[Bioclusters] Bioinformatics workflow?

[Tony Travis]

Jenny Gan wrote:
> Hi,
> 
> We are looking to deploy our Apple Cluster in a week and we are very 
> interested in using Inforsense to compose our own workflows to meet the 
> Bioinformatics needs of our institute.  However I am aware that there 
> are at least couple of open sources ones ( Pegasys and Taverna) out 
> there that look promising but (obviously) lacking the extensive 
> support.  My question is, has anyone here been using workflow program, 
> commercial or opened source, and if so how has it been running for you? 
>  I would appreciate your input very much,

Hello, Jenny.

I'm just starting to use Taverna for bioinformatics and I think it looks 
very promising. I attended a recent UK MyGrid users day in Manchester 
(UK) and saw some impressive applications making use of this technology:

	http://www.mygrid.org.uk

We've used Taverna at the Rowett Institute to make federated queries of 
two BioMart's of microarray data, then normalised them using an 'R' 
program as a remote web service by wrapping it with SoapLab:

	http://www.nesc.ac.uk/events/ahm2003/AHMCD/pdf/115.pdf

This was part of a 'proof of principle' demonstrator project for NuGO:

	http://www.nugo.org

It was more complicated to do this than I thought it would be, but well 
worth the effort of learning how to in the end :-)

I've also looked at the 'Galaxia' PHP workflow engine in TikiWiki:

	http://tikiwiki.org/tiki-index.php?page=GalaxiaWorkflow

This is a general purpose workflow engine, though, not specifically for 
bioinformatics. However, it might be useful for 'server-side' PHP work.

Best wishes,

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
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