Software

STEPS

steps-iconSTEPS is a package for exact stochastic simulation of reaction- diffusion systems in arbitrarily complex 3D geometries. Our 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 it was mainly developed for simulating detailed models of neuronal signaling pathways in stretches of 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 analysing output. The core computational routines are still implemented as C/C++ extension modules for maximal speed of execution.
For more information and downloads, please visit our SourceForge site.

NeuroMac

NeuroMac (Neuronal Morphologies and Circuits) is a computational framework to generate large amounts of virtual neuronal morphologies simultaneously, as well as their resultants microcircuits. For more information and downloads, please visit the NeuroMac page.

Neurofitter

neurofitter-iconNeurofitter is software for parameter tuning of electrophysiological neuron models.
It automatically searches for sets of parameters of neuron models that best fit available experimental data, and therefore acts as an interface between neuron simulators, like Neuron or Genesis, and optimization algorithms, like Particle Swarm Optimization, Evolutionary Strategies, etc.
For more information and downloads, please visit our SourceForge site

NEMO

NEMO is a prototype implementation of a layer-oriented language for describing computational models of ion channels.
For more information please visit the NEMO page.

CSPRC

CSPRC is a MATLAB toolbox for estimating the infinitesimal phase response curve (PRC) by using Compressive Sensing (CS) algorithms.
For more information, please visit the code repository.