[Computational-biology] STochastic Engine for Pathway Simulation release

STEPS Development Team via comp-bio%40net.bio.net (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.


Best regards,

The STEPS Development Team

Website: http://steps.sourceforge.net/
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
http://www.irp.oist.jp/cns/



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