[Computational-biology] STochastic Engine for Pathway Simulation
STEPS Development Team
(by steps.dev from gmail.com)
Thu Jan 14 22:55:25 EST 2010
We are pleased to announce the release of STochastic Engine for
Pathway Simulation (STEPS) version 1.0.
STEPS is a package for exact stochastic reaction-diffusion simulation
in complex 3D geometries. Our core algorithm is an implementation of
Gillespie's SSA extended for membrane reactions and diffusive fluxes
between elements in a tetrahedral mesh. STEPS was developed for
simulation of neuronal signaling pathways in dendritic spines and
around synapses, however it is a general tool that may be used for
studying spatial gradients and morphology in any biochemical pathway.
STEPS supports a number of free and research-licensed powerful mesh-
generation packages that can produce structured 3D tetrahedral meshes
representing the required morphology. STEPS provides further
functionality to retrieve all spatial information from the imported
mesh necessary to initialize and run a simulation.
The user-interface to STEPS is in Python, with core computations
carried out in C++ for maximal speed of execution. The user creates
Python scripts to build a model and control a simulation, optionally
taking advantage of the many powerful scientific computing tools
available for Python to process and visualize data.
STEPS can be downloaded from the sourceforge website (http://steps.sourceforge.net/
) where pre-compiled binaries are available for Mac OS X 10.5-10.6 and
Windows, along with source-code, documentation and support.
The STEPS Development Team
Mailing List: http://lists.sourceforge.net/lists/listinfo/steps-users
Email: steps.dev from gmail.com
Computational Neuroscience Unit
Okinawa Institute of Science and Technology
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