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

[Steve Darnell]

Hi Andreas,

We spoke offline about the HMMER/GPL issue this weekend. I think it is premature to remove the HMMER option from the GSoC wiki page. I would like to clarify the Sean Eddy blog post linked to by Spencer (_**_ emphasis mine):

>From the LICENSE section:

The only thing the GPLv3 really blocks is someone forking a derivative copy of HMMER and distributing it under a different license, such as a closed-source proprietary license; to do that, _*you'd need to negotiate a non-GPL license with us first*_.

>From the COPYRIGHT section:

_*We really don't expect to negotiate any non-GPL licenses, though*_. We want to enable many different people _*to contribute to a single open source HMMER codebase*_, as a shared codebase for bioinformatics and computational biology.

>From the TRADEMARK section:

_*Did I mention, we want to enable a single open source HMMER codebase?*_

==========

Sean Eddy and the Howard Hughes Medical Institute are the main copyright holders. The main goal is clear... maintain a single open source HMMER codebase. The choice of license for HMMER (GPL v3) was to persuade people to contribute back. However, OBF might be able to negotiate other arrangements (perhaps a non-GPL library that can only be distributed with BioJava and any contributions made by the GSoC student must be licensed back to HHMI under GPL?). I do not know how hopeful to be about that possibility, but it cannot hurt to ask.

I would like to dissuade GSoC students from directly contacting Sean Eddy or HHMI about this possibility. This task is most appropriate for a senior BioJava representative and it is up to the "Port an Algorithm to Java" mentors on how to proceed.

Just my $0.02.

Regards,
Steve

--
Steve Darnell
DNASTAR, Inc.
Madison, WI USA

-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Andreas Prlic
Sent: Monday, March 19, 2012 12:19 AM
To: Spencer Bliven; Hannes Brandstätter-Müller
Cc: biojava-l at lists.open-bio.org
Subject: Re: [Biojava-l] GSoC 2012- Port an Algorithm to Java

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/scri
> pts/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_bioinformati
> cs_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
>> _______________________________________________
>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org 
>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org 
> http://lists.open-bio.org/mailman/listinfo/biojava-l



--
-----------------------------------------------------------------------
Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank University of California, San Diego
(+1) 858.246.0526
-----------------------------------------------------------------------

_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/biojava-l