[Bioclusters] TeraGrid as a cost-effective replacement for local clusters

Rob Edwards redwards at salmonella.org
Tue Jul 18 01:24:07 EDT 2006

Hi Don

I have been working with Ivan Judson on developing the Life Sciences  
Gateway for handling some of these issues, particularly blast and  

Ivan has developed a web interface, and I have developed a set of  
perl modules for handling interfacing with the gateway.


On Jul 12, 2006, at 11:18 AM, don gilbert wrote:

> Dear bio-cluster users,
> I'm working on general methods to use Grid systems, esp. US TeraGrid
> as a replacement for maintaining your own local clusters in genome  
> analyses.
> The general idea is to create a set of shared protocols and middleware
> such that many groups can use shared grid systems for genome analyses,
> rather than go thru the maintenance hassles of setting up and  
> maintaining
> each one's own.    The Generic Model Organism Database project  
> (www.gmod.org)
> will be a repository for this shared work, and we hope to have common
> bioinformatics tools and data sets installed for genome work at  
> TeraGrid sites
> E.g. like NC BioPortal, http://www.ncbiogrid.org/,  maybe in  
> collaboration with them --
> their work is now mostly provides a web interface via Pise-Emboss- 
> etc with bio-datasets
>  at TeraGrid sites.  For genome informatics, we expect to use  
> mostly command-line
> type access.
> See here for genome assembly and analyses on TeraGrid:
> http://iubio.bio.indiana.edu/biogrid/genome-on-teragrid-poster.html
> http://iubio.bio.indiana.edu/biogrid/teragrid-genomics06-proposal.pdf
> Anyone interested in using such methods, please feel free to  
> contact me.
> - Don Gilbert
> -- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
> -- gilbertd at indiana.edu -- http://marmot.bio.indiana.edu/
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