[Biojava-dev] Introducing the GSoC project

[Andreas Prlic]

Hi,

Another task for refactoring: The -structure module contains an Element
class, which should be moved to -core as well. It also needs an update,
since some of the data inside is not on the latest state, e.g atomic mass. A
source for up-to-date data is
http://www.iupac.org/publications/pac/83/2/0359/ (Table 2)

>From Peter Rose:

There are two complications with these data:

1.       For 10 elements a range of weights is given. I suggest we use the
average here.

2.       The precision of some of the numbers may exceed float. If so,
should we use double?

Going forward, we should document the source of the data in the source file.

Andreas



On Mon, May 9, 2011 at 4:13 AM, Scooter Willis <HWillis at scripps.edu> wrote:

> 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>
> >_______________________________________________
> >biojava-dev mailing list
> >biojava-dev at lists.open-bio.org
> >http://lists.open-bio.org/mailman/listinfo/biojava-dev
>
>


-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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