[Fedora-nightlife-list] here's an example of NightLife's utility....

[Keith Laidig]

	In response to Jeff Spaleta's recent query about the sorts of  
projects that could make use
of NightLife, I'd like to pose the research in our group as an example  
of the type of work
that could readily use such a resource.

	Short version:

	Our public protein structure prediction server, Robetta, relies upon  
farming our computationally
intensive steps to NCSA's clusters, via CONDOR, to provide timely  
access to our group's methods
for the general academic community.  But we find that our resources  
are stretched thin and at times
we are unable to provide the researchers the sort of quick response  
that allows their research efforts
to proceed.

	If we had access to more computing power, even that available from  
modest periods of inactivity,
we could put that power to work to address many pressing issues in bio- 
medical research such
as HIV/AIDS vaccine design, improvement of existing drugs and/or  
design new drugs, and creation
of new methods to harness biology to address issues such as carbon  
sequestration.

	Overly-long version:

	I run the various computing infrastructures for David Baker's  
computational biophysics
group at the University of Washington, http://www.bakerlab.org.  The  
group's primary computational
focus is the de-novo prediction of the 3-D structure of proteins from  
the linear sequence of amino
acid in the given protein chain.  The algorithm under constant  
development here, Rosetta, is an
embarrassingly parallel, Monte Carlo application that requires  
significant amounts of CPU time
to discover the "best" protein structures in a statistically  
significant fashion.  And this approach
has enjoyed modest success over the past few years.

	The group's success has led to a broad interest in the availability  
of the methods to the
academic community.  The code (which is freely available to academic  
researchers) is challenging
to use correctly and the post-production data crunching can be  
daunting.  As a result we created a
publicly available, automatic service - robetta (http:// 
www.robetta.org) - roughly 4-5 years ago
to allow anyone to use the methods via the service.  We've been  
victims of our popularity and
the server was soon awash in work that pushed the wait times from a  
day or two to almost a year.

	To gain more horsepower, we began a collaboration with NCSA and the  
CONDOR group to farm
our work to their systems - via CONDOR - and that has proven quite  
successful at keeping the wait times
down to the range of "months".

	I'd specifically like to point out that the CONDOR group has been VERY
helpful with our CONDOR issues - their goal is your successful use of  
CONDOR and they're good at
it!  We've been using CONDOR on our local infrastructure for ~8 years  
and are quite happy.  The
transition to CONDOR wasn't as challenging for the scientists as I  
feared and it's integration into Globus
make using remote resources straightforward.

	We have researchers from a wide variety of fields who use this  
service as an integral portion of their
research effort, despite the somewhat slow turn-around time. But this  
summer is the bi-annual, world-wide
CASP contest (http://www.predictioncenter.org/casp8/, blind testing of  
methods, lasts May->August) and,
by popular demand, the automatic service is turned towards the many  
"targets" of the contest which
some use as starting points for their work.  This leaves many  
researchers waiting for their work to be
addressed until the contest is completed.

	If we could access more computing power we would be able to keep the  
service working on the
non-CASP related work during these contests and improve turn-around  
time in general.

	-KEL

-- 
+>  Keith E. Laidig, Ph.D., M.S., M.Phil.    laidig at u.washington.edu
+>  HHMI Affiliate                http://staff.washington.edu/laidig