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

[Amr AL-Hossary]

Let me refer to Dr. Andreas & be back to you.

P.S. please stop sending to both lists.

Amr

-----Original Message----- 
From: Komal Sanjeev
Sent: Sunday, March 18, 2012 9:42 AM
To: Amr AL-Hossary
Cc: biojava-dev at lists.open-bio.org ; biojava-l at lists.open-bio.org
Subject: Re: [Biojava-l] Interested in working with BioJava for GSoC 2012

Hi Amr,

The following has been mentioned in the project description:
"Converting C or C++ source code by hand is not a trivial undertaking and
it is recommended that a C/C++ to Java conversion tool be used to do as
much of the work as possible. It is also an option to consider a JNI
approach for integrating these applications into Java."

I am a bit confused. Kindly tell me what exactly has to be done in the
project.

Thanks,
Komal



On Sun, Mar 18, 2012 at 9:35 AM, Amr AL-Hossary
<amr_alhossary at hotmail.com>wrote:

>   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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