[Biojava-l] Interested in working with BioJava for GSoC 2012

[Amr AL-Hossary]

Dear Komal,

As far as I know, The project is about porting the code to Java, not using existing C code within JNI.
That means you should be able to digest the algorithm first, Build it using Java from scratch, depending on C code as a reference Implementation.

Regards

Amr

-----Original Message----- 
From: Komal Sanjeev 
Sent: Sunday, March 18, 2012 12:59 AM 
To: Andreas Prlic ; biojava-l at lists.open-bio.org 
Subject: Re: [Biojava-l] Interested in working with BioJava for GSoC 2012 

Hi all,

Introducing myself a bit more, I also work as a remote intern for
DARNED<http://darned.ucc.ie/>.
DARNED is a database of RNA Editing, and currently new features are being
added into the project, one of which is incorporating the BLAST feature for
sequence based search. Having worked on a similar project recently, I think
I will be comfortable working with the 'Porting an Algorithm to Java'
project.

The  following is what I understood about the project. Please correct me if
I am wrong.
This(link) <http://biojava.org/wiki/BioJava:CookBook3:NCBIQBlastService> is
the current method used for BLAST, which accesses the NCBI website each
time. The NCBIQBlastService class is currently used. The project aims at
replacing this with code which will perform the search within Biojava. I
downloaded the source codes of BLAST and HMMER. My job will be to convert
these to Java.

Regarding the C/C++ to Java converter, i found this on the internet:
http://tangiblesoftwaresolutions.com/Product_Details/CPlusPlus_to_Java_Converter_Details.html

but it is not free of cost.
Apart from this, I saw that many people discourage the use of C/C++ to Java
tools saying that they are not efficient. Does anyone know of any better
tool which can do this?

Regarding the JNI, would it not be better if the whole code was written in
Java, rather than a part of it being in C/C++? I haven't used it before,
but if it is better than converting the code, I don't have a problem
working with it.

Kindly clear my doubts.
Thanks in advance,
Komal



On Thu, Mar 15, 2012 at 1:17 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Komal,
>
> stay tuned to this list, we still don't know if we will get funded
> from Google this year.
>
> Andreas
>
>
> On Wed, Mar 14, 2012 at 12:27 PM, Komal Sanjeev
> <komalsnehal1991 at gmail.com> wrote:
> > Hi Everyone,
> >
> > I am Komal, an undergraduate student from IT-BHU, India. I'm interested
> in
> > working with BioJava for GSoC 2012. I am particularly interested in
> working
> > on the 'Porting an Algorithm to Java' project.
> > Kindly help me about how I should proceed.
> >
> > Thanks,
> > Komal
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>
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