[BioRuby] Programmatic interfaces to online-only bioinformatic tools

[Ben Woodcroft]

Hi again,

I now believe I'd misunderstood you, sorry. Not enough coffee, my guess is.
I take back my suggestion about changing the default to
lib/bio/cnls_screenscraper.rb. Would it be a good idea to make
lib/bio-cnls_screenscraper.rb by default have some comment about what to do
here, instead of being empty, something like below?

# Please require your code below, respecting the bioruby directory tree. For
instance,
# require 'lib/bio/sequence/awesome_sequence_thingy'
#
# It is bad practice to write other code directly into this file, because
doing so causes confusion if this biogem was ever to get merged into the
main bioruby tree.

Thanks,
ben

On 5 March 2011 11:09, Ben Woodcroft <donttrustben at gmail.com> wrote:

> Hi Raul,
>
> Thanks for the tips - I've added a README and moved things around in the
> tree as per your suggestion, and uploaded to github.
>
> I originally put the code in lib/bio-cnls_screenscraper.rb was because that
> is the file that was created as part of the biogem process. Would changing
> the default to lib/bio/cnls_screenscraper.rb be sensible? Isn't the same
> true of the tests? I moved test/bio-cnls_screenscraper.rb to
> test/bio/cnls_screenscraper.rb as well.
>
> I think it unlikely that my code will make it into the bioruby main tree,
> because of the dependence on the webserver (as well as the usual reasons for
> not including my code!). The reason I used biogem was that it created an
> environment where I could write a distinct chunk of bioruby-associated code
> rapidly. The results will hopefully be published soon (how to cite biogem?)
> and I wanted to make the code available. Slotting it into the bioruby main
> tree isn't something I much care about.
>
> I'm a bit confused by what you mean by "add your case study to the README".
> Perhaps when the DocTeam make the public announcement that will become
> clearer.
>
> Thanks,
> ben
>
>
> On 4 March 2011 20:31, Raoul Bonnal <bonnalraoul at ingm.it> wrote:
>
>> 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
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>>
>>
>>   --
>> Ra
>>
>> linkedin: http://it.linkedin.com/in/raoulbonnal
>> twitter: http://twitter.com/ilpuccio
>> skype: ilpuccio
>> irc.freenode.net: Helius
>> github: https://github.com/helios
>>
>>
>>
>>
>>
>>
>>
>
>