TeraGrid as a cost-effective replacement for local clusters

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-o
n-teragrid-poster.html
http://iubio.bio.indiana.edu/biogrid/teragr
id-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
-- gilbertdindiana.edu -- http://marmot.bio.indi
ana.edu/

_______________________________________________
Bioclusters maillist  -  Bioclustersbioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters

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-o
n-teragrid-poster.html
> http://iubio.bio.indiana.edu/biogrid/teragr
id-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
> -- gilbertdindiana.edu -- http://marmot.bio.indi
ana.edu/
> 
> _______________________________________________
> Bioclusters maillist  -  Bioclustersbioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters

Hello Don:

A publicly accessible API would be a wonderful resource. Do
you have 
some initial code somewhere to play with.

-Malay
_______________________________________________
Bioclusters maillist  -  Bioclustersbioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters

Hi Don

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

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

Rob

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-o
n-teragrid-poster.html
> http://iubio.bio.indiana.edu/biogrid/teragr
id-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
> -- gilbertdindiana.edu -- http://marmot.bio.indi
ana.edu/
>
> _______________________________________________
> Bioclusters maillist  -  Bioclustersbioinformatics.org
> https://bioinformatics.org/mailman/listinfo/bioclusters
>

_______________________________________________
Bioclusters maillist  -  Bioclustersbioinformatics.org
https://bioinformatics.org/mailman/listinfo/bioclusters