[BioRuby] gsoc suggestion: microframework for simple scientific web wrappers

[Yannick Wurm]

Dear all, some specific replies/comments to a subset of the many interesting points raised. 



Pjotr Prins wrote: 
> This is a very good idea, and ties in with earlier bio-ngs work and
> our future plans in pipeline software management.

yes, you could easily imagine that every GUI created also autogenerates a web service-friendly interface (RDF?)


Ben Woodcroft wrote:
> * the ptools rubygem has a 'which' method, which might be of use.
> * bio-commandeer seems of obvious use..

very cool - thanks. 

> Is there any good markup language for describing program inputs and
> outputs? Anything that could be stolen from galaxy?

compatibility with  (or easy conversion of) galaxy wrappers could be very cool!

Check section 3 of their tutorial for an example of their XML description format:
	https://wiki.galaxyproject.org/Admin/Tools/Add%20Tool%20Tutorial
And full(?) description of syntax:
        https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax


Iain Barnett wrote:
> 1. Check CLI and library are separated. If not, separate them. Not only
> does this make calling the library easier, it has the added bonus of
> improving that library and allowing others to develop against it more
> easily too.

Agreed - that is how things should be. Unfortunately, too much bioinformatics software is still is based on bad development practices. Even big packages used by tens of thousands of people. This will slowly change as software sustainability & reproducible research ideas make their way into curricula and more knowledgable people get involved in bioinformatics stuff. So for the next few years at least. the suggestion is unrealistic. 

> There's https://rubygems.org/gems/sinatra-param 

I don't fully understand the sinatra extension stuff but it seems like it would indeed be worth exploring. 

> If you're going to call executables, I'd require them to be installed in a
> special directory local to the app, e.g. /app/bin/ which would make
> handling them easier

That's an interesting point. 


Joachim Baran wrote:
> It might be better to get funding for a full time software developer and bioinformatician to tackle these problems.

Please give me funding for a full-time software developer and bioinformatician :)

Cheers,

Yannick

-------------------------------------------------------
Yannick Wurm - http://yannick.poulet.org
Ants, Genomes & Evolution ⋅ y.wurm at qmul.ac.uk ⋅ skype:yannickwurm ⋅ +44 207 882 3049
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