Using CSA for connection setup

This example sets up a simple network in NEST using the Connection Set Algebra (CSA) instead of using the built-in connection routines.

Using the CSA requires NEST to be compiled with support for libneurosim. For details, see Djurfeldt M, Davison AP and Eppler JM (2014) Efficient generation of connectivity in neuronal networks from simulator-independent descriptions, Front. Neuroinform.

For a related example, see

First, we import all necessary modules for simulation and plotting.

import nest
from nest import voltage_trace
from nest import visualization

Next, we check for the availability of the CSA Python module. If it does not import, we exit with an error message.

    import csa
    haveCSA = True
except ImportError:
    print("This example requires CSA to be installed in order to run.\n" +
          "Please make sure you compiled NEST using\n" +
          "  -Dwith-libneurosim=[OFF|ON|</path/to/libneurosim>]\n" +
          "and CSA and libneurosim are available from PYTHONPATH.")
    import sys

To set up the connectivity, We create a random connection set with a probability of 0.1 and two associated values (10000.0 and 1.0) used as weight and delay, respectively.

cs = csa.cset(csa.random(0.1), 10000.0, 1.0)

Using the Create command from PyNEST, we create the neurons of the pre- and postsynaptic populations, each of which containing 16 neurons.

pre = nest.Create("iaf_psc_alpha", 16)
post = nest.Create("iaf_psc_alpha", 16)

We can now connect the populations using the CGConnect function. It takes the IDs of pre- and postsynaptic neurons (pre and post), the connection set (cs) and a dictionary that maps the parameters weight and delay to positions in the value set associated with the connection set.

nest.CGConnect(pre, post, cs, {"weight": 0, "delay": 1})

To stimulate the network, we create a poisson_generator and set it up to fire with a rate of 100000 spikes per second. It is connected to the neurons of the pre-synaptic population.

pg = nest.Create("poisson_generator", params={"rate": 100000.0})
nest.Connect(pg, pre, "all_to_all")

To measure and record the membrane potentials of the neurons, we create a voltmeter and connect it to all post-synaptic nodes.

vm = nest.Create("voltmeter")
nest.Connect(vm, post, "all_to_all")

We save the whole connection graph of the network as a PNG image using the plot_network function of the visualization submodule of PyNEST.

allnodes = pg + pre + post + vm
visualization.plot_network(allnodes, "csa_example_graph.png")

Finally, we simulate the network for 50 ms. The voltage traces of the post-synaptic nodes are plotted.