From SimBio - A generic environment for bio-numerical simulations

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Simbio Releasenotes


A list of papers that were produced using the SimBio code is available: here.

Compiling SimBio

Here are instructions on how to compile SimBio on different Linux platforms: here.

Directory Structure

Here is an overview of the directory structure of the SimBio source code: here.

Coding Standard

Here is the coding standard for developers of the SimBio source code including naming conventions: here.

File Formats

Here is a list and description of file formats that SimBio currently supports for input and/or output: here.

FE mesh generation

There are multiple possibilities for finite element mesh generation:

Hexahedra meshing

VGRID can be used to generate regular or geometry-adapted hexahedral (cubic) FE meshes. It has been shown that geometry-adapted FE meshes perform better than regular FE meshes in most tested source analysis situations Wolters et al, IEEE Trans Biomed Eng, 2017. Cubic meshes are especially interesting for applications because of the simplicity of generating them (the problem of segmentation and meshing mainly reduces to the problem of segmentation, see, e.g., Wagner et al., NeuroImage, 2016 or Rullmann et al., NeuroImage, 2009

Tetrahedra meshing

With Tetgen, constrained Delaunay tetrahedral meshes of high accuracy for source analysis applications can be constructed, see, e.g., Drechsler et al., NeuroImage, 2009 or Lew et al., Applied Numerical Mathematics, 2009. CURRY8 allows the generation of ordinary Delaunay tetrahedral meshes as used, e.g., in Wolters et al., NeuroImage, 2006.


  1. Nomenclature
  2. Principles of Finite Element Modeling
  3. General Program Functionality
  4. Program proceeding
  5. Program Control
  6. Programmer’s information
  7. Validation
  8. Installation
  9. Examples
  10. Appendix A
  11. Appendix B -EIPP-
  12. Appendix C
  13. Appendix D
  14. References
  15. CAUCHY Papers

download CAUCHY documentation: part 1 part2

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