Welcome to NNGT’s documentation!#

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Overview#

The Neural Networks and Graphs’ Topology (NNGT) module provides a unified interface to access, generate, and analyze networks via any of the well-known Python graph libraries: networkx, igraph, and graph-tool.

For people in neuroscience, the library also provides tools to grow and study detailed biological networks by interfacing efficient graph libraries with highly distributed activity simulators.

The library has two main targets:

  • people looking for a unifying interface for these three graph libraries, allowing to run and share a single code on different platforms

  • neuroscience people looking for an easy way to generate complex networks while keeping track of neuronal populations and their biological properties

Main classes#

NNGT provides four main classes. The two first are aimed at the graph-theoretical community, the third and fourth are more for the neuroscience community. Additional details are provided on the Main module (API) page.

Graph

provides a simple implementation to access and analyse topological graphs by wrapping any graph object from other graph libraries.

SpatialGraph

a Graph embedded in space (nodes 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 graphs and connectivity:

connectivity between the nodes can be chosen from various well-known graph models, specific groups and structures can be generated to simplify edge generation

Populations:

populations of neurons can be used and be set to respect various constraints (for instance a given fraction of inhibitory neurons), they simplify network generation and make it highly efficient to interact with the NEST simulator

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#