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URL: http://steps.sourceforge.net/STEPS/default.php
Proper Citation: STEPS (RRID:SCR_008742)
Description: STEPS is a package for exact stochastic simulation of reaction-diffusion systems in realistic, complex 3D geometries. Our core simulation algorithm is an efficient implementation of a variation on 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.
Abbreviations: STEPS
Synonyms: STochastic Engine For Pathway Simulation
Resource Type: software resource, software application, simulation software
Keywords: reaction-diffusion, stochastic, signaling, molecular, python, software, simulator, reaction kinetics, 3d diffusion, signaling pathway, scripting, bio.tools
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