Naohisa Goto edited this page Jun 14, 2016 · 1 revision

Interfaces to external resources:

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:

Improving docs:

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