[Bioclusters] web based bioinformatics application interface

Juan Perin bioclusters@bioinformatics.org
Tue, 13 Jul 2004 09:55:21 -0400


I'm sure most people are now aware of Bioteams Inquiry package.
It is being sold as a commercial package, but at a very discounted rate for
academic and non-profit institutions.  http://www.bioteam.net/inquiry is the
link to their site.  They actually implement PISE along with an XML
definition configuration, as you imagined, and include a large number of all
the most popular Bioinformatics tools.  We currently purchased this with an
Apple cluster and... So far so good.

They also vectorize much of the source code for the PPC chips, and whenever
possible they are made to take advantage of 'grid engine' and the ability to
run these programs across a cluster or several machines within the 'grid'.


On 7/12/04 6:52 PM, "Michael Gutteridge" <mgutteri@fhcrc.org> 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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