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
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