[Biojava-dev] Idea that needs feedback

[Andy Yates]

Open code submission is very easy if we migrate to GitHub where you can fork the BioJava project, develop it & then ask for the changes to be brought back into the main-line. Information about your individual changes can be provided from GitHub's own wiki system & once it is a verified part of the project that documentation can be brought into BioJava's mediawiki using something like PanDoc.

The tools are already there; they just need to be used

Andy

On 7 Jan 2011, at 20:32, Radhouane Aniba wrote:

> Hi Andreas,
> 
> Thank you for the answer.
> For a simple reason, wiki platform, technically speaking, is not structured.
> Let me explain. If we will rely on a wiki to open code submission for all
> users, I let you imagine what it will give if we, let's say, reach 3000
> source codes using biojava, additionally, everyone will try to add meta
> information describing the code (not talking about code comments), with a
> big number of source codes this will be not homogenous at all.
> 
> What i propose is a system that organize all the contributions, people will
> enter the same information in the same place and the display will be
> standardized and well organized.
> 
> Cross links with wikis and projects webpages are also existant in the
> platform so that people refer always to cookbooks or the project updates.
> What I developed is more oriented "What do you do with Bio* ?"
> 
> Bio* = Biojava, Bioconductor, Bioperl, and corresponding langages.
> 
> 
> Regards,
> 
> Radhouane
> 
> 2011/1/7 Andreas Prlic <andreas at sdsc.edu>
> 
>> Why don't you use the BioJava wiki for that? It's already an open
>> platform and clearly linked to the project.
>> 
>> Andreas
>> 
>> On Fri, Jan 7, 2011 at 10:59 AM, Radhouane Aniba <aradwen at gmail.com>
>> wrote:
>>> Hi Biojava users and contributors,
>>> 
>>> In order to improve collaboration between scientists, computer engineers,
>>> bioinformaticians working with Java and Biojava, I would like to see how
>>> much among you here in this group, would be interested in developing or
>>> making part of a website that plays the role of collaborative platform
>> for
>>> Java/Biojava codes, packages, workflows and contributions, so that we
>>> develop the "re-use" and "don't reinvent the wheel" spirit in one hand,
>> and
>>> to put in practice a more collaborative work and interaction between
>> people
>>> working on Java/Biojava related projects.
>>> 
>>> I already have experience in the development of such platforms and
>> thought
>>> it could be useful and interesting to propose such initiative to people
>> like
>>> you and I working with Java/Biojava.
>>> 
>>> This is in no way a competitive or alternative approach to Biojava
>> mailing
>>> list but a complementary platform for sharing codes / workflows /
>> analysis
>>> scenarios using Java/Biojava.
>>> 
>>> Bioperl and Bioconductor members are joigning the movement and welcomed
>> the
>>> initiative, a prototype is already developed (90%) and I hope Biojava
>>> developers will join the group.
>>> 
>>> 
>>> Would you please take a few moment to answer to this topic so that I can
>>> have an idea on your position in regards of such initiative.
>>> 
>>> Link to the form: http://tinyurl.com/2bxle2d
>>> 
>>> Thank you and happy new year 2011.
>>> 
>>> 
>>> Radhouane
>>> 
>>> --
>>> *Radhouane Aniba*
>>> *Bioinformatics Research Associate*
>>> *Institute for Advanced Computer Studies
>>> Center for Bioinformatics and Computational Biology* *(CBCB)*
>>> *University of Maryland, College Park
>>> MD 20742*
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>> 
>> 
> 
> 
> 
> -- 
> *Radhouane Aniba*
> *Bioinformatics Research Associate*
> *Institute for Advanced Computer Studies
> Center for Bioinformatics and Computational Biology* *(CBCB)*
> *University of Maryland, College Park
> MD 20742*
> _______________________________________________
> biojava-dev mailing list
> biojava-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-dev

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/