[Biojava-l] Fwd: [Biojava-dev] Google Summer of Code 2011

[Peter Troshin]

Dear Nirmal,

Thanks for your interest in GSoC and the project! My name is Peter and I 
am the mentor for the project you are interested in. Andreas has kindly 
sent your email to me.

 >>>I participated in GSoC 2010 for Apache Derby (RDBMS in Java) project 
and successfully finished the project.
I have recently finished a course module on Bio Informatics and have a basic
understanding about few algorithms (Nussinov, Profile HMM, Needle-Wucsh 
etc.),
which made me interested in this area of computer science.

It is very good to have someone with prior experience in GSoC, Java and 
Bioinformatics, this must help you to develop a compelling proposal.


 >>>I would like to contribute to Bio-Java in this summer, would you 
please direct me to
relevant sources which I should start reading on and also possible 
guidelines would
be highly appreciated.

The description of the idea, selection criteria and the coding exercise 
can be found here: http://biojava.org/wiki/Google_Summer_of_Code

The guidelines for GSoC students is available from 
http://open-bio.org/wiki/Google_Summer_of_Code

The ideas behind the project are really simple and most of the methods 
are not new. So you have a benefit of being able to compare the results 
of you implementation with others.
To get a better understanding of what the project involve I’d suggest 
you to read more about each of the calculations involved. Google is your 
friend here. There are plenty of other methods which would be good to 
add to BioJava, to have a better idea of what that might be I'd suggest 
you read through the Expasy web site tools section 
http://expasy.org/tools/ <http://expasy.org/tools/protparam-doc.html>. 
As you studied BioInformatics you should have no difficulties 
understanding these.

I hope I addressed your questions.

Regards,
Peter



-------- Original Message --------
Subject: Fwd: [Biojava-dev] Google Summer of Code 2011
Date: Thu, 24 Mar 2011 20:26:35 -0700
From: Andreas Prlic <andreas at sdsc.edu>
To: Peter Troshin <p.v.troshin at dundee.ac.uk>



Hi Peter,

do you want to reply to this one? Although he is addressing me his
question is about your project..

Thanks,

Andreas


---------- Forwarded message ----------
From: Nirmal Fernando <nirmal070125 at gmail.com>
Date: Wed, Mar 23, 2011 at 7:44 PM
Subject: Re: [Biojava-dev] Google Summer of Code 2011
To: Andreas Prlic <andreas at sdsc.edu>
Cc: Biojava <biojava-l at lists.open-bio.org>, biojava-dev
<biojava-dev at lists.open-bio.org>


On Thu, Mar 24, 2011 at 6:32 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>  Hi,
>
>  As you probably already have heard, the Open Bioinformatics
>  Foundation has been accepted as a mentoring organization for this
>  year's Google Summer of Code. This means we will be able to offer
>  mentoring through BioJava again this year. Accepted students will get
>  a stipend of 5,000$ from Google. Participation is possible from most
>  countries in the world, as long as you are eligible to work in the
>  country in which you'll reside throughout the duration of the
>  program.
>
>  If you are interested in working on a BioJava related project, now
>  is the time to start preparing and discussing your proposals. Last
>  year we had many applications for the projects proposed by mentors.
>  If you want to distinguish your application I recommend to propose
>  your own project. Don't forget to discuss any proposal with us before
>  you submit them. We will try to provide feedback and match you with
>  a suitable Mentor.
>
>  Also see http://biojava.org/wiki/Google_Summer_of_Code and Google's
>  FAQs:
> 
http://www.google-melange.com/document/show/gsoc_program/google/gsoc2011/faqs
>
>
>
The student application deadline is April 8th. Google will announce
>  which proposals got accepted on April 25th.
>
>  Andreas _______________________________________________ biojava-dev
>  mailing list biojava-dev at lists.open-bio.org
>  http://lists.open-bio.org/mailman/listinfo/biojava-dev
>

Hi Andreas,

I'm an undergraduate at Department of Computer Science and
Engineering, University of Moratuwa, Sri Lanka, and I'm hoping to have
an exciting summer with GSoC 2011. I participated in GSoC 2010 for
Apache Derby (RDBMS in Java) project and successfully finished the project.
This is a sample of the work (final output) which I've done for Derby
last summer
(http://nirmalfdo.blogspot.com/p/my-work-at-gsoc-2010.html).

You can find my profile and recommendations at LinkedIn
(http://www.linkedin.com/profile/view?id=54105394&trk=tab_pro).

I have recently finished a course module on Bio Informatics and have a basic
understanding about few algorithms (Nussinov, Profile HMM, Needle-Wucsh 
etc.),
which made me interested in this area of computer science.

While looking at your ideas page "Amino acids physico-chemical
properties calculation"
interested me most, since it involves implementation of algorithms.
The sounding Java knowledge
and the experiences of concurrent programming makes me more comfortable.

I would like to contribute to Bio-Java in this summer, would you
please direct me to
relevant sources which I should start reading on and also possible
guidelines would
be highly appreciated.

Thanks.

--
Best Regards,
Nirmal

C.S.Nirmal J. Fernando
Department of Computer Science & Engineering,
Faculty of Engineering,
University of Moratuwa,
Sri Lanka.
Blog: http://nirmalfdo.blogspot.com/



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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