[Biojava-l] GSoC 2012- Port an Algorithm to Java

[Spencer Bliven]

Unfortunately, HMMER is licensed as GPL. As such, we can't port it to
BioJava or even link against it with JNI. A 2009
post<http://selab.janelia.org/people/eddys/blog/?p=127>indicates that
they are not interested in re-licensing HMMER under a less
restrictive license. I think we should move away from any HMMER-port
project, and focus on porting other important algorithms such as BLAST (public
domain<http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/scripts/projects/blast/LICENSE>
).

I went ahead and removed HMMER from the GSoC wiki
page<http://biojava.org/wiki/Google_Summer_of_Code_2012>.
I was trying to think of other LGPL-compatable bioinformatics
projects<http://en.wikipedia.org/wiki/List_of_open_source_bioinformatics_software>which
would be nice to port to biojava. Maybe a sequence browser, such as
incorporating/linking the Integrated Genome
Browser<http://en.wikipedia.org/wiki/Integrated_Genome_Browser>?
Anyone have ideas other than BLAST?

-Spencer

On Sat, Mar 17, 2012 at 02:50, Ritisha Laungani
<ritishalaungani at gmail.com>wrote:

> Hello,
>
> I am Ritisha Laungani, a pre-final year student currently persuing *MSc
> Tech. Information Systems* at Birla Institute of Technology and Science,
> Goa, India.
>
> I would like to apply for the BioJava project as i have worked into all the
> 3 fields this projects requires- C, Java and Bio!
>
> As far as i understand, in simple terms, the project's goal is to convert
> an existing HMMER source code, which is written in C, to a java code using
> language processing tools.  Do correct me if i am wrong here!
>
> I must admit here that i am new to open source software development and
> also unaware of HMMER. But i would love to learn if given a chance and the
> correct resources!  :)
>
> Eagerly awaiting a reply, which could guide me to the next step.
>
> Regards,
>
> Ritisha Laungani
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