I wanted to wait if we actually get a strong project proposals before contacting the Hmmer folks. At this stage I have seen a lot of interest, but not a single proposal being submitted for this.
Andreas On Sun, Apr 1, 2012 at 10:21 PM, Dhruv Sharma <[email protected]> wrote: > Then I think I'll stick to Hmmer3 implementation as far as GSoC is > concerned. I hope the licensing issues are sorted out soon. > > Thanks! > > > -- > Dhruv Sharma > Student > B.E.(Hons.) Computer Science > BITS, Pilani > India > > > On Mon, Apr 2, 2012 at 9:00 AM, Scooter Willis <[email protected]> wrote: >> >> 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
