Computational Biomechanics Tools

Multibody Dynamics

Branch of computational mechanics that includes both rigid and flexible bodies. The flexible elements are represented with springs and dampers. Multi-body dynamics involves structural dynamics, mechanics, computational mathematics, and control theory. It is the computational method typically used in movement simulation and neuromusculoskeletal models. Solutions involve algebraic and ordinary differential equations.

  • SIMM Musculographics Inc. Software for Interactive Musculoskeletal Modeling Commercial software for developing musculoskeletal models.
  • Open Dynamics Engine (ODE) Open source engine for simulating rigid body dynamics.
  • ADAMS MSC Software Coporation “world’s most widely used mechanical system simulation software” (from website) Many add-ons geared to the automotive industry.
  • LifeMOD The Biomechanics Research Group, Inc. Commercial musculoskeletal modeling software add-on for ADAMS.
  • Simulink The MathWorks Simulink is a platform for multidomain simulation and Model-Based Design for dynamic systems. (From website) Good for control applications in multi-body dynamics.

Finite Element Analysis

Computational method typically used to represent body organs (ie. bone) and organ tissue. For organs, a continuum assumptions is made (the organ is comprised of continuous tissue) and the finite element method solves the partial differential equations of continuum mechanics.

  • TE2THYS Finite volume multi-physics code, focused on coupled behavior (in development)
  • CMISS CMISS is a mathematical modelling package designed for the application of finite element, boundary element, and collocation methods in bioengineering problems. It is developed primarily at the Auckland Bioengineering Institute (University of Auckland). An open source project has started to convert the in-house code.

Mesh Generation

Software used to create meshes of 3-D geometries used in the finite element method.

Conversion Software

Code that converts source code into a common framework.

Conversion of 2-D Images to 3-D Geometries

Typically used to convert two-dimensional medical images such as MRI or CT scans into three-dimensional geometries.

  • 3D Slicer Open source software platform supported by NAMIC and other federal agencies. Provides software tools for many medical image processes including building 3D geometries from medical images (MRI and CT scans).
  • 3D-Doctor
  • Amira
  • MatLab
  • TULIP Freeware image processing software, specializing in moving biological data to quality triangulated surfaces – single and multimateial
  • CMGUI digitizer plugin Open source software that is a part of CMISS (see above). The digitizer plugin is used for manual digitizing of tissue that is difficult to automatically segment.

Geometry Post Processing

  • Geomagic Studio Software for reverse engineering of physical parts. Works well for cleaning up STL files created from 2D medical images ie. smoothing merging etc. Also works well for creating and manipulating NURB surfaces from STL files.
  • MatLab
  • LaGriT-PNNL Contains many utilities for cleaning up your marching-cubes derived surfaces and converting them into computable grids

Extensible Markup Language

Multiscale Modeling Tools

  • CMISS (as above). Components of CMISS have been written for multi-scale or multi-physics modelling. Multi-physics is more developed than multi-scale.



These lists are not meant to be exhaustive. They represent a sample of the tools most commonly used in computational biomechanics. For example, approximately 70 companies offer mesh generation software, but only four such companies are listed here.

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