SimTK - biomolecular and biomechanical physics-based simulation tools from Stanford

Wednesday, March 9, 2011 - 16:30
TH 331
Michael Sherman (Stanford, Simbios)

Simbios is the NIH-funded National Center for Physics-Based Simulation of Biological Structures at Stanford, started in 2004.
Simbios is organized around the idea that the same physical and computational methods are applicable to simulation of biological systems of all scales, from running humans to folding proteins—wherever Newton’s law f=ma holds. A significant part of our mission is to produce a reusable, high performance open source toolkit SimTK that enables biomolecular and biomechanical medical researchers to use physics-based simulation in their research. To be useful SimTK has to use sound software engineering principles, rigorous theory, and the best methods from computational science. SimTK is a community asset and we are looking for collaborators skilled in software engineering, computational science, algorithm development, and biomedical simulation who would like to contribute to it. Simbios has established a cooperative agreement with SFSU Computer Science and would like to engage faculty and students to work with us. I will give a quick overview of Simbios, discuss in some depth a few of the biocomputation challenges we address, and present some of the areas where we see opportunities to collaborate with SFSU CS.


Michael Sherman (Sherm) is the chief software architect for Simbios and a member of its executive staff. He has worked in physics-based simulation for most of his career, starting with simulation for mechanical and aerospace engineering, then robotics and biomechanics, real time simulation for games and virtual worlds, and most recently applying related methods to biomolecular simulation. He is co-founder of two Silicon Valley software companies, one in mechanical engineering (Symbolic Dynamics, developer of the SD/FAST multibody simulation tool, acquired by PTC) and one focused on applying simulation techniques to protein structure determination for drug development (Protein Mechanics). Sherm served as a long-term consultant and chief software architect for several PTC mechanical engineering simulation products. Prior to that he worked at supercomputer startup Elxsi in the 1980s, where he developed and then managed development of operating system software. He started his career at Hewlett Packard in 1978 after receiving a B.S. in Electrical Engineering and Computer Science from U.C. Berkeley.