STOCHSIM: a stochastic simulator of (bio)chemical reactions

STOCHSIM is a stochastic simulator for (bio)chemical reactions. The particles are represented as individual software objects which react according to probabilities derived from concentrations and rate constants. In the version 1.4 of STOCHSIM simple two-dimensional spatial structures have been implemented, in which nearest-neighbour interactions of molecules can be simulated.

STOCHSIM was written by Carl Morton-Firth and Tom Shimizu. I have written TkSTOCHSIM, a cross-platform graphical interface written in Perl/Tk.

More information about STOCHSIM can be found on the website of the Cambridge Computational Cell Biology Group

The program can be downloaded from the StochSim sourceforge site.

TkSTOCHSIM and the Systems Biology Markup Language (SBML)

"The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biochemical reaction networks. SBML is applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and many other areas in systems biology."

The support of SBML by STOCHSIM is still very incomplete.

supported SBML understood, but only partially meaningfull for StochSim unsupported not relevant for this level of SBML
simple complexes yes yes
multistate complexes no no
neighbor-sensitive complexes no no
reactions yes yes
rapid equilibriums no no
dynamic values no yes
bi-dimensional lattices no no
listOfUnitDefinitions no no
listOfFunctionDefinitions not applicable no
listOfCompartments only one compartment only one compartment
compartment.volume yes not applicable
compartment.size not applicable yes
compartment.spatialDimentions not applicable only 3D accepted
compartment.units assumes litre assumes litre
compartment.outside no no
compartment.constant not applicable assumes true
listOfSpecies constraints on species name constraints on species name
species.initialAmount yes yes
species.initialConcentration not applicable Assumes mole per litre
species.units only 'mole' and 'numberof' not applicable
species.substanceUnits not applicable only 'mole' and 'item'
species.spatialSizeUnits not applicable assumes litre
species.boundaryCondition yes coupled to species.constant
species.constant not applicable coupled to species.constant
species.charge no no
species.notes yes yes
listOfParameters no parsing of units no
listOfRules no no
listOfReactions yes yes
reaction.notes yes yes
reaction.listOfReactants only 1 or 2 reactants only 1 or 2 reactants
reaction.listOfProducts only 1 or 2 products only 1 or 2 products
reaction.listOfModifiers no no
reaction.speciesReference.stoichiometry no no
reaction.speciesReference.stoichiometryMath not applicable no
reaction.speciesReference.denominator no not applicable
reaction.kineticLaw Only mass action law no
reaction.kineticLaw.timeUnits no no
reaction.kineticLaw.substanceUnits no no no no
reaction.reversible implied implied
pre-defined functions no no

Here are some models built in STOCHSIM and exported in SBML:

Last modification 22 February 2007. Nicolas LE NOVÈRE
European Bioinformatics Institute EBI Computational Neurobiology group BioModels database Ligand-Gated Ion Channel database European Membrane Protein Consortium Systems Biology Markup Language Nicolas Le Novere homepage