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 <[email protected]>: > 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: [email protected] > [mailto:[email protected]] On Behalf Of Andreas Prlic > Sent: Monday, March 19, 2012 12:19 AM > To: Spencer Bliven; Hannes Brandstätter-Müller > Cc: [email protected] > 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 <[email protected]> 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 >> <[email protected]>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 - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
