Welcome to NNGT’s documentation!#

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Overview#

The Neural Network Growth and Topology (NNGT) module provides tools to grow and study detailed biological networks by interfacing efficient graph libraries with highly distributed activity simulators.

Main classes#

NNGT uses four main classes:

Graph
provides a simple implementation over graphs objects from graph libraries (namely the addition of a name, management of detailed nodes and connection properties, and simple access to basic graph measurements).
SpatialGraph
a Graph embedded in space (neurons have positions and connections are associated to a distance)
Network
provides more detailed characteristics to emulate biological neural networks, such as classes of inhibitory and excitatory neurons, synaptic properties…
SpatialNetwork
combines spatial embedding and biological properties

Generation of graphs#

Structured connectivity:
connectivity between the nodes can be chosen from various well-known graph models
Populations:
populations of neurons are distributed afterwards on the structured connectivity, and can be set to respect various constraints (for instance a given fraction of inhibitory neurons and synapses)
Synaptic properties:
synaptic weights and delays can be set from various distributions or correlated to edge properties

Interacting with NEST#

The generated graphs can be used to easily create complex networks using the NEST simulator, on which you can then simulate their activity.

Indices and tables#