[Biojava-dev] [GSoC] Project Proposal

Wed Apr 6 14:57:59 UTC 2011

Hi,

In addition to the functionalities provided in my proposal, I would like to
build a tool like http://gcua.schoedl.de/ which will be used to display the
codon quality in codon usage frequency values.

It would be nice to get the feedback of the community regarding the
importance of a tool like this to BioJava3.

Thanks.

On Tue, Apr 5, 2011 at 9:34 PM, Nirmal Fernando <nirmal070125 at gmail.com>wrote:

> Hi Peter,
>
> On Tue, Apr 5, 2011 at 9:18 PM, Peter Troshin <p.v.troshin at dundee.ac.uk>
> wrote:
> >
> > Hi Nirmal,
> >
> > First of all thanks for the proposal it looks good.
> > However, I think that one of the benefits of my project idea is that it
> lets you implement a few other methods that are of interest to >you. It is a
> pity that you did not use this opportunity. I strongly encourage to use your
> knowledge and to look at the other properties >that you can implement for
> the benefit of the community. Otherwise it looks like you are not terribly
> interested in Bioinformatics!
>
> Sorry for the disappointment! This week is a bit busy week with me
> having few events at the University, that's why I didn't get much time
> to look for other methods. But I'll try my best to research and
> propose some other methods which will benefit the community.
>
> >
> > Also, I think that the best method of learning BioJava is trying it. So
> I'd put in the project plan that you will write test cases to check >out the
> parts of BioJava that you will be using. Apart from helping you learning it
> in depth it will also help to ensure that the BioJava >code behaves.
>
> Thanks for the tip! :)
>
> >
> > Regards,
> > Peter
> >
> > On 05/04/2011 14:40, Nirmal Fernando wrote:
> >>
> >> Hi All,
> >>
> >> I have prepared my GSoC proposal for BioJava [1]. I highly appreciate
> your valuable feedback.
> >>
> >> Thanks.
> >>
> >> [1]
> >>
> >>
> >>  Google Summer of Code 2011 - Project Proposal
> >>
> >> Organization
> >>
> >>
> >>
> >> *Open Bioinformatics Foundation- BioJava*
> >>
> >> Project
> >>
> >>
> >>
> >> *Calculation of Physicochemical Properties of Amino Acids*
> >>
> >> Student Name
> >>
> >>
> >>
> >> C. S. Nirmal J. Fernando.
> >>
> >> E-mail
> >>
> >>
> >>
> >> nirmal070125 at gmail.com <mailto:nirmal070125 at gmail.com>
> >>
> >> IM
> >>
> >>
> >>
> >> nirmal070125 (Google Talk)
> >>
> >> nirmalfdo (IRC – freenode.net <http://freenode.net>)
> >>
> >> Address
> >>
> >>
> >>
> >> 47, Keels Housing Scheme, Pinwatte, Panadura, Sri Lanka.
> >>
> >> Mobile No.
> >>
> >>
> >>
> >> +94715779733
> >>
> >> *Why I am interested?*
> >>
> >> *
> >> *
> >>
> >> I have recently finished a course module on Bio Informatics and have a
> basic
> >> understanding about bio informatics related algorithms which made me
> interested in this area of computer science.
> >>
> >> *
> >> *
> >>
> >> *Why I am well-suited?*
> >>
> >>
> >> I participated in GSoC 2010 for Apache Derby (RDBMS in Java) project and
> successfully finished the project. The sounding Java knowledge, algorithmic
> knowledge on bio informatics and the experiences of concurrent programming
> make me more comfortable and matching.
> >>
> >>
> >> “Nirmal joined the Apache Derby community as a *Google Summer of Code
> *student for the summer of 2010. In this role, Nirmal wrote a very useful
> tool called PlanExporter. This tool will help users of the *Apache Derby
> *database understand and fix performance issues in their data-rich
> applications. Nirmal fit well into our open-source community, collaborating
> with other engineers, proceeding incrementally, and seeking and taking
> advice cheerfully. Nirmal's contributions to Apache Derby are highly
> respected.”-//*Richard Hillegas* <
> http://www.linkedin.com/profile/view?id=31609548&noCreateProposal=true&goback=%2Enpe_*1_*1_*1_*1>*,
> /Senior Software Engineer, Sun Microsystems./*
> >>
> >>
> >> “Nirmal's work on the Derby PlanExporter tool as part of the Google 2010
> Summer of Code was clear, well-executed and successful. Furthermore, every
> member of the Derby team that I've spoken to has been pleased with Nirmal's
> contributions to the community and we look forward to having Nirmal
> continuing to work with Derby in the future.”- *Bryan Pendleton* <
> http://www.linkedin.com/profile/view?id=492758&noCreateProposal=true&goback=%2Enpe_*1_*1_*1_*1>*,
> /Committer, Apache Derby/.*
> >>
> >> *
> >> *
> >>
> >> *Programming Experiences and Skills*
> >>
> >> ·Completed the “short coding exercise” (all three goals) given by the
> mentor.
> >>
> >> ·Final Year Project: SeMap is our final year project and a four member
> one which is led by me. Objective is to develop a superior framework for
> mapping English Language Semantic Dependency Relationships to sets of
> semantic frames with reasonable accuracy for complex sentences with an
> integrated statistical linguistics based artificial intelligence component
> to allow automatic extensibility.We are working under OpenCog.org, a FOSS
> foundation, under the supervision of Dr. Ben Goertzel. Technologies: [Java,
> Drools]
> >>
> >> *Contributions to Open Source world*
> >>
> >> *
> >> *
> >>
> >> ·Implemented PlanExporter tool which allows Apache Derby users to view
> and understand the query plan followed by the optimizer. Technologies:
> [Java, XML, XSLT, HTML and CSS] (Google Summer of Code – 2010 project)
> >>
> >> ·Solved many issues in Apache Derby
> https://issues.apache.org/jira/secure/IssueNavigator.jspa?
> >>
> >> ·Continuing to work on Apache Derby even after the summer of code.
> >>
> >> **
> >>
> >> *Project Rationale*
> >>
> >> *
> >> *
> >>
> >> The calculation of simple physicochemical properties for biopolymers is
> an important tool in the arsenal of molecular biologist. Theoretically
> calculated quantities like extinction coefficients, isoelectric points,
> hydrophobicities and instability indices are useful guides as to how a
> molecule behaves in an experiment. Many tools for calculating these
> properties exist, including widely used open-source implementations in
> EMBOSS and BioPerl, but only some are currently available in BioJava3. The
> aim of this project is to port or produce new implementations of standard
> algorithms for a range of calculations within BioJava3.
> >>
> >> *Project Scope *
> >>
> >> *
> >> *
> >>
> >> Primarily focus on developing following functionalities:
> >>
> >>   1. Finding molecular weight of a sequence
> >>   2. Finding extinction coefficient of a protein
> >>   3. Finding instability index of a protein
> >>   4. Finding aliphatic index of a protein
> >>   5. Finding GRAVY (Grand Average of Hydropathy) value of a peptide
> >>      or a protein
> >>   6. Finding isoelectric point of a sequence
> >>   7. Finding number of amino acids in a protein (His, Met, Cys)
> >>
> >> **
> >>
> >> *Project Plan*
> >>
> >> *April 20 - May 10*
> >>
> >>    * Read on BioJava3 design http://biojava.org/wiki/BioJava3_Design
> >>    * Read on BioJava3 data model
> >>      http://www.biojava.org/wiki/BioJava3_Proposal
> >>    * Get an understanding on how each BioJava3 module works and their
> >>      functionalities.
> >>    * Find and read on algorithms to provide above mentioned
> >>      functionalities.
> >>    * Identify the possibility of using methods and tools in BioJava3
> >>
> >> *May**11 - May 24*
> >>
> >>    * Implement functions to calculate molecular weight of a sequence
> >>      and extinction coefficient of a protein using multi threads
> >>      where it is possible.
> >>    * Implement functional test cases using Junit.
> >>    * Develop a high level documentation for end users.
> >>
> >> *May 24 - July 10*
> >>
> >>    * Preparing for the mid-term evaluation of the project.
> >>
> >> *
> >> *
> >>
> >> *July 12 - August 15*
> >>
> >>    * Implement functions to calculate,
> >>
> >>          o Instability index of a protein
> >>          o Aliphatic index of a protein
> >>          o GRAVY (Grand Average of Hydropathy) value for a peptide or
> >>            a protein
> >>          o Isoelectric point of a sequence
> >>
> >>          o number of amino acids in a protein (His, Met, Cys)
> >>
> >> ; using multi threads where it is possible.
> >>
> >>    * Implement functional test cases using Junit.
> >>    * Update the high level documentation for end users.
> >>
> >> *August 16 - August 22*
> >>
> >>    * Wrap up the work done, and polishing up the code.
> >>    * Creating Java-doc API
> >>    * Preparing for the final evaluation.
> >>
> >> *August 26*
> >>
> >>    * Final evaluation deadline.
> >>
> >> *Project Deliverables*
> >>
> >> ·Java library with above mentioned functionalities.
> >>
> >> ·Command line executables.
> >>
> >> ·Java doc API of the library.
> >>
> >> ·Functional test cases.
> >>
> >> ·High level end user documentation
> >>
> >>
> >> --
> >> 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/
> >>
> >
> >
>
>
>
> --
> 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/
>

-- 
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/