and from possible mentors.** Google admins will start reviewing organization applications on Monday. The ideas page has 6 project ideas right now - though the ideas are good ones, the quantity won't be particularly impressive to Google. Therefore, if you have an idea for a summer project for a student please use the C& template (it is commented out now but you'll see it when you pull the Ideas section into the editor) and put it up there ASAP. If you're not sure yet who'll mentor, put tentative names there. We don't need a full commitment from mentors until the student application period starts (March 23). Next, for all projects, the leads and/or volunteers should check the reference information for their project: http://open-bio.org/wiki/Google_Summer_of_Code_2009#Open-Bio_projects_involved I just culled these links from the various project websites - it'd be much appreciated if going forward everyone can lend a hand in this. Please review what's there and add or fix as you see fit. *These links must be correct and complete - otherwise potential students may not find you.* Finally, all prospective mentors, primary or secondary, committed or not, and anyone else who would like to volunteer to help out, should subscribe themselves ASAP to the mailing list for communicating GSoC- related administrivia: http://lists.open-bio.org/mailman/listinfo/gsoc I will *not* cross-post all administrative announcements or requests for information, and so you *will* miss information if you don't subscribe yourself there. (Note: students will be subscribed there only *after* acceptance). Those who are considering to mentor, primary or helping out, please also add yourselves to the Mentors section on the Ideas page (and check your link if you're already there): http://open-bio.org/wiki/Google_Summer_of_Code_2009#Mentors Cheers everyone, and fingers crossed! -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From ktym at hgc.jp Wed Mar 18 01:34:50 2009 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 18 Mar 2009 10:34:50 +0900 Subject: [BioRuby] efetch/esearch broken In-Reply-To: References: Message-ID: <1C957035-3095-483C-BE30-CF06FE8FF422@hgc.jp> Hi Craig, Thank you for pointing this out. It was a bug. --- /usr/local/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/ncbirest.rb.orig 2009-03-18 10:33:14.000000000 +0900 +++ /usr/local/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/ncbirest.rb 2009-03-18 10:24:25.000000000 +0900 @@ -147,7 +147,7 @@ class REST list = [] 0.step(limit, step) do |i| - retmax = [step, limit - i].min + retmax = hash["retmax"] || [step, limit - i].min opts.update("retmax" => retmax, "retstart" => i) ncbi_access_wait response = Bio::Command.post_form(serv, opts) Regards, Toshiaki Katayama On 2009/03/06, at 4:16, craigknox wrote: > Hi Everyone, > > I am using the latest bioruby gem (1.3.0) and I am having trouble running efetch. The following is copied directly from the tutorial on "http://bioruby.open-bio.org/wiki/BiorubyTutorial". When I run it, "Bio::PubMed.efetch(entries)" returns a string instead of an array of strings. Additionally, the "retmax" parameter for esearch is not working - it is only returning the default of 100 entries. > > Is the tutorial just out of date or is this a bug? > > Thanks, > Craig Knox > > #!/usr/bin/env ruby > require 'bio' > > keywords = ARGV.join(' ') # I am using "histamine" here > > options = { > 'maxdate' => '2003/05/31', > 'retmax' => 1000, > } > > entries = Bio::PubMed.esearch(keywords, options) > > Bio::PubMed.efetch(entries).each do |entry| > medline = Bio::MEDLINE.new(entry) > reference = medline.reference > puts reference.bibtex > end > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From hlapp at gmx.net Wed Mar 18 18:45:50 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 18 Mar 2009 14:45:50 -0400 Subject: [BioRuby] OBF application for Summer of Code has been rejected Message-ID: <44D1FAFD-B5D7-418B-9FDA-6945219A5481@gmx.net> I hope to find out later why, but our Google Summer of Code application as an umbrella org has been rejected. However, NESCent has been accepted. If you can give your project idea a phylogenetics/phyloinformatics focus, go and put it up on the NESCent ideas page at http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 Do so pretty much **now** - we will start broadcasting and reaching out to students tonight and tomorrow. If someone comes to the site and they don't see a Bio* project that they would have been interested in, they may not check back for updates. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From hlapp at gmx.net Thu Mar 19 22:50:58 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Thu, 19 Mar 2009 18:50:58 -0400 Subject: [BioRuby] Summer of Code 2009 Message-ID: PHYLOINFORMATICS SUMMER OF CODE 2009 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and possibly more importantly, a T-shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Initial project ideas are listed on the website. These range from hardware accerelation for phylogenetic inference, to tree visualization within a wiki, to alignment of next-gen sequencing data, to development of a reusable ontology term markup module for biocuration. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Apply online at the Google Summer of Code website (http://socghop.appspot.com/ ), where you will also find GSoC program rules and eligibility requirements. The 12-day application period for students opens on Monday March 23rd and runs through Friday, April 3rd, 2009. INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early on as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org From flashdog at gmx.net Fri Mar 20 10:53:03 2009 From: flashdog at gmx.net (Flash Dog) Date: Fri, 20 Mar 2009 20:53:03 +1000 Subject: [BioRuby] rotation of protein Message-ID: <49C3758F.6060100@gmx.net> Hello, I have a translation vector and a rotation matrix how can I used it for a protein in a PDB? Best regards, From bonnalraoul at ingm.it Sun Mar 22 11:34:45 2009 From: bonnalraoul at ingm.it (Raoul JP Bonnal) Date: Sun, 22 Mar 2009 12:34:45 +0100 Subject: [BioRuby] euruko 09 but Message-ID: <49C62255.9090909@ingm.it> seems sold out :-( http://app.euruko2009.org/calendar -- Ra From kenglish at gmail.com Mon Mar 23 05:55:26 2009 From: kenglish at gmail.com (Kevin English) Date: Sun, 22 Mar 2009 19:55:26 -1000 Subject: [BioRuby] Error running standalone blast Message-ID: Hello all, New to bioRuby. Following the example I found here: http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1, I wrote the following program to run a standalone blast. I am getting an exception related to rexml... Does anyone know if there is a fix for this? #!/usr/bin/ruby require 'rubygems' require 'bio' factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') ff = Bio::FlatFile.open(Bio::FastaFormat, '/home/kenglish/Data/EST_A.fasta') ff.each do |entry| puts "Searching..." + entry.definition report = factory.query(entry) report.each do |hit| hit.each do |hsp| puts hsp.query_from end end end /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method `record_entity_expansion' for nil:NilClass (NoMethodError) from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' from /usr/lib/ruby/1.8/rexml/element.rb:384:in `each_element_with_text' from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' from /usr/lib/ruby/1.8/rexml/element.rb:388:in `each_element_with_text' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in `rexml_parse_program' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in `rexml_parse' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in `auto_parse' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in `initialize' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in `new' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in `parse_result' from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in `query' from blast1.rb:11 from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in `each' from blast1.rb:9 Thanks in advance for any help... Kevin English From donttrustben at gmail.com Mon Mar 23 07:07:47 2009 From: donttrustben at gmail.com (Ben Woodcroft) Date: Mon, 23 Mar 2009 18:07:47 +1100 Subject: [BioRuby] Error running standalone blast In-Reply-To: References: Message-ID: Hi, I've run into this bug as well and managed to fix it - it is related to a problematic security fix for Debian and Ubuntu. See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502535 or https://bugs.launchpad.net/ubuntu/+source/ruby1.8/+bug/291893 Thanks, ben 2009/3/23 Kevin English > Hello all, > New to bioRuby. > Following the example I found here: > > http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1 > , > I wrote the following program to run a standalone blast. I am getting an > exception related to rexml... Does anyone know if there is a fix for this? > > > #!/usr/bin/ruby > > require 'rubygems' > require 'bio' > > factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') > ff = Bio::FlatFile.open(Bio::FastaFormat, > '/home/kenglish/Data/EST_A.fasta') > > ff.each do |entry| > puts "Searching..." + entry.definition > report = factory.query(entry) > report.each do |hit| > hit.each do |hsp| > puts hsp.query_from > end > end > end > > > /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method > `record_entity_expansion' for nil:NilClass (NoMethodError) > from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' > from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' > from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' > from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' > from /usr/lib/ruby/1.8/rexml/element.rb:384:in `each_element_with_text' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:388:in `each_element_with_text' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in > `rexml_parse_program' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in > `rexml_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in > `auto_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in > `initialize' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `new' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `parse_result' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in > `query' > from blast1.rb:11 > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in > `each' > from blast1.rb:9 > > Thanks in advance for any help... > > Kevin English > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > -- FYI: My email addresses at unimelb, uq and gmail all redirect to the same place. From ngoto at gen-info.osaka-u.ac.jp Mon Mar 23 06:46:24 2009 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Mon, 23 Mar 2009 15:46:24 +0900 Subject: [BioRuby] Error running standalone blast In-Reply-To: References: Message-ID: <20090323064626.A98601CBC423@idnmail.gen-info.osaka-u.ac.jp> Hi, This is not a BioRuby's problem, but REXML DoS vulnerability fix patch's bug. See below for the deital of the REXML DoS fix's bug. http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502535 The issue have already been reported in KNOWN_ISSUES.rdoc bundled within BioRuby 1.3.0. See the section "Problem with REXML DoS vulnerability patch before 09-Nov-2008" http://github.com/bioruby/bioruby/blob/51c3223e033b2992a7bd95da282f88164406ff92/KNOWN_ISSUES.rdoc (quoted from KNOWN_ISSUES.rdoc) > If you have applied a patch taken from > www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/ > before 09 Nov 2008 12:40 +0900, because of the bug in the patch, > parsing of Blast XML results with REXML parser may fail. The bug > is already fixed and new patch is available on the above URL. > Note that some Linux distributions would have incorporated the > patch in their manners, and may have the same problem. To solve the problem, install the new patch, or upgrade to the newest Ruby 1.8.7. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Sun, 22 Mar 2009 19:55:26 -1000 Kevin English wrote: > Hello all, > New to bioRuby. > Following the example I found here: > http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1, > I wrote the following program to run a standalone blast. I am getting an > exception related to rexml... Does anyone know if there is a fix for this? > > > #!/usr/bin/ruby > > require 'rubygems' > require 'bio' > > factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') > ff = Bio::FlatFile.open(Bio::FastaFormat, '/home/kenglish/Data/EST_A.fasta') > > ff.each do |entry| > puts "Searching..." + entry.definition > report = factory.query(entry) > report.each do |hit| > hit.each do |hsp| > puts hsp.query_from > end > end > end > > > /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method > `record_entity_expansion' for nil:NilClass (NoMethodError) > from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' > from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' > from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' > from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' > from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' > from /usr/lib/ruby/1.8/rexml/element.rb:384:in `each_element_with_text' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' > from /usr/lib/ruby/1.8/rexml/element.rb:388:in `each_element_with_text' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in > `rexml_parse_program' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in > `rexml_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in > `auto_parse' > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in > `initialize' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `new' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > `parse_result' > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in > `query' > from blast1.rb:11 > from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in > `each' > from blast1.rb:9 > > Thanks in advance for any help... > > Kevin English > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From kenglish at gmail.com Mon Mar 23 08:23:56 2009 From: kenglish at gmail.com (Kevin English) Date: Sun, 22 Mar 2009 22:23:56 -1000 Subject: [BioRuby] Error running standalone blast In-Reply-To: <20090323064626.A98601CBC423@idnmail.gen-info.osaka-u.ac.jp> References: <20090323064626.A98601CBC423@idnmail.gen-info.osaka-u.ac.jp> Message-ID: I edited line 76 in /usr/lib/ruby/1.8/rexml/entity.rb and changed: document.record_entity_expansion to document.record_entity_expansion unless document.nil? Seems to work now. Thanks for the quick response. Kevin document.record_entity_expansion unless document.nil? On Sun, Mar 22, 2009 at 8:46 PM, Naohisa GOTO wrote: > Hi, > > This is not a BioRuby's problem, but REXML DoS vulnerability > fix patch's bug. > > See below for the deital of the REXML DoS fix's bug. > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502535 > > The issue have already been reported in KNOWN_ISSUES.rdoc > bundled within BioRuby 1.3.0. See the section > "Problem with REXML DoS vulnerability patch before 09-Nov-2008" > > > http://github.com/bioruby/bioruby/blob/51c3223e033b2992a7bd95da282f88164406ff92/KNOWN_ISSUES.rdoc > > (quoted from KNOWN_ISSUES.rdoc) > > If you have applied a patch taken from > > www.ruby-lang.org/en/news/2008/08/23/dos-vulnerability-in-rexml/ > > before 09 Nov 2008 12:40 +0900, because of the bug in the patch, > > parsing of Blast XML results with REXML parser may fail. The bug > > is already fixed and new patch is available on the above URL. > > Note that some Linux distributions would have incorporated the > > patch in their manners, and may have the same problem. > > To solve the problem, install the new patch, or upgrade > to the newest Ruby 1.8.7. > > Naohisa Goto > ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org > > > On Sun, 22 Mar 2009 19:55:26 -1000 > Kevin English wrote: > > > Hello all, > > New to bioRuby. > > Following the example I found here: > > > http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1 > , > > I wrote the following program to run a standalone blast. I am getting an > > exception related to rexml... Does anyone know if there is a fix for > this? > > > > > > #!/usr/bin/ruby > > > > require 'rubygems' > > require 'bio' > > > > factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B') > > ff = Bio::FlatFile.open(Bio::FastaFormat, > '/home/kenglish/Data/EST_A.fasta') > > > > ff.each do |entry| > > puts "Searching..." + entry.definition > > report = factory.query(entry) > > report.each do |hit| > > hit.each do |hsp| > > puts hsp.query_from > > end > > end > > end > > > > > > /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method > > `record_entity_expansion' for nil:NilClass (NoMethodError) > > from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity' > > from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize' > > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each' > > from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize' > > from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value' > > from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text' > > from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?' > > from /usr/lib/ruby/1.8/rexml/element.rb:384:in > `each_element_with_text' > > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call' > > from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something' > > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > > from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each' > > from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each' > > from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something' > > from /usr/lib/ruby/1.8/rexml/element.rb:388:in > `each_element_with_text' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in > > `rexml_parse_program' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in > > `rexml_parse' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in > > `auto_parse' > > from > > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in > > `initialize' > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > > `new' > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in > > `parse_result' > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in > > `query' > > from blast1.rb:11 > > from > /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in > > `each' > > from blast1.rb:9 > > > > Thanks in advance for any help... > > > > Kevin English > > _______________________________________________ > > 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 mkikkawa at gmail.com Mon Mar 23 08:57:33 2009 From: mkikkawa at gmail.com (Masahide Kikkawa) Date: Mon, 23 Mar 2009 17:57:33 +0900 Subject: [BioRuby] rotation of protein In-Reply-To: <49C3758F.6060100@gmx.net> References: <49C3758F.6060100@gmx.net> Message-ID: <093A69F5-7DF2-42A3-B77D-7D69880F0050@gmail.com> Hi, Seems the ruby code in bioruby dealing with PDB does not have specific functions for translation or rotation. Since the ATOM coordinate is stored as Vector, you might be able to use the matrix library.. I would recommend to use moleman2 (written by Gerard J. Kleywegt) to get the job done. > Hello, > I have a translation vector and a rotation matrix how can I used it > for a protein in a PDB? > > Best regards, > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From flashdog at gmx.net Mon Mar 23 12:31:09 2009 From: flashdog at gmx.net (Flash Dog) Date: Mon, 23 Mar 2009 22:31:09 +1000 Subject: [BioRuby] rotation of protein In-Reply-To: <093A69F5-7DF2-42A3-B77D-7D69880F0050@gmail.com> References: <49C3758F.6060100@gmx.net> <093A69F5-7DF2-42A3-B77D-7D69880F0050@gmail.com> Message-ID: <49C7810D.8030000@gmx.net> Hello, Thank you for your email. Unfortunately I can only find a manual, but not the download link. Do you know where can I download moleman2? Thank you in advance. > Hi, > > Seems the ruby code in bioruby dealing with PDB does not have specific > functions for translation or rotation. Since the ATOM coordinate is > stored as Vector, you might be able to use the matrix library.. > > I would recommend to use moleman2 (written by Gerard J. Kleywegt) to > get the job done. > >> Hello, >> I have a translation vector and a rotation matrix how can I used it >> for a protein in a PDB? >> >> Best regards, >> _______________________________________________ >> 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 hlapp at gmx.net Sun Mar 29 18:41:12 2009 From: hlapp at gmx.net (Hilmar Lapp) Date: Sun, 29 Mar 2009 14:41:12 -0400 Subject: [BioRuby] Reminder: Student application deadline for Summer of Code 2009 Message-ID: *** Please disseminate widely to students at your institution. *** *** Note: Among the ideas and mentors are BioPerl, BioRuby, and BioLib *** PHYLOINFORMATICS SUMMER OF CODE 2009 - STUDENT APPLICATION DEADLINE IS APRIL 3 http://hackathon.nescent.org/Phyloinformatics_Summer_of_Code_2009 The Phyloinformatics Summer of Code program provides a unique opportunity for undergraduate, masters, and PhD students to obtain hands-on experience writing and extending open-source software for evolutionary informatics under the mentorship of experienced developers from around the world. The program is the participation of the US National Evolutionary Synthesis Center (NESCent) as a mentoring organization in the Google Summer of Code(tm) (http://code.google.com/soc/ ). Students in the program will receive a stipend from Google (and a T- shirt solely available to successful participants), and may work from their home, or home institution, for the duration of the 3 month program. Each student will have at least one dedicated mentor to show them the ropes and help them complete their project. NESCent is particularly targeting students interested in both evolutionary biology and software development. Project ideas are listed on the website and range from hardware acceleration for phylogenetic inference, to support for phyloinformatics standards within the BioPerl and BioRuby toolkits, to alignment of next-gen sequencing data, to ontology term markup for biocuration, to semantic interoperability of web-services, to 3D-printing of phylogenies. All project ideas are flexible and many can be adjusted in scope to match the skills of the student. We also welcome novel project ideas that dovetail with student interests. TO APPLY: Instructions are at the website (see "When you apply"). You can find GSoC program rules and eligibility requirements at http://socghop.appspot.com . ***The 12-day application period for students ends on Friday, April 3rd, 2009, at 19:00 UTC (3pm EDT, 12pm PDT).*** INQUIRIES: phylosoc {at} nescent {dot} org. We strongly encourage all interested students to get in touch with us with their ideas as early as possible. 2009 NESCent Phyloinformatics Summer of Code: http://hackathon.nescent.net/Phyloinformatics_Summer_of_Code_2009 Google Summer of Code FAQ: http://socghop.appspot.com/document/show/program/google/gsoc2009/faqs Cyberinfrastructure Traineeships (managed separately from GSoC; postdocs also eligible): http://hackathon.nescent.org/Cyberinfrastructure_Summer_Traineeships_2009 To sign up for quarterly NESCent newsletters: http://www.nescent.org/about/contact.php --------- Todd Vision and Hilmar Lapp National Evolutionary Synthesis Center http://nescent.org