[Biojava-l] Suggestion for porting GHMM library

[Dhruv Sharma]

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 <andreas at sdsc.edu> 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 <sharma.dhrv at gmail.com>
> 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  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
*Dhruv Sharma*
*Student
B.E.(Hons.) Computer Science
BITS, Pilani
*
*India*