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 <[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
