Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
package for developing simulations of networks of spiking neurons. It is being developed by Romain Brette and Dan Goodman at the École Normale Supérieure
École Normale Supérieure
The École normale supérieure is one of the most prestigious French grandes écoles...
Paris is the capital and largest city in France, situated on the river Seine, in northern France, at the heart of the Île-de-France region...
.
Details
Brian is aimed at researchers developing models based on networks of spiking neurons. The design is aimed at minimizing users' development time, with execution speed a secondary goal. Users specify neuron models by giving their differential equations in standard mathematical form, create groups of neurons and connect them via synapses. The intent is to make the process as flexible as possible, so that researchers are not restricted to using neuron models already built in to the simulator. The entire simulator is written in Python, using the NumPy and SciPy
SciPy
SciPy is an open source library of algorithms and mathematical tools for the Python programming language.SciPy contains modules for optimization, linear algebra, integration, interpolation, special functions, FFT, signal and image processing, ODE solvers and other tasks common in science and...
numerical and scientific computing packages. Parts of the simulator can optionally be run using C
C (programming language)
C is a general-purpose computer programming language developed between 1969 and 1973 by Dennis Ritchie at the Bell Telephone Laboratories for use with the Unix operating system....
code generated on the fly. Computationally, Brian uses vectorization techniques, so that for large numbers of neurons, execution speed is of the same order of magnitude as C code.
Example
The following code defines, runs and plots a randomly connected network of leaky integrate and fire neurons with exponential inhibitory and excitatory currents.
from brian import *
eqs =
dv/dt = (ge+gi-(v+49*mV))/(20*ms) : volt
dge/dt = -ge/(5*ms) : volt
dgi/dt = -gi/(10*ms) : volt
P = NeuronGroup(4000, eqs, threshold=-50*mV, reset=-60*mV)
P.v = -60*mV
Pe = P.subgroup(3200)
Pi = P.subgroup(800)
Ce = Connection(Pe, P, 'ge', weight=1.62*mV, sparseness=0.02)
Ci = Connection(Pi, P, 'gi', weight=-9*mV, sparseness=0.02)
M = SpikeMonitor(P)
run(1*second)
raster_plot(M)
show
Comparison to other simulators
Brian is primarily aimed at single compartmental model neurons. Simulators focused on multi-compartmental models include Neuron
Neuron (software)
NEURON is a simulation environment for modeling individual neurons and networks of neurons.It was primarily developed by Michael Hines, John W. Moore, and Ted Carnevale at Yale and Duke....
GENESIS is a simulation environment for constructing realistic models of neurobiological systems at many levels of scale including subcellular processes, individual neurons, networks of neurons, and neuronal systems.GENESIS was developed in the Caltech laboratory of Dr. James M...
