[Biojava-l] GSoC:AAPropertiesComputation Updates

[Chuan Hock Koh]

Hi all,

I am a student for this year Google Summer of Code. We are working on
developing tools and APIs for the calculation of physico-chemical properties
via BioJava.

We have come to an end of the second phase of this project. In the first two
phase of the projects, we have developed APIs, test the APIs and also wrote
up documentation (in Cookbook of BioWiki under "Physico-Chemical Proerties
Computation").

We are writing this email to invite for comments/suggestions on the project.
The next few phases of the project can be found here (
http://biojava.org/wiki/GSoC:AAPropertiesComputation#Timeline).

Previously, it was suggested in this mailing list that we should allow users
to define the mass of amino acids instead of always using the standard mass.
We have done so and have documentation on how to do it here (
http://biojava.org/wiki/BioJava:CookBook:AAPROP:xmlfiles).

However, we face a problem here regarding the definition of modified amino
acids. That is in the class of ProteinSequence, it ensures a symbol must be
define in AminoAcidCompoundSet. This would limit the possibilities in
defining the symbol for modified amino acids.


Looking forward to hear from you guys,

AAPropertiesComputation Team
Student: Chuan Hock KOH
Mentors: Peter Troshin & Andreas Prlic

-- 
http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>