1. SimTK: OpenSim Advisor’s Workshop
Welcome to Stanford
Bioengineering
Good morning every one. Let’s get started.
First, and most importantly, thank you for coming. This is exciting for us to host you and learn from each other. In this room we have a fantastic range of biomedical engineers and experts in biomechanical simulation. I’m so pleased that you could come to stanford and meet with my colleagues and me.
My goal is to engage you in a collaboration that will change and improve the way we build and analyze simulations. It’s exciting to think about all we could accomplish using simulations to restore mobility to individuals with disabilities, especially if we work together to create the world’s best simulation system.
It’s easy to say this, but it’s very hard to deliver on the promise. So, my other goal for today and tomorrow is to get your advise on how to best achieve the goal of building the world’s best biomechanical simulation system.
It’s an amazing group of people here. I’d like to take a few minutes to go around the room and have each person introduce themselves.
SimTK: OpenSim Advisor’s Workshop
June 1-2

2. Physics-based Simulation of Biological Structures An NIH National Center for Biomedical Computing Supported by NIH U54GM072970
Let me tell you about the NIH funded center that has motivated this workshop.
I’ll outline the goals of this wokshop and review the agenda for the next two days.
Simulation bring life to biological structures by revealing their motions and functions.
Scott Delp and Russ Altman
Department of Bioengineering
Stanford University
OpenSim Advisor Workshop - June 1-2

3. What are the NCBCs? Key feature of NIH Roadmap.
Goal: to create a software infrastructure for biomedical research
Seven NCBCs
create software tools to advance biomedical research
Driving Biological Problems (DBPs) ensure that computational research in the NCBCs has direct relevance to biomedical research
NCBCs have program for R01 collaborations through Collaborations with National Centers for Biomedical Computing (PAR ).

4. What is Simbios?
Physics-based Simulation of Biological Structures
Goal: to develop and disseminate a Simulation Tool Kit (SimTK) that will:
stimulate groundbreaking biomedical research
enable development and sharing of accurate physics-based models and simulations of biological structures
The initial DBPs of Simbios span a range of scales:
simulating RNA folding
myosin dynamics
neuromuscular dynamics
cardiovascular mechanics

5. Simulation Toolkit GUI Tools | Documentation Tools | Installation
Modeling
Linear Algebra
Multi Body Dynamics
Simbody
PRrobot •
Integrator
ODE
DAE
Contact
Rigid
Penalty
Optimize
Sim Anneal
Genetic
SQ Prog
Control PD
PDEs
Solids
Fluids
Meshing
Monte Carlo
Force Fields

6. Simulation Toolkit GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
PRrobot •
Contact
Rigid
Penalty •
Control PD
Meshing
Force Fields
Linear Algebra
Integrator
ODE
DAE
Optimize
Sim Anneal
Genetic
SQ Prog

7. Simulation Toolkit GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
PRrobot •
Contact
Rigid
Penalty •
Meshing
Force Fields
Linear Algebra
Integrator
ODE
DAE
Optimize
Sim Anneal
Genetic
SQ Prog
PDEs
Solids
Monte Carlo

8. Simulation Toolkit GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
PRrobot •
Contact
Rigid
Penalty •
Meshing
Force Fields
Linear Algebra
Integrator
ODE
DAE
Optimize
Sim Anneal
Genetic
SQ Prog
PDEs
Solids
Monte Carlo

9. Simulation Toolkit GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
PRrobot •
Contact
Rigid
Penalty •
Control PD
Meshing
Force Fields
Linear Algebra
Integrator
ODE
DAE
Optimize
Sim Anneal
Genetic
SQ Prog
PDEs
Solids
Fluids
Monte Carlo

10. Course Graining of Myosin Neck
Normal Mode Analysis of low frequency gross motions
I constructed two models, one with all compact LCs, another with extended LCs for IQ domains 3 and 6.
Myosin neck has 13,887 atoms
Neck is 23nm long
David Parker

11. Simulation Toolkit GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
PRrobot •
Contact
Rigid
Penalty •
Control PD
Meshing
Force Fields
Linear Algebra
Integrator
ODE
DAE
Optimize
Sim Anneal
Genetic
SQ Prog
Monte Carlo

12. Simulation Toolkit GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
TAO •
Optimize
Sim Anneal
Genetic
SQ Prog
Force Fields
Contact
Rigid
Penalty •
PDEs
Solids
Fluids
Control PD
Meshing
Linear Algebra
Integrator
ODE
DAE
Monte Carlo

13. OpenSim GUI Tools | Documentation Tools | Installation Modeling
Multi Body Dynamics
Simbody
TAO •
Optimize
Sim Anneal
Genetic
SQ Prog
Contact
Rigid
Penalty •
PDEs
Solids
Fluids
Control PD
Meshing
Linear Algebra
Integrator
ODE
DAE
Monte Carlo

14. What will OpenSim provide?
SIMM features in modern open source software
- building and analyzing musculoskeletal models
- standard format for exchanging models
Simbody - open source dynamics engine
Pipeline to create simulations from motion analysis data
Tools to analyze simulations
Extensibility (plugins)
New actuators, controllers, analyses, …
Software continuity for your lab

15. What will OpenSim provide?
The tools models you contribute
The tools we define in this workshop to be the most important

16. Goals for this workshop
Exchange scientific knowledge and ideas among individuals who perform advanced simulations
Identify the major computational challenges that must be met to achieve our scientific goals
Define the features of a simulation toolkit and an application that will be broadly adopted in biomechanics
Clarify the barriers to success and devise means to overcome them
Have a fantastic time at it!

17. Agenda for Thursday
8:30 –9:30 SimTK and OpenSimm overview (Scott Delp)
Goals for the meeting
Feedback from participants
9:30 – 10:30 Presentations by participants (10 minutes each)
Clay Anderson
Darryl Thelen
Rick Neptune
Ton van den Bogert
10: :00 Break
11: :15 Presentations by participants (10 minutes each)
Jill Higginson
Brian Garner
Wendy Murray
Steve Piazza
Tom Buchanan
12:15 - 1:30 Lunch

18. Agenda for Thursday 12:15 - 1:30 Lunch
1:30 – 2:30 Presentations by participants (10 minutes each)
Robert Kirsch
Jeff Reinbolt
Rahman Davoodi
Gerry Loeb
2:30 – 3:30 Working groups
1. Barriers to adoption of SimTK (and solutions)
2. Design of course to teach simulation using SimTK
3. Grand challenges for biomechanical simulation
4. Summary of scientific goals and features needed to achieve them.
3:30 - 4:00 Break
4:00 - 5:00 Reports from working groups
5:00-5:30 Feedback from participants; adjust Friday schedule
6:30 Dinner for visitors

19. Agenda for Friday 8:30 NIH program overview for collaborating R01s
8:45 SimTK.org (Paul)
9:00 Simbody (Sherm)
9:30 OpenSim (Clay)
10:00 General feedback from Advisors
11:00 Depart for Airport
or Set up a project on SimTK.org

21. GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
TAO •
Optimize
Sim Anneal
Genetic
SQ Prog
Force Fields
Contact
Rigid
Penalty •
PDEs
Solids
Fluids
Control PD
Meshing
Linear Algebra
Integrator
ODE
DAE
Monte Carlo

22. Challenges Multi-scale modeling (vs multiple scale modeling)
Multi-physics modeling
Testing models with experimental data
GUI Tools | Documentation Tools | Installation
Modeling
Multi Body Dynamics
Simbody
TAO •
Optimize
Sim Anneal
Genetic
SQ Prog
Force Fields
Contact
Rigid
Penalty •
PDEs
Solids
Fluids
I hope you have seen how physics-based simulation can bring biological structures to life and provide insight into their function.
Some of the major challenges are .. Multi-scale modeling, multiphysics, testing models with experimental data.
The imaging and simulation communities have much to share.
Control PD
Meshing
Linear Algebra
Integrator
ODE
DAE
Monte Carlo

23. Simbios Collaborators
James Spudich
David Paik
Chris Bruns
Leonidas
Guibas
Pat Hanrahan
Osussama
Khatib
Jean-Claude
Latombe
Jung-Chi Liao
Adrian Lew
Allison Arnold
Jeanette Schmidt
Rachel
Weinstein
Kathy Miller
Charles Taylor
Christopher
Zarins
Eftychios
Sifakis
Padma
Sundaram
David Parker
Paula Petrone
Russ Altman
Scott Delp
Peter Pinsky
Michael
Levitt
Alain Laederach
Alex Labute
Clay Anderson
Silvia Blemker
Blanca Pineda
Ron Fedkiw
Peter
Feenstra
Bryan Keller
Jack Middleton
Vijay Pande
Sandy Napel
Ayman Habib
Randy Radmer
Daniel
Herschlag
Michael Sherman

24. Simbios Resources SimTK.org: optional features
adopt our CMake system and get:
nightly builds for Windows, Mac & Linux
automated testing
at-a-glance build results
automated nagging for problems
The CMake system is functional now and available on a beta testing basis
Further infrastructure development will include a system for installation, uninstall, and automated updates

25. Simbios Resources SimTK tools for building physics-based simulations:
robust, high performance, pre-built binary computational methods
Linear algebra, numerical integration, multibody dynamics, molecular force fields, finite element solvers, etc.
shareable models
application building tools
narrow, domain targeted applications
all open source and available in SimTK.org

26. Contacts to learn more about Simbios
Websites: and
Simbios Team:
Jeannette Schmidt, Executive Director:
Michael Sherman, Chief Software Architect:
David Paik, Executive Editor Biomedical Computation Review
Simbios PIs:
Russ Altman, co-PI:
Scott Delp, co-PI:
NIH Officers:
Peter Lyster, Program Officer:
Jennie Larkin, Lead Science Officer:

27. Simbios Resources SimTK.org: website and federated infrastructure
promotes collaborative environment for user communities of physics-based modeling
SimTK: tool kit with freely available tools and models for building physics-based simulations
Simbiome: “yellow pages” with trusted information on resources for the community
Biomedical Computation Review
journal of biomedical computation with a focus on cross cutting issues that are important to the entire community.

28. SimTK/SimTK.org uses and users
Repository of advanced algorithms
Modeling
Applications with easy-to-use GUI
for computer scientists, applied mathematicians, etc.
for modelers such as engineers, physicists, bio-physicists
for end users, such as clinicians or bench scientists