[Biojava-l] Question About BioJava

[Thomas Down]

On Thu, Jan 25, 2001 at 08:30:53PM -0500, Nick Heudecker wrote:
> Hi,
> 
> I've noticed that the BioJava news hasn't been updated since August
> 2000.  Is this project still being maintained?  If so, I have some
> questions:

Absolutely.

Sorry if the news section's a bit old.  There's been lots
of development in the CVS repository since the 1.0x releases.
For instance:

  - More recognition of mutability in the core interfaces,
    and pervasive use of a simple event model for change
    notification/vetoing

  - New sequence I/O framework

  - Parsers for blast and fasta output, and PDB files

  - Client for the DAS protocol (still developing, but usable)

  - Enhanced dynamic programming toolkit.

  - And lots lots more (apologies if I've left out someone's
                        favourite feature).

>  -) Where do you see BioJava heading in the next 12/18 months?  

Well, in the next few weeks our priority is to have a final
test cycle on the current CVS code, and make a 1.1 release
(and update the news section of the website ;).

Beyond that, it depends what individual developers want
to work on.  I'm keen to see pervasive use of some form
of naming and directory interface in the next release.  I'd
guess that we're also going to see a lot more work related
to storing sequences in big databases -- purely as a consequence
of the amount of data now available.

Another area where there's plenty of room for biojava to
expand is proteomics and 3D structure.

>  -) How has the bioinformatics community reacted to the BioJava project?

That's hard to answer really but:

  - Looking at the mailing list archives, we've seen a steady
    growth in traffic.  The number of contributers is also
    increasing.

  - We've also been seeing a steady interest in requests to
    the web site:

     http://www.biojava.org/stats/www2001/index.html

    I guess we'd better update it a bit...

>  -) How can I contribute?  I'm a pretty good developer and I'd like to get
> involved.  I'm interested in doing GUI and 3D development.  

Check out the latests CVS version and experiment.  We're happy
to accept contributions of code relating to almost any biocomputing
activity.  In GUI terms:

  - We have a (really experimental) start of a sequence viewing
    GUI in the org.biojava.bio.gui.sequence package.  It would be
    good to see some more development on that.

  - Right now we don't have an object model for storing 3D structure
    data.  But, of course, it would be good to have one.

If you're interested in working on any piece of code, just mail
the list and see what people think.  If you've got code ready
to check in, Matthew Pocock (mrp@sanger.ac.uk) is the person to
talk to about read-write access to the CVS repository.

Let me know if you've got any more questions,

   Thomas.