[Biojava-dev] [Biojava-l] Leadership

[Richard Holland]

The plan was to create separate new BJ3 jars for task-specific code,
exactly as you suggest for phylogenetics. I'd support a biojava-phylo
jar of some kind, and I agree it would probably depend on the BJ3
biojava-core module for sequence handling. The existing BJ code was not
originally going to be refactored into separate jars, unless Andreas has
other plans!

Scooter Willis wrote:
> 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 <mailto: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
>     <mailto:holland at eaglegenomics.com>
>     http://www.eaglegenomics.com/
>     _______________________________________________
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> 
> 

-- 
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/