[Biojava-l] Work completed for GSoC:AAPropertiesComputation

[Peter Troshin]

Hi guys,

New release sounds great! It nicely wraps up the work completed during 
this year's Google Summer of Code. Thank you for making it!

Perhaps, I should say a few words about another, recently added piece of 
the functionality for prediction of disordered regions from a protein 
sequence.

This work is wrapped up as a /biojava3-protein-disorder/ module. For 
now, this module contains one method for the prediction of disordered 
regions. This method is based on the Java implementation of RONN 
<http://www.strubi.ox.ac.uk/RONN> predictor.

This code has been originally developed for another project and made its 
way into the BioJava.
As the main code behind this is a Java implementation of RONN, 
unimaginatively we call it /JRONN/. JRONN is based on RONN version 3.1 
which is still current in time of writing (August 2011) and so gives the 
same predictions as RONN.

Main motivation behind JRONN development was providing an implementation 
of RONN more suitable to use by the automated analysis pipelines and web 
services. Robert Esnouf has kindly allowed us to explore the RONN code 
and share the results with the community.

Original version of RONN is described in Yang,Z.R., Thomson,R., 
McMeil,P. and Esnouf,R.M. (2005) RONN: the bio-basis function neural 
network technique applied to the detection of natively disordered 
regions in proteins. Bioinformatics 21: 3369-3376 
<http://bioinformatics.oxfordjournals.org/content/21/16/3369.full>

Please refer to the cookbook entry 
http://biojava.org/wiki/BioJava:CookBook#biojava3-protein-disorder for 
more information about disorder prediction module.

Happy coding,
Peter

P.S. I think the documentation for biojava3-protein-disorder module is 
ok, unless someone can suggest any improvements.

P.P.S. Andreas, it would be great if you could remove the content of 
this directory
http://www.biojava.org/download/maven/org/biojava/biojava3-protein-disorder
to get rid of outdated artefacts.



On 25/08/2011 18:06, Andreas Prlic wrote:
> 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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