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

[Andreas Prlic]

Thanks Steve, good points.

Let's conclude this discussion with the take home message that
converting GPLed code to BioJava has licensing issues and requires
additional negotiations. Before embarking on such a project the
mentors will have a discussion about licensing with HHMI (or any other
license holder for other algorithms).

Andreas





2012/3/19 Steve Darnell <darnells at dnastar.com>:
> 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
>>> _______________________________________________