Sharing ORNL HPC informatics within the biomedical research community
OLCF Director of Science Jack Wells spoke recently to the annual Bio-IT World Conference & Expo in Boston, sharing Oak Ridge National Laboratory’s supercomputing experience.
Now in its 11th year, Bio-IT hosted over 2,500 biomedical researchers and drug development representatives from over 30 countries. The aim of the conference is to expand life science informatics and achievements.
By incorporating information technology tools into biomedical research, the Bio-IT community has grown rapidly, pushing into areas such as personalized medicine and evidence-based medicine. Wells was asked to present case studies of applications using Titan to give this community a better sense of the problems that can be tackled by leadership computing.
“It is important to bring knowledge about the leadership computing user programs to communities that are not working with us,” Wells explained. “Our participation in this meeting is an example of our outreach and the community’s interests.”
In his presentation, “Accelerating Bioscience and Technology with Titan, the World’s Fastest Supercomputer,” Wells explained that petascale computing is drastically speeding up early science results. Thanks to its hybrid architecture, which combines GPUs (originally created to accelerate computer gaming) with traditional CPUs, Titan has shown a tenfold increase in performance over its supercomputing predecessor, Jaguar.
“This new computing power is enabling new science applications,” Wells noted. “Researchers in a variety of fields need to hear about our impact so that they can dream and come up with the problems that they might want to solve on Titan.”
One powerful tool available to Titan users in biology, materials science, and nanotechnology is an application known as LAMMPS, for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a molecular dynamics code that simulates the movement of atoms through time.
Wells pointed to two studies in which LAMMPS is being used for biomedical research on Titan.
In one, Titan is helping ORNL researchers simulate the effects of sunlight on organic photovoltaic materials—materials that can generate electricity when exposed to sunlight—in hopes of creating a lightweight, highly flexible, low-cost source of renewable energy.
The other study involves the dewetting of liquid crystal films or the ability of liquid crystals to self-assemble into complex solid structures. The outcome, researchers envision, is a film-like structure that acts as a biomedical sensor adapted to detecting bacteria, antibodies, or other specific structures within the body.
Titan is also accelerating new drug discovery. Recently ORNL computational biophysicists used virtual high-throughput software to simulate the docking process of 2 million molecular compounds against a targeted cellular receptor—a feat performed in 72 hours on Titan that would have taken conventional test tubes months, or even longer. This research will eventually result in more efficient drugs, with fewer side effects, at a fraction of the current time to market. (https://www.olcf.ornl.gov/2012/10/18/big-computing-cures-big-pharma/)
Wells sees this ample opportunity for Titan to power biological research discoveries in the future.
“Thanks to the opportunities that Titan enables, we expect to grow new user partnerships within the Bio-IT community from disciplines such as genetics, drug design, and molecular biology and biophysics,” he said.—by Jeremy Rumsey
