Biotech and pharmaceutical organizations are increasingly looking to apply Grid computing to their research efforts.
Typically, life science software that run on Grids include a wide range
of applications, with the most common ones being molecule screening
algorithms and DNA sequence analysis routines.
The nature of these applications makes them good candidates for Grid
computing. For example, in the case of molecule screening, the typical
computational problem involves checking to see if any of the millions
to billions of molecules in collection have the right 3-D shape and
chemical properties to potentially be used to fight a disease. The
common approach here is to give every Grid node the disease target
against which each molecule will be tested. Then, the Grid application
divides up the collection of molecules and distributes them to the
nodes. This type of application is often called a molecular docking
With the DNA sequence routines, the nodes hold portions of a genome
database and then the genetic sequence to be compared is sent to all
the nodes to be checked against the larger database.
Such applications are widely used throughout the biotech and
pharmaceutical industry. Still, the actual use of Grid computing varies
greatly from organization to organization. However, there are two
distinct scenarios for using Grids within the life sciences.
In one common approach, a company sets up an internal Grid that
complements its existing high performance computing operations. In the
other approach, an organization, such as a university or a group
dedicated to fighting a particular disease, asks people to essentially
donate spare PC compute cycles to speed up research efforts.
Notable examples in the first category include Grid projects at Novartis and Johnson & Johnson.
For example, about 18 months ago, Novartis' Grid effort started with a
50-node pilot project that quickly grew to a Grid that included about
2,700-plus office PCs. The Grid ran common bioinformatics routines
including sequence analysis and molecular docking algorithms. Once the
pilot was up and running, the company claimed the Grid's processing
power was about 5 teraflops (5 trillion floating point operations per
second). If that performance were sustained and benchmarked, it would
be on a par roughly with the world's 30th most powerful supercomputers.
Processing power is one thing, results are another. The Grid project
didn't have specific goals, but it was thought that the extra
processing power might help Novartis identify up to 10 times more
potential drug targets per year.
The Grid immediately helped in making a scientific discovery. Running a
docking program, the Grid screened the corporate library of compounds
and found a previously unknown potential cancer inhibitor called a
protein kinase CK2 inhibitor. The results were published in the Journal
of Medicinal Chemistry.
In many life science companies, Grid efforts have been departmental in
nature. But noting the increased computing resources that a wider-scale
effort would deliver and the potential for making faster scientific
discoveries, some companies are making Grids a corporate venture.
That is the case with Johnson & Johnson, which earlier this year
expanded its research and development Grid efforts from discrete
departmental projects into a company-wide initiative. The idea was to
deploy a single global Grid that would host many applications and be
The Grid project is being carried out under the purview of the J&J
Pharma R&D IM (Information Management) group. A pilot project
started earlier this year was expected to grow the Grid from about 450
nodes to 3,000 nodes by the third or fourth quarter of this year.
Outside of the corporate arena, Grids are also being used by
organizations to help conduct basic research into common diseases. Many
of these efforts are philanthropic projects run by research
There are many of these projects, which are similar to SETI@Home where
people are asked to download some software and let the organization
take advantage of the spare CPU cycles on a home computer. Examples of
these types of Grids include the Scripps Research Institute's
FightAids@Home project, the Smallpox Research Grid Project and the
World Community Grid.
Most of these efforts are molecule screening projects. For instance,
the goal of the Smallpox Research Grid Project is to screen about 35
million molecules against a handful of target proteins.
The World Community Grid project takes a slightly different research
approach. Its participants are helping examine how proteins fold. The
information derived about protein folding is useful when trying to find
treatments and cures for disease such as cancer, HIV/AIDS, malaria and
Most of these philanthropic efforts have a technology partner including
companies like IBM, United Devices and others. These partners supply to
underlying Grid infrastructure and management tools that allow the
organization to coordinate and run its research on a Grid. Often times,
there is also a life science software partner that, for example, makes
an application Grid-enabled.
The trend in this philanthropic Grid area is simply to get more people to participate.
The bottom line is that Grid computing is increasingly being called on
within biotech and pharmaceutical companies, as well as by research
organizations, to accelerate research in the life sciences. Most of
these efforts have the ultimate goal of finding new drugs to treat and
About Salvatore Salamone
Salvatore Salamone is the senior IT editor at Bio-IT World (www.bio-itworld.com
He will be chairing a three day IT Solutions for Drug Discovery
conference track May 17 to May 19 at the Bio-IT World Conference &
Expo, to be held in the Hynes Convention Center in Boston. Several of
the talks in that conference track will focus on the use of Grid
computing in the life sciences. More information about the conference
can be found at www.bio-itworldexpo.com