[Biojava-dev] BioJava3 contribution

[Andreas Prlic]

Hi Fabrice,

Regarding the tertiaty structure representation we should work
together. There is a seet of tools available already in the current
biojava 1.7 which I was intending to maintain and migrate to biojava v
3. Let me know if you have specific RNA related requests...

Andreas

On Mon, Oct 20, 2008 at 6:51 AM, Richard Holland
<holland at eaglegenomics.com> wrote:
> Excellent! Thanks for your offer of help!
>
> Yes, an advanced RNA module would be very helpful indeed. You should
> probably call it 'rna'.
>
> As long as everyone who intends to work on BJ3 declares their intentions
> here, as you just have, then basically it's first come first served. I won't
> be doing any official supervision other than keeping an eye on committed
> code once in a while to make sure it all looks OK. So feel free to start
> coding straight away!
>
> All new modules should probably start by:
>
> 1. copying the existing dna module to something new, like 'rna' in this
> case.
> 2. remove all the hidden .svn directories from the copy,
> 3. update the pom.xml in the copy (do a search-and-replace on dna and change
> to the new name, rna in this case), delete the existing source packages in
> src/main/java (org.biojava.dna) and create suitable new ones
> (org.biojava.rna in this case).
> 4. empty out the target/ folder then svn add the new module
> 5. svn:ignore the target/ directory in your new module,
> 6. include your new module in the list at the end of the pom.xml in the root
> directory of the biojava3 branch.
>
> cheers,
> Richard
>
>
>
> 2008/10/20 Fabrice Jossinet <f.jossinet at ibmc.u-strasbg.fr>
>
>> Dear Richard,
>>
>> I'm answering to your "official call", to propose you my help for the
>> development of the biojava3 code. With the modularity of Maven, I also would
>> like to proposes you my help for the development of a module that will use
>> the biojava3 code to manage more specialized RNA stuff (secondary and
>> tertiary structures, base-pairs classifications, modified nucleotides, RNA
>> alignments,....).
>>
>> What will be the next step for me? Will you make a selection?
>>
>> Best Regards
>>
>> Fabrice Jossinet
>>
>> --
>> Dr. Fabrice Jossinet
>> Laboratoire de Bioinformatique, modelisation et simulation des acides
>> nucleiques
>> Universite Louis Pasteur
>> Institut de biologie moleculaire et cellulaire du CNRS
>> UPR9002, Architecture et Reactivite de l'ARN
>> 15 rue Rene Descartes
>> F-67084 Strasbourg Cedex
>> France
>>
>> Tel + 33 (0) 3 88 417053
>> FAX + 33 (0) 3 88 60 22 18
>>
>> f.jossinet at ibmc.u-strasbg.fr
>> fjossinet at gmail.com
>> http://www-ibmc.u-strasbg.fr/arn/Westhof/index.html
>> http://fjossinet.u-strasbg.fr/
>>
>>
>>
>>
>>
>
>
> --
> Richard Holland, BSc MBCS
> Finance Director, Eagle Genomics Ltd
> M: +44 7500 438846 | E: holland at eaglegenomics.com
> http://www.eaglegenomics.com/
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