# Welcome to Stanford Bioengineering Sim TK Open Sim

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Welcome to Stanford Bioengineering Sim. TK: Open. Sim Advisor’s Workshop June 1 -2

Physics-based Simulation of Biological Structures An NIH National Center for Biomedical Computing Supported by NIH U 54 GM 072970 Scott Delp and Russ Altman Department of Bioengineering Stanford University Open. Sim Advisor Workshop - June 1 -2

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 R 01 collaborations through Collaborations with National Centers for Biomedical Computing (PAR-05 -063).

What is Simbios? Physics-based Simulation of Biological Structures • Goal: to develop and disseminate a Simulation Tool Kit (Sim. TK) 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

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

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

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

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

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

Course Graining of Myosin Neck Normal Mode Analysis of low frequency gross motions Myosin neck has 13, 887 atoms Neck is 23 nm long David Parker

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

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

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

What will Open. Sim 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

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

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!

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

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

Agenda for Friday 8: 30 8: 45 9: 00 9: 30 10: 00 11: 00 NIH program overview for collaborating R 01 s Sim. TK. org (Paul) Simbody (Sherm) Open. Sim (Clay) General feedback from Advisors Depart for Airport or Set up a project on Sim. TK. org

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

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 Sim Anneal Genetic Simbody Linear Algebra Force Fields Optimize TAO Integrator • ODE DAE SQ Prog Contact PDEs Rigid Solids Penalty Monte Carlo Control PD • Fluids Meshing

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

Simbios Resources Sim. TK. org: optional features • adopt our CMake system and get: – – nightly builds for Windows, Mac & Linux automated testing at-a-glance build results automated email 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

Simbios Resources Sim. TK • 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 Sim. TK. org

Contacts to learn more about Simbios Websites: http: //simbios. stanford. edu and https: //simtk. org Simbios Team: • Jeannette Schmidt, Executive Director: [email protected] edu • Michael Sherman, Chief Software Architect: [email protected] edu • David Paik, Executive Editor Biomedical Computation Review Simbios PIs: • Russ Altman, co-PI: russ. [email protected] edu • Scott Delp, co-PI: [email protected] edu NIH Officers: • Peter Lyster, Program Officer: [email protected] nih. gov • Jennie Larkin, Lead Science Officer: larkinj [email protected] nih. gov

Simbios Resources • Sim. TK. org: website and federated infrastructure – promotes collaborative environment for user communities of physics-based modeling • Sim. TK: 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.

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

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