I think HMMER implementation should be viewed as the source code of interest. When they went from HMMER2 to HMMER3 significant changes in what answer you get.
On 4/1/12 8:15 PM, "Andreas Prlic" <[email protected]> wrote: >That could work in terms of license and would be an interesting >feature to have. I am still slightly concerned that the scale of the >project might be too big and it might be difficult to accomplish this >during the limited time of the project. > >Andreas > >On Sun, Apr 1, 2012 at 2:32 PM, Dhruv Sharma <[email protected]> >wrote: >> Hi Andreas, >> >> In response to our last discussion, I would like to suggest porting >>General >> Hidden Markov Model (GHMM) library (http://ghmm.org/) from C to Java. >> >> The library is licensed under LGPL and is currently available as RC1 >> version. The code is not very big and it is very much possible to port >>100% >> code to Java which would make it not only efficient in comparison to >>use of >> converters or JNI but also make it platform independent. >> >> Would it be possible to add this library to BioJava? >> >> If yes, I would surely like to work on it. >> >> >> >> >> On Sun, Apr 1, 2012 at 11:24 PM, Andreas Prlic <[email protected]> wrote: >>> >>> Hi Dhruv, >>> >>> We are quite flexible regarding the projects and what we are really >>> looking for are sound projects and motivated students. As such our >>> project suggestions are quite open. We will interact with accepted >>> students from remote, so a certain degree of self-sufficiency will be >>> required from the side of the student. >>> >>> If you already see tons of problems coming up during your initial >>> assessment of the project, perhaps focus your proposal on something >>> smaller and more achievable. There are quite a number of interesting >>> algorithms out there and it does not have to be one of the ones >>> suggested by us. >>> >>> Andreas >>> >>> >>> >>> On Sat, Mar 31, 2012 at 1:46 PM, Dhruv Sharma <[email protected]> >>> wrote: >>> > Hi, >>> > >>> > I am Dhruv Sharma, a senior undergraduate student pursuing >>>B.E.(Hons.) >>> > Computer Science at BITS, Pilani, India. >>> > >>> > I am very much interested in 'porting BLAST algorithm to Java' as a >>>GSoC >>> > 2012 project. I am proficient and primarily work using Java and C. >>>Also, >>> > I >>> > have past experience of working in C++ before migrating to Java. >>> > However, I >>> > am new to GSoC and haven't used version control in the past. >>> > >>> > My recent project was based on developing a web application in Java >>>for >>> > posting data to remote CS-BLAST web >>> > service<http://toolkit.tuebingen.mpg.de/cs_blast/> with >>> > FASTA sequence, parse and auto-filter its results using the release >>>date >>> > from RCSB PDB <http://www.rcsb.org/pdb/home/home.do> and download the >>> > PDB >>> > files. >>> > >>> > Since, the project aims at converting the legacy C/C++ code to Java, >>> > already suggested approaches on the Bio-Java page and my observations >>> > are:- >>> > >>> > 1) Using C++ to Java converters for 100% conversion. I have tried >>> > converting the ncbi-blast-2.2.26 source code using a few freely >>> > available >>> > converters but all of them either crashed or failed to convert even >>> > after I >>> > resolved certain header file dependency issues that emerged. Most >>> > failures >>> > occurred at function calls to non-standard C++ libraries. >>> > >>> > 2) Using JNI as an alternative solution. JNI programming would be a >>> > tedious task and would anyway require understanding of the purpose of >>> > underlying C++ code. Hence,has little advantage over rewriting the >>> > equivalent Java code. A significant advantage can be seen when there >>>is >>> > no >>> > efficient Java alternative of the C++ code. However, platform >>>dependence >>> > would still exist. >>> > >>> > According to my understanding of the problem, a hybrid approach can >>>be >>> > taken up which includes using code converters for simpler files, >>>manual >>> > coding for tricky areas and using JNI for typical C++ code involving >>> > non-standard libraries. But, I am still not clear about my exact >>>course >>> > of >>> > action. >>> > >>> > Can you please tell me if my analysis of the problem is correct? >>>Please >>> > also comment on the feasibility of my suggested approach and please >>>make >>> > any suggestions as they would help me in improving my application >>>draft >>> > that I would soon be sharing for review. >>> > >>> > As BLAST is a collection of programs, so, keeping in mind the length >>>of >>> > code to be ported, can we work on certain selectively critical >>>programs >>> > in >>> > it from the GSoC's perspective? >>> > >>> > >>> > Thanks. >>> > >>> > -- >>> > *Dhruv Sharma* >>> > *Student >>> > B.E.(Hons.) Computer Science >>> > BITS, Pilani >>> > * >>> > *India* >>> > _______________________________________________ >>> > Biojava-l mailing list - [email protected] >>> > http://lists.open-bio.org/mailman/listinfo/biojava-l >> >> >> >> >> -- >> Dhruv Sharma >> Student >> B.E.(Hons.) Computer Science >> BITS, Pilani >> India >> > >_______________________________________________ >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
