Biosimulation Education and Training
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BioSimulationCourse

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BioSimulationCourseAnnouncement.doc
Mar 3, 2007
Author: Paul Mitiguy
BioSimulation Course Announcement

BioSimulationCourseSyllabus.doc
Apr 4, 2007
Author: Paul Mitiguy
BioSimulation course syllabus

A. BioSimulationCourseLectureVideos

a) Lectures: Preliminary coding requirements

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Lecture 02 -- C/C++ coding standards, compilers, numerical simulation basics
Apr 4, 2007
Author: Blanca Pineda
Video for Lecture 2 (You need QuickTime to view the video)

Lecture 03 -- Using Visual Studio
Apr 4, 2007
Author: Blanca Pineda
Video for Lecture 3 (You need QuickTime to view the video)

b) Lectures

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Lecture 04 -- Preliminaries for using Simbody
Apr 4, 2007
Author: Blanca Pineda
Video for Lecture 4 (You need QuickTime to view the video)

Lecture 05 -- Introduction to Simbody classes, Rotation, Vec3, and Transforms
Apr 4, 2007
Author: Blanca Pineda
Video for Lecture 5 (You need QuickTime to view the video)

Lecture 06 -- Simbody continued, Mass distribution
Apr 4, 2007
Author: Blanca Pineda
Video for Lecture 6 (You need QuickTime to view the video)

Lecture 07 -- Experimental and analytical determination of mass, center of mass, and inertia properties
Apr 4, 2007
Author: Blanca Pineda
Video for Lecture 7 (You need QuickTime to view the video)

Lecture 08 -- Biomechanical Modeling and Geometry
Apr 4, 2007
Author: Blanca Pineda
Lecturer: Jeff Reinbolt; video for Lecture 8 (you need QuickTime to view the Video)

Lecture 09 -- Molecular Modeling and Geometry
May 5, 2007
Author: Blanca Pineda
Lecturer: Russ Altman; video for Lecture 9 (You need QuickTime to view the video)

Lecture 10 -- Mass Properties of Nucleic Acids and Proteins
May 5, 2007
Author: Blanca Pineda
Lecturer: Chris Bruns; video for Lecture 10 (You need QuickTime to view the video)

Lecture 11 -- What is a force
May 5, 2007
Author: Blanca Pineda
Video for Lecture 11 (You need QuickTime to view the video)

Lecture 12 -- Modeling Forces Generated by Muscles and Tendons
May 5, 2007
Author: Blanca Pineda
Lecturer: Clay Anderson; video for Lecture 12 (You need QuickTime to view the video)

Lecture 13 -- Molecular Modeling and Forces
May 5, 2007
Author: Blanca Pineda
Lecturer: Russ Altman; video for Lecture 13 (You need QuickTime to view the video)

Lecture 14 -- An Introduction to Molecular Dynamics for Biomolecules
May 5, 2007
Author: Blanca Pineda
Lecturer: David Parker; video for Lecture 14 (You need QuickTime to view the video)

Lecture 15 -- Simbody Forces
May 5, 2007
Author: Blanca Pineda
Video for Lecture 15 (You need QuickTime to view the video)

Lecture 16 -- Types of Mobilizers
May 5, 2007
Author: Blanca Pineda
Video for Lecture 16 (You need QuickTime to view the video)

Lecture 17 -- Kinematics of Human Motion
May 5, 2007
Author: Blanca Pineda
Lecturer: Jeff Reinbolt; video for Lecture 17 (you need QuickTime to view the Video)

Lecture 18 -- Constraints and Molecule Modeling
Jun 6, 2007
Author: Blanca Pineda
Lecturer: Michael Sherman; video for Lecture 18 (you need QuickTime to view the Video)

B. Labs

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Lab1GettingStartedWithSimTK.zip
Apr 4, 2007
Author: Paul Mitiguy
Lab 1: Getting started with SimTK

Lab2GettingStartedWithSimbody.zip
Apr 4, 2007
Author: Paul Mitiguy
Lab 2: Getting started with Simbody

Lab3MassPropertiesOfMoleculesWithSimbody.zip
May 5, 2007
Author: Paul Mitiguy
Lab 3: Mass properties of molecules with Simbody

Lab4MassPropertiesOfRigidBodiesWithSimbody.zip
May 5, 2007
Author: Paul Mitiguy
Lab4: Mass Properties Of Rigid Bodies With Simbody

Lab4ZHumanBodySegmentMassProperties20070515.zip
May 5, 2007
Author: Paul Mitiguy
Lab4Z: Human Body Segment Mass Properties

Lab5ForcesAndTorquesWithSimbody.zip
May 5, 2007
Author: Paul Mitiguy
Lab5: Forces and torques with Simbody

C. Coding Standards and Libraries

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CodingStandardsCpp.pdf
Apr 4, 2007
Author: Paul Mitiguy
C/C++ Coding standards for BioSimulation

LibrariesAndHeadersForSimTKWinIntel.zip
May 5, 2007
Author: Paul Mitiguy
Libraries and Headers for SimTK Win Intel.zip

LibrariesAndHeadersForVTKWin.zip
Feb 2, 2007
Author: Paul Mitiguy
Libraries and headers for VTK Win

D. Other

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ZZMicrosoftVisualStudioDllsRequiredBySimbody.zip
Apr 4, 2007
Author: Paul Mitiguy
Microsoft Visual Studio Dlls required by Simbody

BioSimulationInstructors

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BioSimulationClassroomScheduleSpring2007.doc
Apr 4, 2007
Author: Paul Mitiguy
BioSimulation Classroom Schedule Spring 2007

Molecular Dynamics

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ConstraintsAndMoleculesByMichaelShermanBioE21520070601.zip
Jul 7, 2007
Author: Paul Mitiguy
Constraints in Simbody; Molecular modeling; by Michael Sherman 20070601

MolecularForcesByDavidParker20070518.pdf
May 5, 2007
Author: Paul Mitiguy
Molecular Forces By David Parker May 18, 2007

MoleculeMassPropertiesCMBruns2007May04.pdf
May 5, 2007
Author: Christopher Bruns
Molecule Mass Properties By Chris Bruns May 4, 2007

Neuromuscular Biomechanics

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EnforcingNewtonsLawForBiomechanicsSimulationByChandJohn.pdf
Apr 4, 2007
Author: Chand John
A new way to make F equal ma in biomechanics motion data for simulation by Chand John

EstimatingBodySegmentParametersInAnimals.pdf
Apr 4, 2007
Author: Paul Mitiguy
Estimating Body Segment Parameters In Animals

HumanBodyInertialPropertiesCopyrightJeffReinbolt20070427.pdf
May 5, 2007
Author: Paul Mitiguy
Human Body Inertial Properties Presentation by Jeff Reinbolt

MuscleAndTendonForcesClayAnderson20070511.doc
May 5, 2007
Author: Paul Mitiguy
Muscle and tendor forces and equations by Frank (Clay) Anderson

MuscleTendonForcesClayAnderson20070511.pdf
May 5, 2007
Author: Paul Mitiguy
Muscle and Tendon Forces Presentation By Clay Anderson

NeuromuscularBiomechanicsInertialPropertiesHandout.pdf
Apr 4, 2007
Author: Paul Mitiguy
Neuromuscular Biomechanics Inertial Properties Handout - Jeff Reinbolt

Planning for course

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BioSimulationTrainingCourseOverview.ppt
Nov 11, 2006
Author: Paul Mitiguy
Bio-Simulation Course Overview (Powerpoint)

BioSimulationTrainingCourseSimbiosRetreat.ppt
Nov 11, 2006
Author: Paul Mitiguy
Bio-Simulation Course Overview (Powerpoint for Simbios Retreat)

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Last updated
Sep 14, 2009

SimTK is maintained through Grant R01GM124443 01A1 from the National Institutes of Health (NIH). It was initially developed as part of the Simbios project funded by the NIH as part of the NIH Roadmap for Medical Research, Grant U54 GM072970.

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