BioFVM

BioFVM: Finite Volume Solver for Biological Problems. Version: 1.1.0 Release date: 23 February 2016 Homepage: http://BioFVM.MathCancer.org Downloads: http://BioFVM.sf.net Summary: This update introduces write support for MultiCellDS digital snapshots, based upon the 0.5 draft of the standard. See http://MultiCellDS.org for further information on this multicellular data standard. Also, as of this version, BioFVM is moving from the Apache 2.0 license to the (3-clause) BSD license, to ensure compatibility with GPL v2. Lastly, this release fixes a small bug where new basic_agents were not given a volume. This would cause discrete source/sinks to release/uptake 0 substrate. The default constructor now sets the volume to 1.0, so that source/sink rates correspond to per-cell rates unless the cell volume is set (in which case the rates are per-cell volume). New features: + Added detailed metadata output options for MultiCellDS. + Added several MultiCellDS write functions. + Added write support for MultiCellDS digital snapshots (draft standards 0.5). + Included a new matlab function for reading BioFVM-generated MultiCellDS data. (read_MultiCellDS_xml.m) + template_project.cpp updated to include MultiCellDS saves. + Changed license to Modified BSD (3-clause) to be GPL 2 and GPL 3 compatible. Bugfixes: + basic_agent::volume set to 1 in the default constructor, so that uptake and secretion rates are now (by default) per-cell, rather than per-cell volume, and so that cell sources and sinks aren't set to zero if the user doesn't specify cell volumes. + Full source for the tutorial is now included in a cleaner documentation folder. + Documentation folder includes an HTML file with links to tutorials on MathCancer.blogspot.com. + Licenses for BioFVM and pugixml are now more explicitly included in a licenses directory.