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 >> > _______________________________________________ > Biojava-l mailing list - [email protected] > 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 - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
