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.
method paper: http://dx.doi.org/10.1093/bioinformatics/btv730
- simultaneously solve diffusion of many substrates
- powerful even on desktop workstations
- OpenMP parallelization
- minimal dependencies
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