[Biojava-l] Fwd: Biojava3-genetics

[Andreas Prlic]

Hi Richard,

I am forwarding your message to the mailing list, since that is the best
place to meet other people interested in genetics application.

The BioJava source code is available via anonymous svn or the download page
on the wiki.

Andreas

---------- Forwarded message ----------
From: Finkers, Richard <richard.finkers at wur.nl>
Date: Sat, Apr 17, 2010 at 12:46 AM
Subject: RE: Biojava3-genetics
To: Andreas Prlic <andreas at sdsc.edu>


Hi Andreas,

To start with, associations with e.g. sequence variation (454) and phenotype
data within larger sets of genetically different individuals. This will be
code which I will have to write the coming year for one of my projects. I am
planning to use this in combination the sequence and phylogeny based biojava
modules.

I also might consider migrating some of my current code to this module. This
includes graphical representations of genetic data but also some statistical
analysis for which we use the package R for the calculations but the rest of
the data handling / formatting is done in Java.

Some of the functionality, that I am thinking about, is available from other
packages but I did not find the (java) source code.

Richard




-----Original Message-----
From: andreas.prlic at gmail.com on behalf of Andreas Prlic
Sent: Fri 2010-04-16 19:39
To: Finkers, Richard
Cc: biojava-dev at lists.open-bio.org
Subject: Re: Biojava3-genetics

Hi Richard,

any contribution is welcome. What do you have in mind in particular? Perhaps
there is already something there along those lines...

Andreas

On Thu, Apr 15, 2010 at 11:43 PM, Richard Finkers <Richard.Finkers at wur.nl
>wrote:

> Dear List,
>
> I would be interested in adding a module for genetic analysis to the
> biojava3 project. Are there others who are interested in this as well and
> with who should I discuss this further?
>
> Thanks,
> Richard
>
>
> --
> Dr. Richard Finkers
> Researcher Plant Breeding
> Wageningen UR Plant Breeding
> P.O. Box 16, 6700 AA, Wageningen, The Netherlands
> Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB
> Wageningen, The Netherlands
> Tel. +31-317-484165 Fax +31-317-418094
> http://www.plantbreeding.wur.nl/ <http://www.plantbreeding.wur.nl>
> https://www.eu-sol.wur.nl/ <https://www.eu-sol.wur.nl>
> https://cbsgdbase.wur.nl/ <https://cbsgdbase.wur.nl>
> http://solgenomics.wur.nl/ <http://solgenomics.wur.nl>
> http://www.disclaimer-uk.wur.nl/
>
>


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