Getting Started

A quick overview of simulating neural networks

A NEST simulation tries to follow the logic of an electrophysiological experiment - the difference being it takes place inside the computer rather than in the physical world.

In NEST, the neural system is a collection of nodes and their Connections. Nodes correspond to neurons and devices and connections by synapses. Different neuron and synapse models can coexist in the same network.

To measure or observe the network activity, you can define so-called Devices that represent the various instruments (for measuring and stimulating) found in an experiment. These devices write their data either to memory or to file.

The network and its configuration are defined at the level of the simulation language interpreter (SLI) as well as the PyNEST level.

Check out our PyNEST tutorial, which will explain how to build your first neural network simulation in NEST.

How do I use NEST?

As the experimenter, you need a clear idea of what you want to learn from the experiment. In the context of a network Simulation, this means that you have to know which input you want to give to your network and which output you’re interested in.

You can use NEST either with Python (PyNEST) or as a stand alone application ( nest). PyNEST provides a set of commands to the Python interpreter which give you access to NEST’s simulation kernel. With these commands, you describe and run your network simulation.

A basic network setup in PyNEST

You can use PyNEST interactively from the Python prompt or from within ipython. This is very helpful when you are exploring PyNEST, trying to learn a new functionality or debugging a routine. Once out of the exploratory mode, you will find it saves a lot of time to write your simulations in text files. These can in turn be run from the command line or from the Python or ipython prompt.

Fundamentally, you can build a basic network with the following functions:

# Create the models you want to simulate
neuron = nest.Create("model_name")

# Create the device to stimulate or measure the simulation
device = nest.Create("device_name")

# Modify properties of the neuron and device
nest.SetStatus(neuron, {"key" : value})
nest.SetStatus(device, {"key" : value})

# Tell NEST how they are connected to each other (synapse properties can be
# added here)
nest.Connect(device, neuron, syn_spec={"key": [value1, value2]})

# Simulate network providing a specific timeframe.
nest.Simulate(time_in_ms)

NEST is extensible and new models for neurons, synapses, and devices can be added. You can find out how to create your own model using NESTML and c++.

Connections

Connections between nodes (neurons, devices or synapses) define possible channels for interactions between them. A connection between two nodes is established, using the command Connect.

Each connection has two basic parameters, weight and delay. The weight determines the strength of the connection, the delay determines how long an event needs to travel from the sending to the receiving node. The delay must be a positive number greater or equal to the simulation stepsize and is given in ms.

Devices

Devices are network nodes which provide input to the network or record its output. They encapsulate the stimulation and measurement process. If you want to extract certain information from a simulation, you need a device which is able to deliver this information. Likewise, if you want to send specific input to the network, you need a device which delivers this input.

Devices have a built-in timer which controls the period they are active. Outside this interval, a device will remain silent. The timer can be configured using the command SetStatus.

Simulation

NEST simulations are time driven. The simulation time proceeds in discrete steps of size dt, set using the property resolution of the root node. In each time slice, all nodes in the system are updated and pending events are delivered.

The simulation is run by calling the command Simulate(t), where t is the simulation time in milliseconds. See below for list of physical units in NEST.

Physical units in NEST

  • time - ms
  • voltage - mV
  • capacitance - pF
  • current - pA
  • conductance - nS
  • Spike rates (e.g. poisson_generator) - spikes/s
  • modulation frequencies (e.g. ac_generator) - Hz

Next Steps