title: BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations.
abstract: Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology.
  
  
  
  We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and decay in large 3D domains. It has been parallelized with OpenMP, allowing efficient simulations on desktop workstations or single supercomputer nodes. The code is stable even for large time steps, with linear computational cost scalings. Solutions are first-order accurate in time and second-order accurate in space. The code can be run by itself or as part of a larger simulator.
  
  
  
  BioFVM is written in C ++ with parallelization in OpenMP. It is maintained and available for download at http://BioFVM.MathCancer.org and http://BioFVM.sf.net under the Apache License (v2.0).
  
  
  
  paul.macklin@usc.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Ahmadreza
authors.initials: A
authors.lastname: Ghaffarizadeh
authors.affiliation: Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Friedman
authors.affiliation: Center for Applied Molecular Medicine, University of Southern California, Los Angeles, CA 90033, USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Macklin
mesh_terms: D001692:Biological Transport; D003198:Computer Simulation; D021621:Imaging, Three-Dimensional; D008962:Models, Theoretical; D012984:Software; D049490:Systems Biology