[BioLib-dev] GSoC: Mapping JAVA libraries to Perl/Ruby/Python using Biolib+SWIG+JNI

[Pjotr Prins]

Hi Luiz,

On Tue, Mar 30, 2010 at 02:33:43PM -0300, Luiz Irber wrote:
> my name is Luiz Carlos Irber Júnior, currently a computer engineering
> undergrad (last semester) at Universidade Federal de São Carlos,
> Brazil. I have experience writing C bindings for Python with Cython
> (staff.get-e.org/?p=users/luizirber/python-eet.git) and C++ bindings
> too (but sadly it was on a company that didn't release the source).

Meanwhile, Brazil has a great track record in OSS! Thank you for
taking an interest in this challenging project.

> Looking for the available projects at OpenBio, I found this one, and
> started to research. I read the suggested link on the wiki, and
> http://www.swig.org/Doc1.3/Java.html too, but when I tried to find
> Fountain to actually try something... I couldn't find it. While
> searching I found that
> http://genetics.hpi.uni-hamburg.de/FOUNTAIN.html doesn't exist
> anymore, and apparently the source code isn't available anymore. What
> other Java libraries do you recommend for this project? Or where else
> can I find FOUNTAIN?

Hmmm. I guess we have to contact the authors for that. It looks like
the Bioinformatics thing. After publication the authors disappear. But
maybe it is temporary.

For Biolib we are really interested in making JAVA available to SWIG
over JNI. Any JAVA/Scala/Jython bioinformatics library could act as a
proof of concept. As far as I am concerned you can bring up something
completely different, as long as it covers some real JAVA-like
functionality that would map SWIG through the JNI.

If it is Fountain itself you are interested in I will contact the
original authors and see if we can get it.

What do you think?

Pj.