[Biojava-dev] BioJava3 contribution

[Fabrice Jossinet]

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/
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>




--
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/