[BiO BB] Anybody knows the usage stats for different apps in sequence alignment & molecular dynamics?

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Thu Jan 15 10:05:38 EST 2004

++ CCGB--
>>       Our misison is to enable individual researchers and small
>>       labs to speed up their research and level the playing field with the 'big
>> guys' who can afford throwing 100K per one
>>       acceleration module...
> My impression is that computational speed is the limiting factor for only a small
> number of groups.  I think that most researchers remain interface and data
> management bound.
> I could be way off base with this, and I'm curious to hear about other
> experiences:  I believe that (as is usually true with high performance computing)
> 5% of the researchers take up 95% of the cluster time, and the other 95% are doing
> the best they can to manage even a rather small set of results.
> Am I wrong?

No you are not wrong, but perhaps we are just privilaged? Anyone want to borrow my
idle time?

Most of my time is scripting / debugging jobs to run. The machines sit idel most of
the time, and finish in reasonable time for everything I need.

I would be more likely to pay for a process pipeline manager - naturally I would
preffer a free one.

Any projects to make a process pipeline tool in php?

Should -
* allow workflows to be created / edited / monitored through web.
* be tied into cron.
* rely on gnu make under the hood.
* be tied into cvs for 'job module' developement.
* provide error reporting by mail.
* provide log review.

> Are lots of people sitting on their hands waiting for BLAST (and
> HMMER, and InterPro, and meta-java-dock-o-matic-whatever) to
> complete?
> -Chris Dwan
>  The University of Minnesota
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