[Biojava-dev] [GSoC] Project Proposal

Tue Apr 5 15:48:58 UTC 2011

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!

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.

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/
>