BioFVM Files

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.