HPC Approaches in Life Sciences

Presenter: Thomas Cheatham
University of Utah, U.S.
tec3@utah.edu

Presenter: Erik Lindahl
University of Stockholm, Sweden
erik.lindahl@scilifelab.se

This joint presentation will highlight computational science developments and challenges from the perspective of two different MD simulation community codes (AMBER and GROMACS). Issues related to performance, data management, and simulation management will be covered.

Thomas Cheatham is a Professor in the Department of Medicinal Chemistry in the College of Pharmacy and Director of Research Computing at the Center for High Performance Computing (CHPC) in University IT at the University of Utah. His research involves large ensembles of biomolecular simulations with a focus on RNA. He is involved nationally with a variety of cyberinfrastructure interests including XSEDE, Blue Waters, ACI-REF and the Campus Research Computing Consortium. At CHPC, beyond broadly supporting research computing on campus, we deploy and operate both open and protected environments for computing and analyses of open and restricted data (including HIPAA and human genomic data), and large scale virtualized, "bare metal", HPC, storage and advanced networking resources.

Erik Lindahl is professor of Biophysics at Stockholm University Sweden, with a second appointment as professor of Theoretical Biophysics at the KTH Royal Institute of Technology. His research is focused on understanding membrane protein structure and function, in particular complex conformational transition and method development both for molecular dynamics simulations and cryo-EM structure determination. The lab leads the development of GROMACS, which is one of the large programs used for parallel molecular dynamics simulations on a wide range of supercomputers, distributed resources and accelerators such as GPUs or many-core chips.