[Bioclusters] Bioinformatics workflow?

Tony Travis ajt at rri.sari.ac.uk
Sun Oct 2 03:14:17 EDT 2005

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:


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:


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


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:


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

Best wishes,

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
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687

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