[Bioclusters] web based bioinformatics application interface

Michael Gutteridge bioclusters@bioinformatics.org
Mon, 12 Jul 2004 15:52:02 -0700

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:

<description>Some application</description>
    <option name=bar required=no>
        <helptext>Set the bar option</helptext>
    <option name=baz required=no>
        <helptext>Use filename for baz option</helptext>

( Yeah- really poor approximation of XML there, but hopefully that 
gives the general gist. Wouldn't need to be XML, either, just seemed 

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 Gutteridge		Fred Hutchinson Cancer Research Ctr.
System Administrator   mgutteri@fhcrc.org