[Biojava-dev] [Biojava-l] Leadership

[Andreas Prlic]

Hi Scooter,

Thanks for volunteering. I like the idea of modularizing BioJava in
the next version. The details of how to do this still need to be
discussed on the dev mailing list. If you want to be involved into
anything phylo related then this is great and any contribution will be
welcome.

About merging in 3rd party code that is under a different license: For
this you need to get  permission from the original copyright owners or
rewrite the code ....

Andreas


On Tue, Apr 14, 2009 at 8:02 AM, Scooter Willis <willishf at ufl.edu> 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>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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>>
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