STEPS 1.3.0

STochastic Engine for Pathway Simulation

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LICENSE TYPE:
GPL v3 
USER RATING:
5.0/5 1
DEVELOPED BY:
STEPS Development Team
HOMEPAGE:
steps.sourceforge.net
CATEGORY:
ROOT \ Science and Engineering \ Bioinformatics
STEPS is a package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries. Our core simulation algorithm is an implementation of Gillespie's SSA, extended to deal with diffusion of molecules over the elements of a 3D tetrahedral mesh.

While it was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it is a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role.

We have implemented STEPS as a set of Python modules, which means STEPS users can use Python scripts to control all aspects of setting up the model, generating a mesh, controlling the simulation and generating and analyzing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution.

STEPS is distributed under the GPL v3 license.

Last updated on December 8th, 2011

requirements

#STochastic engine #pathway simulation #stochastic simulation #STochastic #pathway #simulation #3D

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