Software for computational neuroscience

Installation media available!

The following tools are among the software currently available in NeuroFedora:


sudo dnf install auryn-{mpich,openmpi}

A simulator for spiking neural networks with plastic synapses. Only built with MPI support.


sudo dnf install bionetgen

Software for rule-based modeling of biochemical systems.

Brian (v1)

Please see COPR.

A clock-driven simulator for spiking neural networks.


sudo dnf install python3-brian2

A clock-driven simulator for spiking neural networks.

CalC: Calcium calculator

sudo dnf install calcium-calculator

A modeling tool for simulating intracellular calcium diffusion and buffering.


sudo dnf install COPASI

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


sudo dnf install genesis-simulator

The GEneral NEural Simulation System.


sudo dnf install moose

Multiscale Neuroscience and Systems Biology Simulator.


sudo dnf install MUSIC

MUSIC, the MUltiSimulation Coordinator.


sudo dnf install python3-nest nest

The neural simulation tool. Built with MPI support. Please see this page for details.


sudo dnf install python3-neuron neuron

A flexible and powerful simulator of neurons and networks. Currently not built with MPI support. /usr/bin/oc has been renamed to /usr/bin/hoc (rhbz 1696118).


sudo dnf install neurord

Stochastic reaction-diffusion simulator.


sudo dnf install python3-nineml

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


sudo dnf install python3-PyLEMS

LEMS interpreter implemented in Python.


sudo dnf install python3-lfpy

Module for extra cellular potentials of multicompartment neuron models on NEURON.


sudo dnf install smoldyn

A particle-based spatial stochastic simulator

Installing multiple tools at once

While each tool can be installed individually, for convenience, a "package group" has also been set up. Installing the group installs all the tools in it:

sudo dnf groupinstall --with-optional "Neuron Modelling Simulators" --skip-broken

This pulls in: COPASI, bionetgen, calcium-calculator, genesis-simulator, moose, neurord, python3-PyLEMS, python3-brian2, python3-nest, python3-neuron, python3-nineml, and smoldyn.

Software that is in the queue for inclusion is listed here.