Tutorial 11

9/3 1:30 - 4:00, Hewlett 103

Particle-Based Cellular Simulation with Smoldyn

Steven S. Andrews and Nathan Addy

Molecular Sciences Institute and Fred Hutchinson Cancer Research Center.

Smoldyn is a computer program for cell-scale biochemical reaction network simulations. It simulates each molecule of interest individually to capture natural stochasticity and for nanometer-scale spatial resolution. Smoldyn can simulate 104 to 105 molecules over several minutes of real time reasonably conveniently. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real chemical system. Smoldyn is similar to the popular MCell program, but is more accurate, more computationally efficient, and has somewhat different features (for example, Smoldyn is probably better for quantitative biophysical research, whereas MCell is probably better for studying neural signaling). Smoldyn is open source, easy to use, and runs on Mac, Linux, and Windows. This tutorial will cover: (1) Survey of spatial modeling methods and software, (2) Tour of Smoldyn capabilities, (3) Smoldyn applications, and (4) Hands-on tutorial. We encourage participants to bring laptop computers. Smoldyn installation CDs will be available although participants will have more time to learn to use Smoldyn if they install it beforehand. Smoldyn is freely available at http://www.smoldyn.org.

Registration Registered attendees please register for this Tutorial.