Software for computational neuroscience

The following tools are among the software currently available

Auryn

A simulator for spiking neural networks with plastic synapses.

Built with MPI support.

bionetgen

Software for rule-based modeling of biochemical systems.

Brian (version 1)

A clock-driven simulator for spiking neural networks (in COPR).

Brian2

A clock-driven simulator for spiking neural networks.

COPASI

A software application for simulation and analysis of biochemical networks and their dynamics.

Genesis

The GEneral NEural Simulation System.

Moose

Multiscale Neuroscience and Systems Biology Simulator.

NEST

The neural simulation tool.

Built with MPI support. Please see this page for details.

NEURON

A flexible and powerful simulator of neurons and networks

Currently not built with MPI support, and does not provide Python bindings (both are WIP). /usr/bin/oc has been renamed to /usr/bin/hoc (rhbz 1696118).

neurord

Stochastic reaction-diffusion simulator.

nineML-python

A tool for reading, writing and generally working with 9ML.

PyLEMS

LEMS interpreter implemented in Python.

smoldyn

A particle-based spatial stochastic simulator

Software that is in the queue for inclusion is listed here