[BioRuby] Programmatic interfaces to online-only bioinformatic tools

[Raoul Bonnal]

Dear Ben,
I'm very happy that you like the plugin system, thanks!

Yesterday we created the doc team which is charge to supervise every doc content for BioRuby.
@DocTeam: please make a public announce.

Our role is to make their life easier, so write tests, documentation in code and useful comments so,  I invite you to add your case study to the README for a better comprehension of the tool, or where the docteam will decide.

Also a reminder for all developers:
try to respect/reflect the bioruby directory tree, in this particular case:

lib/bio-cnls_screenscraper.rb
  require 'bio/cnls_screenscraper'

mkdir lib/bio 
touch lib/bio/cnls_screenscraper.rb and add your code here.

Don't forget, git add .

This would help in the future for an easier incorporation into bioruby, if we decide that a particular plugin can be assimilated (BORG)

PS: probably I need to make this concept more clear on biogem, sorry it's my fault.

On 03/mar/2011, at 01.47, Ben Woodcroft wrote:

> Hi there,
> 
> I'm after an opinion on best practice for accessing those bioinformatic
> tools that are only accessible via web-interfaces, without any way of
> downloading the program itself. As I often want to throw an organisms's
> whole proteome at the tool (in my case ~5500 proteins), doing it one at a
> time is obviously not feasible. Do people think that writing a wrapper that
> hammers the website in question is a nice thing to do, provided I wait 1
> second in between each upload (1 protein/upload)? From what I can
> understand, processing each protein is not computationally demanding and
> results are returned almost instantaneously when querying the server
> manually, unlike a blast server.
> 
> Some background:
> I'm really like this bioruby plugin thing - thanks to those involved in its
> creation. I've written a bioruby plugin
> https://github.com/wwood/bioruby-cnls_screenscraper which queries
> http://nls-mapper.iab.keio.ac.jp/cgi-bin/NLS_Mapper_form.cgi that does what
> I've described above. Not quite as well documented as it might be, but it
> appears to work and isn't too complicated.
> 
> Thanks,
> ben
> 
> -- 
> Ben J Woodcroft, BE (Hons)
> 
> PhD Candidate
> Ralph Laboratory
> The University of Melbourne
> Melbourne, Australia
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby

--
Ra

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