[Biojava-l] GSoC Intent - Amino Acids Physico-Chemical Properties Calculation

[Peter Troshin]

Hi Justin,

Welcome to the BioJava mailing list and thank you for your interest in 
the project.

It sounds like you have plenty of experience in programming, which is 
definitely a plus. Do not worry about you lack of experience in 
multi-threaded programs, in the end there must be something for you to 
learn too! I hope that this project can give you what you are looking 
for – the experience of implementing algorithms in pure Java and 
integrating with the relatively large BioJava code base.

However, do not underestimate the difficulty of the algorithms for 
calculating the physico-chemical properties. Although the algorithms may 
not be particularly complex, but in order to understand them you would 
need some knowledge in chemistry, molecular biology and maths. 
Programming skills only will not be sufficient for this project.

Good luck with your application.

Regards,
Peter





On 04/04/2011 16:34, Xaroth wrote:
> Hello everyone and project mentor Peter Troshin,
>
> My name is Justin Pugh. I am a 3rd year Computer Science student at the
> University of Central Florida. I am proficient in C and Java and I prefer to
> do all of my coding work in Java. I've recently learned about the Google
> Summer of Code program and I've been spending the past week or so looking
> over the available open-source projects. I am excited about participating in
> the GSoC because I have been anxious to be a part of a larger project than
> the small-scope programs that I have to write for classes. Sadly, I do not
> have any experience doing any programming projects on this scale but I am
> very interested in learning. The largest project I have completed was to
> write a compiler and virtual machine for PL/0. I'm currently working on
> writing a game from scratch as a vehicle for implementing some AI techniques
> and I am learning a lot about making use of others' code provided in
> libraries and integrating it into my own through the use of jMonkeyEngine
> (an open source java-based 3d game engine). I want to take my skills to the
> next level with GSoC.
>
> Out of all the projects I have looked at, BioJava has stood out the most for
> me (in particular, the Amino Acids Physico-Chemical Properties Calculation
> idea). I wanted to work on something written entirely in Java so I wouldnt
> have to spend any time learning a new language and I would be able to focus
> more on the actual project. I feel like I am able to wrap my head around the
> Amino Acids Physico-Chemical Properties Calculation proposal and I think it
> falls within my ability to get it done and even more - to have fun with it
> and be able to spend time refining it. I do not know anything about the
> calculations which must be implemented, but I am of course willing to learn
> them. I have only had small instruction in the area of multi-threaded Java
> programming but I hope this will not be a severe handicap for me.
>
> I plan on spending the next couple days doing some research and developing
> my proposal. I just wanted to announce my intent to submit an application
> and to introduce myself to the group. Please let me know your opinions
> regarding my ability to complete this project - I am open to criticism and
> pointers! :)
>
> Thank you for your time,
> -Justin Pugh
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