Brain Simulations

There are two important distinctions of simulators, with respect to level of detail and to scale. Simulations can be simplified, which means they only represent few properties of the system, or biologically detailed/realistic, which means they model more biological aspects, such as ion channels and multiple compartments in neurons and synapses. The network can be reduced or broad-scale. Computational time depends on scale and level of detail.

Neuron and GENESIS are used for in silico simulations of biologically realistic simulations with multiple compartments. The NEST simulator is used for point-neurons (single compartments) up to neurons with few-compartments. For more detailed descriptions see articles in scholarpedia: NEST, Neuron, and GENESIS.

Another simulator is iqr, which is written in C++ and is used typically for models of cognitive systems. Systems can be graphically designed and controlled. The simulator allows real-time interfacing with robotic devices and sensors. It can be extended via shared libraries with new neuron and synapse types, and custom interfaces to hardware. The source code is distributed under an open-source license at sourceforge. 32 and 64bit binaries are available for Debian/Ubuntu, Suse, and Red Hat.

Here comes an overview over simulators, adapted from Ulysses Bernadet's PhD thesis, "The Neurobiological Basis of Perception and Behavior: The iqr large-scale neuronal System Simulator and its Application", 2006.

Simulator	focus	documentation	license	platform
CSIM/PCSIM	large-scale	manual	GPL	cross-platform
emergent	large-scale	book, wiki, tutorials	GPL	cross-platform
GENESIS	compartmental	book and web	GPL	cross-platform
iqr	large-scale	manual	GPL	*nix
Matlab Neural Network Toolbox	large-scale	good	commercial	Matlab
NCS	large-scale	manual	?	*nix
NEST	large-scale	API	open-source (NEST license)	linux
Neuron	single-cell to network	book and web	open source	cross-platform
Spike-Net	large-scale	manual	GPL	*nix
SPLIT	compartmental	scientific articles	?	?