network_LIF

C code for a generic balanced network of leaky integrate-and-fire neurons, with sparse and random connections and synaptic dynamics. Most of the details about the network model can be found in the article 'Dynamics of Sparsely Connected Networks of Excitatory and Inhibitory Spiking Neurons' by Nicolas Brunel and published in Journal of Computational Neuroscience May 2000, Volume 8, Issue 3, pp 183-208. The only difference with the model described in that article is that the code incorporates dynamics for synaptic currents.

The code tries to be simple, clean, and readable.

Dependencies

To compile the code, you will need the GNU scientific library installed in your system. In Debian-like systems you can install the library with

sudo apt-get install libgsl-dev

Installation and compilation

Just get the code and compile the code with either make or scons in the network_LIF folder:

git clone https://github.com/djmarti/network_LIF
cd network_LIF
make

Problems?

This code compiles and runs well in my Linux boxes, but you may get some errors depending on the compiler you use (i.e., clang instead of gcc). Please let me know if you have problems, and I'll try to update the code to make it more portable.

Running the code and measuring network activity

After compilation you will get an executable file called simulate_one_trial. This program simulates the activity of the network for 20 seconds and saves in text files different measures of activity. The files generated are:

• The spike activity of the 100 neurons , saved under a file like spikes_N_10000_mu_24_delay_0p50_T1_0p5_T2_100.dat. The sample contains excitatory and inhibitory neurons in the same fraction as the overall network: the first f 100 neurons are excitatory (indices i=0,...,100 f - 1) and the remaining (1 - f) 100 are inhibitory (indices i=100 f, ..., 100 - 1). The name of the file contains information about the specific parameters used in the simulation. See filename suffixes below for more details on how to decode this information. The file contains all the spikes emitted during the simulation, with each line containing the time when a spike was emitted (first column) and the identifier of the neuron that emitted the spike (second column).
• The population activity of the excitatory and inhibitory populations, measured on non-overlapping sliding windows of width 0.5 ms.
• The average spike-train autocorrelation.
• The autocorrelation of the population activities (excitatory and inhibitory).

Specifying parameters

You can specify the values of different network parameters with command line options, as well as by editing a configuration file. The configuration file is called brunel2000.conf and sets the default values. The command line options can be used to override the default values without having to edit the config file.

Usage: ./simulate_one_trial [OPTIONS]

Simulate a network of spiking neurons and save spike activity,
population rates, and autocorrelations.

  General settings:
    -c, --config-file=FILE              read configuration parameters from FILE
    -v, --verbose                       be verbose.

  Network parameters:
    -N, --number-of-neurons=INT         set the total number of neurons
    -C, --number-of-connections=INT     set the number of connections per cell
    -f, --fraction-excitatory=REAL      set the fraction of excitatory cells
                                        in the network
    -J, --synaptic-efficacy=REAL        set the synaptic efficacy of excitatory
                                        connections
    -g, --inh-to-exc-weight-ratio=REAL  set the ratio between inhibitory to
                                        excitatory efficacies (absolute value)
    -T, --membrane-time-constant=REAL   set the membrane time constant (in ms)
    -r, --refractory-period=REAL        set the refractory period (in ms) 
    -D, --synaptic-delay=REAL           set the synaptic delay (in ms) 
    -t, --synaptic-time-constant=REAL   set the time constant of fast synapses
    -I, --external-current=REAL         set the homogeneous external current (in mV)

  Miscellaneous:
    -h, --help                          display this help and exit

You can modify the default values by editing brunel2000.conf, which is well commented and contains self-explanatory variable names.

Suffixes

Most of the datafiles generated in the simulation contain a long suffix that specifies the parameter values used in the simulation. An example of suffix is N_10000_mu_24_delay_0p50_T1_0p5_T2_100, which tells us that:

• the network size (N) is 10000,
• the constant external input (mu) is 24 mV,
• the synaptic delay is 0.5 ms,
• the short synaptic time scale (T1) is 0.5 ms,
• the long synaptic time scale (T2, if present) is 100 ms.

Note that decimal points are replaced by 'p' whenever they occur, to avoid issues with the operating system.

All datafiles also contain a header in the first two lines of the file where the parameters are again specified.

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.