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STEPS specifications


Unique identifier OMICS_11478
Alternative name STochastic Engine for Pathway Simulation
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.2.0
Stability Stable
Maintained Yes


No version available


  • person_outline STEPS

Publication for STochastic Engine for Pathway Simulation

STEPS citations


Parallel STEPS: Large Scale Stochastic Spatial Reaction Diffusion Simulation with High Performance Computers

Front Neuroinform
PMCID: 5301017
PMID: 28239346
DOI: 10.3389/fninf.2017.00013

[…] been reported (Gladkov et al., ; Dematté, ); both show 100~200-fold speedup gains compared to the CPU-based serial Smoldyn implementation.Here we introduce an MPI-based parallel implementation of the STochastic Engine for Pathway Simulation (STEPS) (Hepburn et al., ). STEPS is a GNU-licensed, stochastic spatial reaction-diffusion simulator implemented in C++ with a Python user interface. The main […]


25th Annual Computational Neuroscience Meeting: CNS 2016

BMC Neurosci
PMCID: 5001212
PMID: 27534393
DOI: 10.1186/s12868-016-0283-6

[…] afficking [3]. In this work, we have extended the model by adding the molecular network regulating CaMKII activity, which is known to influence LTD. This new model was solved stochastically by STEPS (STochastic Engine for Pathway Simulation) to simulate the influence of noise in the LTD signaling network [4]. Some of the most important new components of this network include phosphatase 2A (PP2A), […]


Spines slow down dendritic chloride diffusion and affect short term ionic plasticity of GABAergic inhibition

Sci Rep
PMCID: 4796789
PMID: 26987404
DOI: 10.1038/srep23196

[…] iffusion of Cl− was simulated as 3D random transfer of Cl− particles from one tetrahedron to another using spatial Gillespie’s Stochastic Simulation Algorithm. The algorithm was implemented in STEPS (STochastic Engine for Pathway Simulation) which is a software for exact simulations of reaction-diffusion systems. The tetrahedral mesh was imported into STEPS. The diffusion coefficient (DCl = 2 μm2/ […]


Comparison of Models for IP3 Receptor Kinetics Using Stochastic Simulations

PLoS One
PMCID: 3629942
PMID: 23630568
DOI: 10.1371/journal.pone.0059618

[…] ented in the section ‘Models’. Our work does not include parameter estimation (as, for example, ) since raw data on channel kinetics of IP3Rs in neurons is not publicly available.In this work, STEPS (STochastic Engine for Pathway Simulation) (, ; version 1.1.2 was used for simulation. With STEPS, it is possible to perform full stochastic simulation of reactions and d […]


STEPS: Modeling and Simulating Complex Reaction Diffusion Systems with Python

Front Neuroinform
PMCID: 2706651
PMID: 19623245
DOI: 10.3389/neuro.11.015.2009

[…] systems at the level where stochasticity, spatial gradients within complex boundary conditions and diffusion all come into play at the same time, we have developed a simulation platform called STEPS (STochastic Engine for Pathway Simulation) that uses an extension of Gillespie's SSA to deal with diffusion of molecules in 3-dimensional reconstructions of neuronal morphology and tissue (Wils and De […]


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STEPS institution(s)
Theoretical Neurobiology, University of Antwerp, Wilrijk, Belgium; Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Kunigami, Okinawa, Japan
STEPS funding source(s)
STEPS development was supported by HFSPO (RGP0074/2003) and OISTPC.

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