Software for computational neuroscience

Installation media available!

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

Arbor

sudo dnf install arbor-{,mpich,openmpi}

The Arbor multi-compartment neural network simulation library.

Auryn

sudo dnf install auryn-{mpich,openmpi}

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

bionetgen

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.

Brian2

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.

COPASI

sudo dnf install COPASI

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

Genesis

sudo dnf install genesis-simulator

The GEneral NEural Simulation System.

jLEMS

sudo dnf install jlems

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

mod2c

sudo dnf install mod2c

NMODL to C adapted for CoreNEURON simulator.

Moose

sudo dnf install moose

Multiscale Neuroscience and Systems Biology Simulator.

MUSIC

sudo dnf install MUSIC

MUSIC, the MUltiSimulation Coordinator.

NEST

sudo dnf install python3-nest nest

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

NetPyNE

sudo dnf install python3-netpyne

A Python package to facilitate the development, parallel simulation, optimization and analysis of multiscale biological neuronal networks in NEURON.

NEURON

sudo dnf install python3-neuron neuron neuron-devel

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).

neurord

sudo dnf install neurord

Stochastic reaction-diffusion simulator.

NiaPy

sudo dnf install python3-niapy

Python microframework for building nature-inspired algorithms.

nineML-python

sudo dnf install python3-nineml

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

PyLEMS

sudo dnf install python3-PyLEMS

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

LFPy

sudo dnf install python3-lfpy

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

SciUnit

sudo dnf install python3-sciunit

A Test-Driven Framework for Formally Validating Scientific Models Against Data.

STEPS

sudo dnf install python3-steps{,-mpich,-openmpi}

STochastic Engine for Pathway Simulation.

smoldyn

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.