Simbios Simbios ™ The National Center for Physics-Based Simulation of Biological Structures at Stanford SimTK Framework CCA for Physics Based Simulation of Biological Structures Jack Middleton, Michael Sherman CCA Meeting, 28 April 2005

2 Topics Review of Simbios center Review of SimTK How CCA fits into SimTK Architecture Use of GForge Time for questions & discussion

Simbios Simbios ™ The National Center for Physics-Based Simulation of Biological Structures at Stanford

4 Simbios Part of huge NIH initiative –Establish national biocomputing infrastructure One of 7 centers –$20M/5yrs each, one 5yr renewal possible Ours is to pursue physics-based simulation Not just a research grant

5 Simbios mission Enable biomedical scientists to develop and share accurate models and simulations of biological structures—from molecules to organisms. Strategy: develop, disseminate, support a “simulation toolkit” SimTK.

6 Simbios goals Integrate field of physics-based modeling in biomedicine –Avoid duplication of effort –Permit multiscale modeling –Accelerate research in Biocomputation Biomodeling Laboratory biology Medicine

7 Simbios goals (cont.) Support several DBPs to ensure accuracy and utility Exploit existing technologies Serve as global development platform for new technology Keep up with advances in high performance computing architecture Serve distinct user communities –Varying levels of computational savvy –Different areas of domain knowledge

Simbios Organization And … Education Infrastructure (SimTK.org) Dissemination Administration

9 Some SimTK Goals High speed, high quality scientific computation Reliable, convenient, industrial-grade open source development & distribution Sharing of data, numerical methods, models, simulation results Integration with other national computation efforts, exploit existing standards Support several distinct user communities

10 Distinct User Communities 1.Algorithm inventor 2.Modeler 3.Scientist/clinician 4.Application developer

11 Tactics Separate “modeling” from “computation” Support many small, purpose-built, narrow applications Build centralized infrastructure at SimTK.org

12 High level architecture Resources Physics & Logic Problem solving COMPUTATION MODELS APPLICATIONS

13 Models vs. Components Models –Physics, math, logic –Hierarchical construction –Subsystems correspond to physical world objects or concepts –Conceptual, not computational! Components –Computational resources CPUs, memory, numerical methods Supports parallelization –Flat, peer structure –Primary abstraction is “services” (called Ports in CCA) Components providing same Ports are interchangeable –High performance, no overhead

14 Model + Solver  Model W( A ) W( A ) ∂ W( A )/ ∂ A solvermodelresult a=f( A )/m ∫∫ [ ● ] W( A ) dynamics D[●]D[●] ∂ W/ ∂ A sensitivity Study: find muscle attachments A that minimize work W for one gait step optimization A best min [ ● ]

15 Structure of an executing app InvestigationModel Subsystems CCA Components Provides Uses Logic State Component Realization Cache State Variables Application go() Model Manifest States Subsystems Problem Solving (Applications) Physcis & Logic (Modeling) Computation (Components)

16 SimTK Goals for CCA High quality computational toolbox –Solvers (ODE, PDE, DAE, optimizer, sensitivity etc.) –Useful numerical utilities Easily swap compatible components for: –Comparison of computational methods –Utilize clusters (eventually grids) Cross Language –C/C++ (create and use existing components) –FORTRAN (use existing components) –Java, Python, TCL (NA)

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18 Open source version of Source Forge Supports: –Host multiple projects, track bugs, requests, patches –Access control –Surveys, announcements, discussion groups, statistics –Source code repositories, mailing lists Requires some maintenance: –Setup Postgres, Apache, access control –Debug PHP scripts, cron scripts GForge

19 Questions and Issues SimTK must run on native Windows Where is latest CCA spec? Updated CCA website Where are existing components?