STEPS is a free and open source package for exact stochastic simulation of reaction-diffusion systems in arbitrarily complex 3D geometries.
The 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 STEPS was mainly developed for simulating detailed models of neuronal signaling pathways in dendrites and around synapses, it's also a general tool and can be used for studying any biochemical pathway in which spatial gradients and morphology are thought to play a role.
· Python 2.5 or later
What's New in This Release: [ read full changelog ]
· First version to include E-Field and related objects. Allows simulation of the potential across a membrane specifed as a collection of triangles comprising a surface in the tetrahedral mesh. See documentation for more information.
· Addition of solver TetODE for spatial deterministic simulations. Uses the CVODE
· library for solutions.
· Addition of surface diffusion in mesh-based solvers (Tetexct and TetODE), which models a diffusive flux between triangles that form part of a patch surface, analogous to
· volume diffusion between tetrahedral elements in a compartment.
· Several other smaller additions and fixes.