Brian is an open source
Python package for developing simulations of networks of spiking neurons.
Details
Brian is aimed at researchers developing models based on networks of
spiking neurons. The general design is aimed at maximising flexibility, simplicity and users' development time.
[Goodman and Brette 2009] Users specify neuron models by giving their
differential equations in standard mathematical form as
strings, create groups of neurons and connect them via
synapse
In the nervous system, a synapse is a structure that allows a neuron (or nerve cell) to pass an electrical or chemical signal to another neuron or a target effector cell. Synapses can be classified as either chemical or electrical, depending o ...
s. This is in contrast to the approach taken by many neural simulators in which users select from a predefined set of neuron models.
Brian is written in Python. Computationally, it is based around the concept of code generation: users specify the model in Python but behind the scenes Brian generates, compiles and runs code in one of several languages (including Python,
Cython
Cython () is a superset of the programming language Python, which allows developers to write Python code (with optional, C-inspired syntax extensions) that yields performance comparable to that of C.
Cython is a compiled language that is ty ...
and
C++). In addition there is a "standalone" mode in which Brian generates an entire C++
source code
In computing, source code, or simply code or source, is a plain text computer program written in a programming language. A programmer writes the human readable source code to control the behavior of a computer.
Since a computer, at base, only ...
tree with no dependency on Brian, allowing models to be run on platforms where Python is not available.
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 brian2 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="v>-50*mV", reset="v=-60*mV")
P.v = -60 * mV
Pe = P 3200Pi = P 200:Ce = Synapses(Pe, P, on_pre="ge+=1.62*mV")
Ce.connect(p=0.02)
Ci = Synapses(Pi, P, on_pre="gi-=9*mV")
Ci.connect(p=0.02)
M = SpikeMonitor(P)
run(1 * second)
plot(M.t / ms, M.i, ".")
show()
Comparison to other simulators
Brian is primarily, although not solely, aimed at single compartment neuron models. Simulators focused on multi-compartmental models include
Neuron
A neuron (American English), neurone (British English), or nerve cell, is an membrane potential#Cell excitability, excitable cell (biology), cell that fires electric signals called action potentials across a neural network (biology), neural net ...
,
GENESIS, and its derivatives.
The focus of Brian is on flexibility and ease of use, and only supports simulations running on a single machine. The
NEST
A nest is a structure built for certain animals to hold Egg (biology), eggs or young. Although nests are most closely associated with birds, members of all classes of vertebrates and some invertebrates construct nests. They may be composed of ...
simulator includes facilities for distributing simulations across a cluster.
Footnotes
References
* Goodman, D. and Brette, R. (2008)
"Brian: a simulator for spiking neural networks in Python" ''Front. Neuroinform.'' 2:5.
* Goodman, D.F.M. and Brette, R. (2009)
"The Brian simulator" ''Front. Neurosci.''
External links
Brian homepage
Computational neuroscience
Scientific simulation software
Free science software
Neuroscience software
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