1. Training for Physics-Based Bio-simulation SimBios: NIH Center for Biomedical Computation Physics-based Simulation of Biological Structures Funding: NIH Roadmap Grant U54 GM072970 This PowerPoint presentation and the BioE215 course syllabus are available at https://simtk.org/home/training Last updated November 19, 2006

2. BioE215: Course Objectives Model, analyze, and interpret the mechanics of biological systems Identify important parameters for physics-based modeling of biology Understand the role of computational tools in simulating biological structures, including generating and solving the physical equations with SimTK software Gain physical insights into basic principles with computer experiments Use techniques, skills, and tools necessary for bio-simulation Design/conduct computer experiments and analyze/interpret results Modeling Biological Systems Simulation

3. BioE215: Prerequisites Basic knowledge of: – Biology (e.g. BIOSCI 41) – Mechanics (e.g., E15 or Physics 41) – ODEs (e.g., Math 53 or E155A or CME 102) Significant C or C ++ programming (e.g., CS106B or CS106X)

4. Modeling & Simulating with F=ma F = ma Linear eqns Variables Collisions Post process Geometry JointsConstraints Forces Integration Motion and Forces Initial values

5. BioE215 Lab 2: SimTK.org Download Simbody library and code to simulate Newton’s apple from SimTK.org Simulate Newton’s apple – Plot numerical results (Excel, Matlab, …) – Visualize results with Simbody/VTK Modify Newton’s apple for projectile motion – Simulate with Simbody and plot results – Visualize results with Simbody/VTK

6. BioE215 Lab 3: Numerical Integration ODE and DAE numerical integrators Choosing a numerical integrator – Choosing a step-size – Error control (variable vs. fixed) – Error parameters (relative/absolute error) – Numerical integration verification Impact on integrator of modeling stiff springs/bonds with rigid bodies Numerical integration in Simbody

7. BioE215: List of Labs Lab 1: Getting Started with SimTK Lab 2: Newton’s apple with Simbody Lab 3: Numerical integration Lab 4: Modeling bio-geometry in Simbody Lab 5: Modeling bio-forces with Simbody Lab 6: Modeling bio-joints (mobilizers and Simbody) Lab 7: Modeling constraints in Simbody Lab 8: Simbody studies: Kinematics Lab 9: Simbody studies: Dynamics

8. Teaching Philosophy “I hear and I forget. I see and I remember. I do and I understand.” Confucius 500 B.C. This is a DO course.

9. Course Opportunities & Challenges Opportunities Truly cross-disciplinary Material for a great course Challenges New Course, New field, New team, New software Strengths Modeling and simulation expertise Simbios faculty and staff Instructor/TA and development team

10. Conclusion Jeanette Schmidt Michael Sherman Russ Altman Scott Delp David Paik Blanca Pineda Mark Friedrichs Jung-Chi Liao Alain Laederach Jeff Reinbolt Charley Taylor Thank you Jonathan Dugan Bill Katz Bryan Keller Chris Bruns Jack Middleton Clay Anderson Ayman Habib Chand John Allison Arnold Eran Guendelman … Copyright 2006 BioX at Stanford