Contributing

Interfaces to external resources:

• API for Ensemble (suggested by Jan Aerts)
• API for UCSC (Hiroyuki Mishima and Jan Aerts)
• API for InterMine (svn://subversion.flymine.org/flymine)
• API for BioMart etc.
• API for Semantic Web resources (BioGateway, Bio2RDF etc.) -- this is what we tried during the last BioHackathon

Modern bioinformatics:

• handling NGS data - wrappers and parsers for tools and libraries
• Proteomics
• Immunoinformatics - immunology prediction servers (described by someone during the Skype meeting)
• Handling pipelines

Classical bioinformatics:

• Do benchmark for existing BioRuby modules to find bottlenecks for improving performance (good example was posted by Martin Hansen and I think this kind of improvements should be welcomed)

• Setting up NCBI's BLAST WWW like interface (with SGE or Cloud backends) is still demanded. People who are working with not-yet-public genome often need to setup this kind of server (easy generic blast server creation in progress). How about to create a general Rails plugin using BioRuby which can be easily setup and can perform various sequence similarity search (by BLAST, BLAT, EXONERATE, Bowtie, whatever...) with simple configuration (use DSL to setup target DBs and the computational farm). This project should also target on the downstream processes -- phylogenetic annotations, mapping RNA-Seq data, summarizing statistics, visualization, integration with genome browsers etc. -- and cool UI design, to be chosen as a yet another BLAST+alpha interface.

• Improve Phyml support (partial codeml support exists, but many semi-obsolete functions are found in the code). Making a phyml-factory is lower priority than making good parsers for all phyml outputs.

Visualization modules:

• BioGraphics (already started by Jan) - genome mapping / comparative genomics?

• Interface for Cytoscape - so that we can easily generate beautiful graph visualization within BioRuby (e.g. from Semantic Web data) Note: some samples are already provided by Cytoscape group

Improving docs:

• Make the website sexier, updated & KISS (consolidate documentation in a single place!)

• Writing some tutorials on how you used the BioRuby - this should be done by newbie who will have difficulty with finding solutions on the Internet. They can ask mentors how to solve their problems and summarize the result in HOWTO-like tutorials. Some blogs and Wiki pages are the only existing resources as far as I know (and also clearly pointed by Yannick Wurm)

• Completing and cleaning up the current bioruby HOWTOs, for example by removing/replacing PERL code from HOWTO:Trees

• Example scripts: that mirror what exists in bioperl and in the biopython cookbook. (eg http://www.bioperl.org/wiki/Render_blast4)

• We should also need to have a document on "how to use GitHub for forking BioRuby", "how to create your own BioRuby plugins" etc.

Wishlist/Suggestions. Add yours here, or integrate them above.