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 jlems

Java interpreter for the Low Entropy Model Specification (LEMS) language.


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

Python interpreter for the Low Entropy Model Specification (LEMS) language.


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.