Software for computational neuroscience

The following tools are among the software currently available

nest

The neural simulation tool.

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

Brian2

A clock-driven simulator for spiking neural networks.

Moose

Multiscale Neuroscience and Systems Biology Simulator.

Genesis

The GEneral NEural Simulation System.

PyLEMS

LEMS interpreter implemented in Python.

nineML-python

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

neurord

Stochastic reaction-diffusion simulator.

Brian (version 1)

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

bionetgen

Software for rule-based modeling of biochemical systems.

COPASI

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

Auryn

A simulator for spiking neural networks with plastic synapses.

Built with MPI support.

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).

smoldyn

A particle-based spatial stochastic simulator

Software that is in the queue for inclusion is listed here