Software for computational neuroscience

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

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

The GEneral NEural Simulation System.

Moose

sudo dnf install moose

Multiscale Neuroscience and Systems Biology Simulator.

NEST

sudo dnf install python3-nest nest

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

NEURON

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).

neurord

sudo dnf install neurord

Stochastic reaction-diffusion simulator.

nineML-python

sudo dnf install python3-nineml

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

PyLEMS

sudo dnf install python3-PyLEMS

LEMS interpreter implemented in Python.

LFPy

sudo dnf install python3-lfpy

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

smoldyn

sudo dnf install smoldyn

A particle-based spatial stochastic simulator

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