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Bio::TogoWSBio::TogoWS entry point for PDBj, NCBI, DDBJ, EBI, KEGGrequire ‘ bio ’t = Bio::TogoWS::REST.newputs t.entry('genbank', 'AF237819')puts t.search('uniprot', 'lung cancer')
BioRuby is Agile
● OpenBio* developers are the Stakeholders
Speed up in the iteration proccess● Speed up in the iteration proccess
● Frequent meetings (mail, skype/voice chat, irc)
● Test Everything (required for new features)
– Improve quality , maintainability and guarantee portability
– Ruby Unit Testing Framework , Rspec
● GitHub
● Low barries for new developers
● 32 forks and 100 people watching us
Agile Manifesto
Moving to Agile Programming
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Refactoring
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Ongoing Work
● Semantic Web (started @ BioHackathon 2010)
Expose data in RDF● Expose data in RDF
● Consuming SPARQL end points efficiently
● Ruby 1.9.2 support of BioRuby ( GSoC & OBF)
● Improved performances
● Develop an API for NeXML I/O, and, RDF triples for BioRuby (GSoC &
NESCent)NESCent)
● Implementation of algorithm to infer gene duplications in BioRuby
(GSoC & OBF)
PlugIn system
● We want a BioRuby core stable on every OS
But… we want to use experimental code ASAP● But… we want to use experimental code ASAP
● BioRuby + BioRuby Plugin + Rails we can have multiple
applications with an unique core and specific features
– User or Application
● Suggest Guidelines for plugin namespace
● On GitHub you can find our plugins looking for
bioruby -plugin -NAME
PlugIn system
The plugin system will be delivered with the next
BioRuby releaseBioRuby release
BioGraphics – Jan Aerts-
For biologists:
bioruby --plugin install graphics
For geeks:For geeks:
bioruby --plugin install git://github.com/user/repo.g it
It’s very experimental
What We Need
● Better integration with R
● Better support for data visualization (interpretation)
● Detailed Roadmap
Publications
BioRuby: Bioinformatics software for the Ruby programming language (submitted)
Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and
workflows (accepted)
Toshiaki Katayama et all.
Toshiaki Katayama, Mitsuteru Nakao and Toshihisa Takagi (2010)
TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services, Nucleic Acids