[Biojava-l] GSoC Application Discussion and Help - Porting BLAST to Java

[Andreas Prlic]

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*
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