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

[Andreas Prlic]

A worst case scenario could be to host an independent and GPLed
project on the BioJava SVN. However I  see your point. These licensing
issues contribute to the complexity around such a project and make it
much more difficult.

In terms of other algorithms, BioJava already contains a multiple
sequence alignment algorithm, as such I would rather see that one
getting extended, than a 2nd algorithm being implemented.

Andreas

On Sun, Mar 18, 2012 at 1:47 PM, Spencer Bliven <sbliven at ucsd.edu> wrote:
> 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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-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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