[Bioclusters] web based bioinformatics application interface

Joe Landman bioclusters@bioinformatics.org
Mon, 12 Jul 2004 19:29:24 -0400

Hi Michael:

  Such a thing exists and it is called Pise. See 
http://www.pasteur.fr/recherche/unites/sis/Pise/  and in short order 
(hopefully) you will be able to pull a nice RPM for it from Luc's page 
http://www.biolinux.org/ .    If you don't like this interface, have a 
look at http://genome.tugraz.at/Software/ClusterControl/ .  There are 
other under development including http://www.mygrid.org.uk/ and various 
portal based things about.  There are even a few commercial 
implementations of the above, though the original open source codes are 
evolving rapidly.


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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Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615