[Biojava-l] Biohackathon report

[Thomas Down]

For those who hadn't already heard about it, O'Reilly have
recently run a `hackathon' event, with representatives of all
the open-bio projects, plus a number of other bioinformatics
programmers.  Mathew Pocock and myself attended as BioJava
representatives.  The main thing which came out in the meeting
was agreement on a set of basic sequence-fetching methods,
which should be supported by Bio{Perl,Python,Java,Ruby}.  A
draft document can be downloaded from:

    http://www.technophage.com/open-bio-database.pdf

During the meeting, the following additions
were made to the biojava-live CVS tree.

  - On Sunday, before we started checking in any post-Hackathon
    code, I tagged the repository with `release-1_2-branch'.
    This doesn't necessarily mean that the branch point will
    exactly correspond to the 1.20 release, but given that
    a number of new modules have been checked in, I wanted a
    stable branch.

  - Brian Gilman (a new contributor to the BioJava tree) has
    done some work on an implementation of the `registry'
    component.  This can be found in the package
    org.biojava.directory

  - Matthew Pocock has been re-vamping the IndexedSequenceDB
    code to handle a new index format, which has been agreed
    as a standard for all the Bio* projects (i.e. you should
    be able to create indices with Biopython and access them
    with BioJava).

  - I've checked in a SequenceDB implementation backed
    by the BioSQL database schema (previously known as
    bioperl-db).  This currently works with PostgreSQL
    and MySQL (I don't recommend the latter since most
    MySQL installations still don't support transaction
    commit-rollback.  But it does work).  An Oracle
    port should be easy in the future, if anyone's
    interested in that.  I'll be posting some more detailed
    information about this in the next few days, but for
    now, if anybody wants to try it, the code can be found
    in org.biojava.bio.seq.db.biosql.


Also coming soon:

  - We'd like to use Martin Senger's OpenBQS code as a base
    for a bibliographic reference object model within BioJava.
    This should be checked in in the next week or so.


New mailing list:

  - For people interested in knowledge representation, there's
    now a `developer-oriented' mailing list for discussion
    about such topics:

         http://bioperl.org/mailman/listinfo/biograph