[Biojava-dev] Introducing the GSoC project

[Scooter Willis]

Ah Fu

Some elements that model the attributes of the amino acids and the protein
should go in core module. The obvious ones are mass and the
physio-chemical attributes of the amino acids. Algorithms that determine a
quantitative value from the attributes that is not absolute finite would
go in the module use are developing. It would help if you can identify
portions of the code that need to go in core as they properly model the
amino acid and protein and would be code that others can use in their
module. I can assist with the code that would go into core where I have
had on my list of things to do a way to properly handle PTM modeling of
amino acids such that the mass and chemical composition would be correct
for those with a mass spectrometry interest. I have code in another
library for a project at work that deals with the PTM issue but would
rather use an external well defined data model for PTM's. Lasts years Gsoc
project had a PTM element for PDB and we may be able to use that as a
model on how to integrate PTM support into core.

Thanks

Scooter

On 5/9/11 6:39 AM, "Chuan Hock Koh" <kohchuanhock at gmail.com> wrote:

>Hi all,
>
>As Andreas have highlighted, I am one of the student for this year's
>Google
>Summer of Code.
>
>I will be implementing physico-chemical computation of protein sequences
>within the biojava framework. I will soon be embarking on the coding of
>some
>basic properties such as molecular weight, instability index, isoelectric
>point etc.
>
>If you have any suggestions for any properties you would like to be
>implemented, we would love to hear from you. Please take a look at the
>following page for what we currently have in mind.
>http://biojava.org/wiki/GSoC:AAPropertiesComputation
>
>Looking forward to hearing from you guys!
>Ah Fu
>
>
>
>
>On Sat, May 7, 2011 at 10:22 AM, Andreas Prlic <andreas at sdsc.edu> wrote:
>
>> Hi -devs,
>>
>> I would like to kick off our work on this year's Google summer of code
>> by introducing  Ah Fu and his project to the -dev list. Welcome Ah Fu
>> and we are looking forward to a fun summer working on this together
>> with you!
>>
>> In case anybody is interested in the project details, Ah Fu has
>> already set up a project page on the wiki:
>> http://biojava.org/wiki/GSoC:AAPropertiesComputation
>>
>> Similar to last year we are planning to track the weekly progress there.
>>
>> The plan is to keep important and high level discussions here on this
>> list, but keep details offline. We are also having a skype call every
>> Thursday at 8 AM PST, in case anybody is interested in joining.
>>
>> Andreas
>>
>
>
>
>-- 
>http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp
>.nus.edu.sg/~ChuanHockKoh/index.html>
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