BioFVM is an open source diffusive transport solver for biological problems. It can solve for the diffusion of tens or hundreds of substrates on large 3-D domains. For simplicity, the code has minimal external dependencies.

BioFVM was first published in:

A. Ghaffarizadeh, S.H. Friedman, and P. Macklin. BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. Bioinformatics 32(8): 1156-8, 2016.

DOI: 10.1093/bioinformatics/btv730

method paper:


  • simultaneously solve diffusion of many substrates
  • powerful even on desktop workstations
  • OpenMP parallelization
  • cross-platform
  • minimal dependencies

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BSD License

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Science/Research, Education, Developers, Engineering

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