[Biojava-l] Work completed for GSoC:AAPropertiesComputation

[Andreas Prlic]

Hi Ah Fu and Peter,

Thank you both for your dedicated work over the summer. It is great to
see the new modules coming out of this and this further extends the
list of useful things you can use BioJava for. Let's try to make
access to these new features as easy as possible by making a new
release within the next two weeks.

I suggest to have a code freeze by Thursday September 1st (today in a
week), then I will make the release during the days after. Until then
lets make sure that the documentation is up to date and any
outstanding commits are being made.

Andreas




On Wed, Aug 24, 2011 at 7:12 PM, Chuan Hock Koh <kohchuanhock at gmail.com> wrote:
> Hi All,
>
> The Google Summer of Code has come to an end. Please allow me to share with
> you what was achieved during this summer by me, Andreas Prlic and Peter
> Troshin.
>
> 1) A set of APIs to compute Physico-Chemical properties of protein
> sequences. Please see CookBook (
> http://biojava.org/wiki/BioJava:CookBook:AAPROP:main) on how to use them.
> Following is a list of properties that could be generated:
>
>   - Molecular weight
>   - Extinction coefficient
>   - Instability index
>   - Aliphatic index
>   - Grand Average of Hydropathy
>   - Isoelectric point
>   - Amino acid composition
>
>
> 2) A executable jar to do the same thing as point 1. Please see CookBook (
> http://biojava.org/wiki/BioJava:CookBook:AAPROP:commandprompt) for examples
> on usage.
>
> 3) A set of APIs to compute PROFEAT properties of protein sequences. Please
> see this paper (
> http://nar.oxfordjournals.org/content/34/suppl_2/W32.abstract) for more
> details about PROFEAT properties. Also, do see CookBook (
> http://biojava.org/wiki/BioJava:CookBook:AAPROP:profeat) on how to use them.
>
> 4) Another thing worth noting is that as requested by the BioJava community,
> we have enabled the customization for the computing of molecular weight for
> point 1 and 2. Please see CookBook (
> http://biojava.org/wiki/BioJava:CookBook:AAPROP:xmlfiles) for more
> information.
>
> 5) Also, a SOAP web service for physico-chemical properties computation
> (point 1) was developed within the JABAWS framework for portable web
> services (http://www.compbio.dundee.ac.uk/jabaws/). This web service can be
> installed on your own computing infrastructure with ease. If you intend to
> use this web service, please contact us for further details.
>
> I would continue to improve and work on this package even after this summer.
> Therefore, if you have any feedback or comments. Please feel free to drop me
> a mail. Thanks!
>
> Regards,
> Chuan Hock Koh (aka Ah Fu), Andreas Prlic and Peter Troshin
>
> --
> http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh<http://compbio.ddns.comp.nus.edu.sg/~ChuanHockKoh/index.html>
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