[Biojava-l] [Biojava-dev] Leadership

[Scooter Willis]

Andreas

Congrats on taking on the responsibility of steering BioJava in a positive
direction.

I needed the ability to generate phylogenetic trees from aligned sequence
data and found that the work was started in a google summer project but
looking at the code it wasn't finished and appeared to focus only on loading
trees not creating them. I ended up taking the tree generation code out of
jalview and removing as much jalview dependencies as possible and have it as
a nice tight collection of classes. My assumption without any deep legal
review is that because jalview is open source that the code can be used and
contributed to another open source project like BioJava. I will also plan on
contributing the code changes back to Jalview.

One of the challenges I ran into with the JalView code is performance for
building the tree when using 1800+ sequences(takes a very very long time) so
I am doing some code optimization and finishing up testing on a fairly
significant performance speedup doing Neighbor_Join with a slightly
different approach that makes it N2 instead of N3. I have a couple things to
fix in tree joinging code and then will compare results for the quality of
the tree compared to the original distance matrix. I should know more this
week.

I think I remember a BioJava discussion about trying to seperate parts and
pieces to that if you try and use a particular feature set of BioJava you
are not forced into absorbing the entire BioJava collection of Jars. In my
case I would want a biojava-phylogenetic.jar that has all things related to
tree creation and/or tree viewing etc. If the common data format for
handling sequences is RichSequence or Sequence then I would expect to have
one other Jar requirement of biojava-core.jar. Not sure if any work has been
done to refactor the BioJava code base into multiple jar files in the same
way apache does its jars for great java code geared to a specific problem
domain.

Let me know what I can do to assist moving forward.

Thanks

Scooter Willis

On Tue, Apr 14, 2009 at 4:33 AM, Richard Holland
<holland at eaglegenomics.com>wrote:

> Hello again.
>
> Well, nobody objected, and several people supported the idea, so I would
> now like to formally hand over control of the BioJava project to Andreas
> Prlic with immediate effect.
>
> It's been good fun working with the project over the last 5 years, and
> although I'll no longer be in charge, I will still remain on the mailing
> lists and contribute code/ideas/bugfixes/etc. whenever I get the chance.
>
> I'll also continue to attend BOSC, including this year in Stockholm, so
> I'm looking forward to meeting up with everyone there for a beer or two.
>
> Thanks for the help and support everyone's given, and I'm sure you'll
> join me in wishing Andreas the best of luck with the project. He'll be
> an excellent leader and with him in charge I believe the project will go
> from strength to strength.
>
> cheers,
> Richard
>
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
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