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SimTK 0.5 A progress report 14 July 2005

SimTK 0.5 A progress report 14 July 2005. Simbios mission. Enable biomedical scientists to use, develop and share accurate models & simulations of biological structures—from molecules to organisms. Strategy: Develop, disseminate, support an open-source “biosimulation toolkit” SimTK

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SimTK 0.5 A progress report 14 July 2005

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  1. SimTK 0.5 A progress report 14 July 2005

  2. Simbios mission Enable biomedical scientists touse, develop and shareaccurate models & simulations ofbiological structures—from molecules to organisms. Strategy: Develop, disseminate, support an open-source “biosimulation toolkit” SimTK Support several “driving biological problems” to ensure accuracy & utility

  3. The people Clay Anderson Jack Middleton Chris Bruns ? Ayman Habib Bryan Keller Michael Sherman Blanca Pineda Jeanette Schmidt

  4. Topics • Introduction (done) • Goals for SimTK • The shape of the box • How and why to participate • What do we have now? • What’s next? • Demos & discussion

  5. Some goals for SimTK • One-stop App shopping for lab scientists and clinicians • Exchangeable subsystems for modelers • Access to reliable computational methods & hardware support • Platform for computational research • Apples-to-apples comparisons • Demonstrate superiority in real applications • Encourage collaboration with others, incl. NCBCs • Develop into a self-sustaining community

  6. SimTK User Communities • Algorithm inventor • Modeler • Scientist/clinician • Application developer But:generality is not a benefit to a specialist! So …

  7. How to focus? • Low hanging fruit? • Pressing needs? • How can we attract initial users? • What can we offer soon?

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

  9. SimTK.org The SimTK box ApplicationsProblem solving • “Buy-in” at several levels ModelingPhysics, mathematics, logic ComputationResource management

  10. SimTK.org SimTK.org SourceForge–like “federated” model (uses GForge) Applications Modeling Computation

  11. SimTK.org • Familiar SourceForge federated model via GForge • Friendly seach, browse, download & install for end users • Self-governing projects within a defined framework • Best-in-class project hosting • SubVersion source code control • CMake/Dart2 for multiplatform build/test • Installation & download support • Mailing lists, project management, etc. • Inviting to collaborators at different levels of “openness” • privateopen binariesopen sourceopen development • Control over who can access what when • Peer review/certification for SW & people • Curation is a major task and great service

  12. SimTK.org Applications Layer • Goal: best computational methods delivered to end-users through narrow, domain-specific, researcher-friendly GUIs • Issues • Curation & quality control • Delivery • Tools • Easy to combine elements into a narrowly-focused app • Exploit available hardware for speed • Example apps for developers Applications Modeling Computation

  13. SimTK.org Modeling Layer • Goal: robust, shareable subsystems • Models composed hierarchically from interchangeable subsystems • Issues • Many • A later discussion … Applications Modeling Computation

  14. Applications Modeling Computation SimTK.org Computation Layer Goals • Support both production & research • Reliable, best-of-class numerical methods • Interchangeable components • Encapsulation and hiding of computational expertise • Exploit parallel hardware • Put high performance in the hands of bench scientists & modelers

  15. Applications Modeling Computation SimTK.org Hardware focus • Avoid impossible problems! • For now tackle technical, not people problems • Sharing is hard (big cluster, grid) • Sole ownership by researcher/clinician • Off-the-shelf notebooks, PCs, small clusters • Windows, Mac, Linux • Effective use of dual- and dual-dual core machines • Goal: end-user sees 10X speedup for $20K • Typical node? • 4 tightly coupled 64-bit CPUs (e.g. 2 X dual core Opterons) • Acceleration via GPUs (e.g. 2 X NVIDIA Quadro) • $12K now, much cheaper soon

  16. Applications Modeling Computation SimTK.org Scientists like instruments Mass Spec Biostructuresimulation

  17. Applications Modeling Computation SimTK.org Biosimulation is HPC • High Performance Computing • Physics-based, multiscale, computationally intense • E.g., fusion simulation, astrophysics, climatemodeling • Similar computational structure acrossdomains, incl. biology • Focus: how to speed up a single computation using parallel hardware • Extensively pursued by DOE (DARPA & NSF too) • Much available public domain software & expertise • DOE “ACTS” collection • Common Component Architecture (CCA)

  18. Licensing • Anything we write or fund: open source, BSD-like license • Anyone can do anything; just don’t blame us! • Commercial involvement is crucial to long-term health and broad dissemination! • Contributors have legitimate reasons for privacy • Welcome at all levels; easy to open up once in SimTK • Open source ≠ open development! • Much great software already exists in physics-based simulation • Reliable access to it is a huge problem

  19. Some ways to participate now • Manage your projects in SimTK.org • SubVersion source code control (Clay’s SimTK Engr. J. 5(4)) • Mailing lists, news, bug tracking, documentation, references • You control who has access • Disaster recovery (backed up nightly) • Easy collaboration with others • A major benefit: continuity • For lab: software still available after developer moves on • For developer: open source means continued access to your work from your new institution • Contribute software and ideas • E.g., what essential numerical libraries should be maintained in SimTK?

  20. Some SimTK people & projects • Contributions • Delp lab: NMBL simulation & control tookit; NMBL app (Clay Anderson, Ayman Habib) • Khatib lab: PrRobot multibody code (KC Chang, thanks to James Warren) • Altman lab • SStructView (RNA 2d structure viewer by Ramon Felciano) • Gomopy molecular dynamics (Randy Radmer) • FEATURE (many contributors) • DOE: CCA & Sundials suite (Radu Serban, Rob Armstrong, Ben Allan) • VTK (Kitware; NAMIC NCBC) • Source control only • Pande lab: Ion Simulator (Mark Englehardt), Normal modes (Paula Petrone) • Altman lab: Mike Liang’s research • Staff projects • SimTK.org web site (Bryan Keller) • ToRNAdo RNA viewer (Chris Bruns) • Modeling layer prototype (Sherm) • SimTK CCA infrastructure (Jack Middleton)

  21. Plans for SimTK 1.0 • The rest of the box • Complete multiplatform build/test/release/download system • Modeled after VTK’s system • Peer rating system • Defined evaluation & certification process (ideas, please!) • Content • Some useful apps • Basic computational libraries • Robust conventional HPC with multiprocessor/small cluster support • Open source multibody dynamics

  22. Applications Modeling Computation Applications Modeling Computation SimTK.org SimTK.org SimTK.org Applications Modeling Computation Demos • A brief tour of SimTK.org • A turnkey downloadable App: ToRNAdo • Single purpose Java app • Built using available visualization/windowing/ installation tools • A toy App • C++ main program using wxwindows, vtk • Uses prototype modeling layer with exchangeable subsystems (particles or leg) • Particles built in to App • Leg uses PrRobot multibody code from Oussama Khatib’s lab (thanks to James Warren!) • Uses exchangeable computational components • DOE CVODE implicit integrator as CCA component • Conventional RK4 from a library • Dumb explicit Euler built-in to App • All share same interface • Many ways to play!

  23. SimTK.org tour

  24. To do RNA: ToRNAdo • What is ToRNAdo? • Work in progress (hence “To do”) • Prototype SimTK application • Java application • Goals: • Visualize lumped molecule representations • Explore user interface concepts • Interactively refold RNA structures • Generate reusable application components

  25. Why Java web start? • Turn-key applications • One click -> running program • Automatic program updates • Only downloads new parts if an update has occurred • Transparent support for multiple platforms • (e.g. Windows, Mac, Linux, Solaris) • “Real” C/C++ applications can be wrapped in a thin Java shell.

  26. 1 2 3 4 Select application in web browser Ignore progress dialogs Accept security certificate(s) Use application

  27. External components of toRNAdo • VTK visualization tool kit • written in C++ • bound to Java using JNI • also bound to python, Tcl • open source license • JAMA numerical methods • public domain • symmetric eigenvectors and SVD • Swing widgets • part of Java • JOGL • Java OpenGL bindings • BSD license • Java Web Start

  28. Cobbled together from: PrRobot (Khatib) NMBL bones (Delp) VTK (NAMIC) CVODE (DOE) CCA (DOE) wXwindows Linux Toy app GUI Investigation Model Model MechanicalSubsystem ForceSubsystem State Integrator ParticleSubsystem Lower LegSubsystem CVODE(CCA Component) RK4 (Library) Explicit Euler (Built in)

  29. Thank you! • Links • Center: simbios.stanford.edu • Software: simtk.org • Journal: journal.simtk.org • Magazine: BiomedicalComputationReview.org

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