Phylohackathon 1/Subgroup Proposals

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Here we list subgroups and their proposed tasks which are not selected currently for the (next) hackathon. They may still be selected to replace one of the subgroups proposed for invitation, and a subgroup initially proposed for invitation may be pushed back into this pool. The ideas listed here may be selected for invitation to a later hackathon.

  1. NEXUS reference implementations: create reference implementations for reading and writing NEXUS format in popular programming languages and toolkits
    • Targeted languages and toolkits: Perl (Bioperl), Java (Biojava), Python (Biopython), Ruby (Bioruby), Prolog (Blipkit), R (Bioconductor?)
    • Participants(*): T.B.D.
  2. PhyloXML reference implementations: create reference implementations for reading and writing PhyloXML format in popular programming languages and toolkits
    • Targeted languages and toolkits: Perl (Bioperl), Java (Biojava), Python (Biopython), Ruby (Bioruby), Prolog (Blipkit), R (Bioconductor?)
    • Participants(*): T.B.D.
  3. Phylogenetic trees (and character data?) in GMOD: create all missing pieces to enable storing and retrieving NEXUS (and PhyloXML?) formatted data to and from, respectively, Chado.
    • Participants(*): Chris Mungall, David Emmert, Don Gilbert, T.B.D.

(*) participant code: italics = nominated, normal = accepted/interested, bold = confirmed