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RandomLib
benchmark
documents
examples
.hgignore
CompartmentGrowthProcess.cpp
CompartmentGrowthProcess.hpp
CompartmentProcess.cpp
CompartmentProcess.hpp
DiffusionInfluencedReactionProcess.cpp
DiffusionInfluencedReactionProcess.hpp
DiffusionInfluencedReactionProcessInterface.hpp
DiffusionProcess.cpp
DiffusionProcess.hpp
ErythrocyteProcess.cpp
ErythrocyteProcess.hpp
H5Support.hpp
H5VisualizationLogProcess.cpp
HistogramLogProcess.cpp
HistogramLogProcess.hpp
INSTALL
IntensityLoggerProcess.cpp
IteratingLogProcess.cpp
IteratingLogProcess.hpp
Makefile
MassActionProcess.cpp
MassActionProcess.hpp
MicroscopyTrackingProcess.cpp
MicroscopyTrackingProcess.hpp
MicrotubuleProcess.cpp
MicrotubuleProcess.hpp
MoleculeLogProcess.cpp
MoleculeLogProcess.hpp
MoleculePopulateProcess.cpp
MoleculePopulateProcess.hpp
MoleculePopulateProcessInterface.hpp
OscillationAnalysisProcess.cpp
OscillationAnalysisProcess.hpp
Packer.hpp
PeriodicBoundaryDiffusionProcess.cpp
PeriodicBoundaryDiffusionProcess.hpp
PolymerFragmentationProcess.cpp
PolymerFragmentationProcess.hpp
PolymerizationParameterProcess.cpp
PolymerizationParameterProcess.hpp
PolymerizationProcess.cpp
PolymerizationProcess.hpp
PriorityQueue.hpp
README
ReactionProcess.cpp
ReactionProcess.hpp
ReactionProcessInterface.hpp
SpatiocyteCommon.hpp
SpatiocyteNextReactionProcess.cpp
SpatiocyteNextReactionProcess.hpp
SpatiocytePolymer.hpp
SpatiocyteProcess.cpp
SpatiocyteProcess.hpp
SpatiocyteProcessInterface.hpp
SpatiocyteStepper.cpp
SpatiocyteStepper.hpp
SpatiocyteVisualizer.cpp
SpatiocyteVisualizer.hpp
Species.cpp
Species.hpp
TagProcess.cpp
TagProcess.hpp
Thread.cpp
Thread.hpp
Vector.hpp
VisualizationLogProcess.cpp
VisualizationLogProcess.hpp

README

INSTALL: detailed installation instructions
spatiocyteGuide.odt: document describing model building essentials

Details of the method:

1. Arjunan, S. N. V. and Tomita, M. (2010). A new multicompartmental
   reaction-diffusion modeling method links transient membrane attachment of
   E. coli MinE to E-ring formation. Syst. Synth. Biol. 4(1):35-53.

2. Arjunan, S. N. V. and Tomita, M. (2009). Modeling reaction-diffusion of
   molecules on surface and in volume spaces with the E-Cell System. 
   International Journal of Computer Science and Information Security.
   3(1): 211–216