[Bioclusters] web based bioinformatics application interface

Chris Dagdigian bioclusters@bioinformatics.org
Tue, 13 Jul 2004 07:11:47 -0400

PISE does exactly what you are thinking about :)



Michael Gutteridge wrote:
> Hi all...
> Hopefully this isn't too far off the charter... my apologies if it is, 
> but this seems to be a good community for this question.
> One of the services I'd like to be able to provide to our users is a 
> web-based front end to many of the different applications (blast, 
> clustal*, etc. running on our Torque/Maui cluster) to allow greater 
> access to those in the community that are intimidated by the Unix 
> shell.  I'm thinking of a web page that allows a user to log in, choose 
> an application, and fill in a form (containing arguments, options, and 
> filenames) to have a job run on the cluster.
> On a one-by-one basis, this isn't a huge deal, but it got me to thinking 
> about generalizing the problem.
> What I think would be Really Cool (tm) is to have a web-based 
> application that would read a configuration file that "knows" how the 
> underlying application functions, present various form elements as 
> appropriate for the options & arguments of the underlying application, 
> then handle wrapping in a qsub to the cluster.
> So, for application "foo" taking options "bar" and "baz <filename>" 
> you'd write something that had information about those options:
> <application>
> <name>foo</name>
> <description>Some application</description>
>    <option name=bar required=no>
>        <helptext>Set the bar option</helptext>
>    </option>
>    <option name=baz required=no>
>        <helptext>Use filename for baz option</helptext>
>        </value=filepath>
>        <depends>bar</depends>
>    </option>
> </application>
> ( Yeah- really poor approximation of XML there, but hopefully that gives 
> the general gist. Wouldn't need to be XML, either, just seemed apropos)
> Anyway, the web-application reads that and generates a page with a 
> checkbox for the "bar" option, a checkbox and text-input box for the 
> "baz" option, etc.  So the web-application does some input validation 
> before the commands are generated.
> Any suggestions here?  Anyone used or seen something like this? Even 
> some google search words would be helpful (haven't found the combination 
> of words that return anything useful so far).
> Thanks much!
> Michael
> Michael Gutteridge        Fred Hutchinson Cancer Research Ctr.
> System Administrator   mgutteri@fhcrc.org
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