[Biojava-dev] BioJava3 contribution

[Andreas Prlic]

Hi Fabrice,

The biojava 1 features could only accept integer positions as start
and stop. For protein structures an amino acid is uniquely identified
by a number and an insertion code. As such in the biojava 1 world it
was not possible to implement this for the protein structures. If we
have a cleaner interface definition for that in biojava 3 should be no
prob.

Andreas

On Mon, Oct 20, 2008 at 1:40 PM, Fabrice Jossinet <fjossinet at orange.fr> wrote:
> Hi Andreas,
> yes of course, I really would like to work with you (I like your work with
> SPICE). I wanted to contact you about this point before to start. Concerning
> the tertiary structure representation, I need to annotate an RNA tertiary
> structure with base-pairs families (as described in
> http://www.ncbi.nlm.nih.gov/pubmed/12177293 or in
> http://prion.bchs.uh.edu/bp_type/ ) and structural motifs (like those listed
> in the SCOR database
>  http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=308814). The idea
> is to attach these features to a 3D in the same way than the features
> attached to a sequence (1D).
> What do you think?
> Fabrice
> Le 20 oct. 08 à 21:18, Andreas Prlic a écrit :
>
> 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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>
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>
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>
>
>
>
>
> --
> 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/
>
>
>