[Biojava-dev] Idea that needs feedback

[LAW Andy]

I *think* that Radhouane is suggesting that we set up a more "downstream" system than that. Perhaps more of a PLEAC-type system for Bio* code.

"Here's how I did X using Y" rather than focussing on the whys and wherefores of the internal code hackery within Bio* projects.


On 10 Jan 2011, at 10:28, Andy Yates wrote:

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

Later,

Andy
--------
Yada, yada, yada...

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