[Biojava-dev] BioJava3 contribution

[Richard Holland]

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/