SCHRÖDINGER
EASY ACCESS
Researchers
combined
Schrödinger
software with
cloud computing
to simulate how
the antibiotic
staurosporine
interacts with the
kinase CDK2.
LEARNING TO LOVE
THE CLOUD
Cloud computing could provide FASTER AND CHEAPER
solutions to some problems, but chemists remain wary
ELIZABETH K. WILSON, C&EN WEST COAST NEWS BUREAU
THE PHENOMENON of cloud computing—essentially outsourcing companies’ or
facilities’ Internet-like services to do jobs
that were once handled by supercomputers
or smaller clusters of on-site computers—
has swept the pharmaceutical industry.
The rest of the scientific community,
however, has been slower to embrace the
cloud, questioning whether it can be an
effective tool for computational research.
Academic and government scientists have
been wary of the significant alterations
they’d need to make to their software
codes, which were originally designed to be
used on clusters or supercomputers.
And a cloud, which could contain tens of
thousands of individual processors, serves
some types of computational problems
better than others. It lends itself well, for
example, to the simultaneous screening of
millions of compounds for drug discovery.
But for other problems that require a lot of
communication between processors, such
as calculating the electronic structure of
large molecules, the cloud performs poorly
compared with in-house clusters.
The many traditional bottlenecks to
swift, unfettered computation include
machine access, communication between
processors, and cost. The cloud, with its
instant availability, almost limitless proces-
sors, and low overhead, offers potentially
an adjunct associate
electrical engineering
and computer sciences
professor at the Uni-
versity of California,
Berkeley. But propo-
nents of cloud comput-
ing, including Fox, are
working to change that.
WHAT’S IN A CLOUD?
Banks of computer servers owned by
companies or institutions make up
the “cloud,” essentially an Internet-like service to which users can
connect and do computing tasks.
greater data management capacity, speed,
and lower cost.
But at least for now, the applications for
chemists are limited to very specific tasks,
says Shane Canon, who directs research on
Magellan, a cloud test facility at Lawrence
Berkeley National Laboratory’s National
Energy Research Scientific Computing
Center. Magellan also serves as a cloud test
bed project at Argonne National Laboratory’s Argonne Leadership Computing
Facility. It was funded through the Department of Energy by the American Recovery
& Reinvestment Act of 2009 to the tune of
$32 million.
Still, “the response from the science
community was tepid,” says Armando Fox,
SCIENTISTS FROM all corners of the
university, including chemists, physicists,
and biologists, have applied for access to
the ACISS cloud. Guenza thinks the facility
will allow her lab to perform molecular dy-
namic simulations of coarse-grained mac-
romolecular systems with an increasing
number of molecules and different time-
scales. These simulations, she adds, “are
useful for the study of important systems
with applications in emerging technology
and in biology.”
“We envision ACISS becoming a major
tool for our lab,” Guenza says. “Through
ACISS, our trajectory data and codes will
be easily shared among the members of our
group and remotely with our collaborators.”
Geraldine Richmond, a University of
Oregon chemistry professor who is also
participating in ACISS, performs molecular
dynamics simulations of molecular pro-
cesses at liquid surfaces. Her lab’s compu-
tational methods—which include a mix of
classical, ab initio, and density functional
theory—have very high central processing
unit (CPU) and memory requirements.
“We are delighted to have access to the
ACISS cloud,” Richmond says. “For my research group, the cloud will allow for much
higher throughput,” she says. “The cloud
