pyLM
v1.1
A Python Problem Solving Environment for the simulation of stochastic biological systems
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peekFile | |
pyLM | The problem solving environement which interfaces to Lattice Microbes simulation software |
CME | |
CMESimulation | A CME simulation that contains reactions and species |
ipyInterface | |
LMLogger | |
NullHandler | |
RDME | |
CMESimulation | A CME simulation that contains reactions and species |
RDMERegion | A class that represents a type region of an RDME simulation |
RDMESimulation | A class that contains all regions, reactions, diffusions and rules for a RDME simulation |
units | |
pySTDLM | A standard library of functionality that is commonly used in biological simulations |
CellArranger | |
CellArranger | A base class for laying out cells in a 3D space |
RandomArranger | An arranger that randomly orients a number of cells in a regin until either a count or a volume fraction target is met |
RandomSphericalArranger | An arranger that randomly orients a number of cells in a sphere inside a regin until either a count or a volume fraction target is met |
TightGridArranger | An arranger that orients cells in square grid |
LooseGridArranger | An arranger that orients cells in square grid with padding in between |
Cells | |
CellShape | Base class for a particular cell type for use in CellArranger (and later more) |
SphereCell | A representation for a spherical cell |
BoxCell | A representation for a spherical cell |
CapsuleCell | A representation for a spherical cell |
CapsuleShellCell | A representation for a spherical cell |
Distributions | |
ParticleGenerator | A particle generator that adds particles to a particular region of a simulation |
Fitting | |
Comparator | |
MomentComparator | |
TraceComparator | |
Fitter | |
SweepFitter | |
SimulatedAnnealingFitter | |
NetworkVisualization | |
OnTheFly | |
PostProcessing | |
SBMLReader | |
StandardCells | |
StandardReactions | |
StandardReactionSystems |