[Bioclusters] Bioinformatics workflow?

[Joaquin Zaragoza]

Dr. Temkin,

How is your schedule on October 20th or 21st for my defense?

-joaquin


-----Original Message-----
From: bioclusters-bounces+jzaragoza=lbk.ars.usda.gov at bioinformatics.org
[mailto:bioclusters-bounces+jzaragoza=lbk.ars.usda.gov at bioinformatics.org]
On Behalf Of J.W. Bizzaro
Sent: Sunday, October 02, 2005 3:09 PM
To: Clustering, compute farming & distributed computing in life science
informatics
Subject: Re: [Bioclusters] Bioinformatics workflow?

Hi Jenny,

At first I thought you were referring to Pegasus:

   http://pegasus.isi.edu/

But then I realized you meant Pegasys:

   http://bioinformatics.ubc.ca/pegasys/

PegasUs and Taverna are designed to work over a grid (heterogeneous systems 
often connected via WAN).  If you're just trying to create a workflow on a 
homogeneous cluster, something like Condor with DAGMan will probably work
fine:

   http://www.cs.wisc.edu/condor/dagman/

But maybe you're also looking for something with a "connect the dots" 
interface.  Pegasys and Taverna are of course two examples of this.  Here's 
another one that I'm aware of:

   http://wildfire.bii.a-star.edu.sg/wildfire/

And the following are (AFAIK) independent of grid and external scheduling
systems:

http://www.scicraft.org/
http://scitegic.com/products_services/pipeline_pilot.htm

BioPipe doesn't (yet, AFAIK) have a connect-the-dots GUI, but it's based on 
BioPerl:

   http://biopipe.org/

Cheers,
Jeff

Jenny Gan wrote:
> 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,

-- 
J.W. Bizzaro
Bioinformatics Organization, Inc. (Bioinformatics.Org)
E-mail: jeff at bioinformatics.org
Phone:  +1 508 890 8600
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