GitHub - ecell/ecell3-spatiocyte

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Name		Name	Last commit message	Last commit date
Latest commit History 422 Commits
RandomLib		RandomLib
benchmark		benchmark
documents		documents
examples		examples
.hgignore		.hgignore
CompartmentGrowthProcess.cpp		CompartmentGrowthProcess.cpp
CompartmentGrowthProcess.hpp		CompartmentGrowthProcess.hpp
CompartmentProcess.cpp		CompartmentProcess.cpp
CompartmentProcess.hpp		CompartmentProcess.hpp
DiffusionInfluencedReactionProcess.cpp		DiffusionInfluencedReactionProcess.cpp
DiffusionInfluencedReactionProcess.hpp		DiffusionInfluencedReactionProcess.hpp
DiffusionInfluencedReactionProcessInterface.hpp		DiffusionInfluencedReactionProcessInterface.hpp
DiffusionProcess.cpp		DiffusionProcess.cpp
DiffusionProcess.hpp		DiffusionProcess.hpp
ErythrocyteProcess.cpp		ErythrocyteProcess.cpp
ErythrocyteProcess.hpp		ErythrocyteProcess.hpp
H5Support.hpp		H5Support.hpp
H5VisualizationLogProcess.cpp		H5VisualizationLogProcess.cpp
HistogramLogProcess.cpp		HistogramLogProcess.cpp
HistogramLogProcess.hpp		HistogramLogProcess.hpp
INSTALL		INSTALL
IntensityLoggerProcess.cpp		IntensityLoggerProcess.cpp
IteratingLogProcess.cpp		IteratingLogProcess.cpp
IteratingLogProcess.hpp		IteratingLogProcess.hpp
Makefile		Makefile
MassActionProcess.cpp		MassActionProcess.cpp
MassActionProcess.hpp		MassActionProcess.hpp
MicroscopyTrackingProcess.cpp		MicroscopyTrackingProcess.cpp
MicroscopyTrackingProcess.hpp		MicroscopyTrackingProcess.hpp
MicrotubuleProcess.cpp		MicrotubuleProcess.cpp
MicrotubuleProcess.hpp		MicrotubuleProcess.hpp
MoleculeLogProcess.cpp		MoleculeLogProcess.cpp
MoleculeLogProcess.hpp		MoleculeLogProcess.hpp
MoleculePopulateProcess.cpp		MoleculePopulateProcess.cpp
MoleculePopulateProcess.hpp		MoleculePopulateProcess.hpp
MoleculePopulateProcessInterface.hpp		MoleculePopulateProcessInterface.hpp
OscillationAnalysisProcess.cpp		OscillationAnalysisProcess.cpp
OscillationAnalysisProcess.hpp		OscillationAnalysisProcess.hpp
Packer.hpp		Packer.hpp
PeriodicBoundaryDiffusionProcess.cpp		PeriodicBoundaryDiffusionProcess.cpp
PeriodicBoundaryDiffusionProcess.hpp		PeriodicBoundaryDiffusionProcess.hpp
PolymerFragmentationProcess.cpp		PolymerFragmentationProcess.cpp
PolymerFragmentationProcess.hpp		PolymerFragmentationProcess.hpp
PolymerizationParameterProcess.cpp		PolymerizationParameterProcess.cpp
PolymerizationParameterProcess.hpp		PolymerizationParameterProcess.hpp
PolymerizationProcess.cpp		PolymerizationProcess.cpp
PolymerizationProcess.hpp		PolymerizationProcess.hpp
PriorityQueue.hpp		PriorityQueue.hpp
README		README
ReactionProcess.cpp		ReactionProcess.cpp
ReactionProcess.hpp		ReactionProcess.hpp
ReactionProcessInterface.hpp		ReactionProcessInterface.hpp
SpatiocyteCommon.hpp		SpatiocyteCommon.hpp
SpatiocyteNextReactionProcess.cpp		SpatiocyteNextReactionProcess.cpp
SpatiocyteNextReactionProcess.hpp		SpatiocyteNextReactionProcess.hpp
SpatiocytePolymer.hpp		SpatiocytePolymer.hpp
SpatiocyteProcess.cpp		SpatiocyteProcess.cpp
SpatiocyteProcess.hpp		SpatiocyteProcess.hpp
SpatiocyteProcessInterface.hpp		SpatiocyteProcessInterface.hpp
SpatiocyteStepper.cpp		SpatiocyteStepper.cpp
SpatiocyteStepper.hpp		SpatiocyteStepper.hpp
SpatiocyteVisualizer.cpp		SpatiocyteVisualizer.cpp
SpatiocyteVisualizer.hpp		SpatiocyteVisualizer.hpp
Species.cpp		Species.cpp
Species.hpp		Species.hpp
TagProcess.cpp		TagProcess.cpp
TagProcess.hpp		TagProcess.hpp
Thread.cpp		Thread.cpp
Thread.hpp		Thread.hpp
Vector.hpp		Vector.hpp
VisualizationLogProcess.cpp		VisualizationLogProcess.cpp
VisualizationLogProcess.hpp		VisualizationLogProcess.hpp

Repository files navigation

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

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