This project provides simulation code associated with the publication

T. Schwalger, M. Deger, and W. Gerstner. Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size. PLoS Comput. Biol., 13(4):e1005507, 2017.

The core simulation code is written in C. There are two libraries:

• glm_netw_sim_0.8.c for the microscopic (neuron-based) simulation
• glm_popdyn_1.1.c for the mesoscopic (population-based) simulation

The C libraries can be used either via a Python interface or directly in a C program.

Prerequisites for compiling c code

• gcc
• fftw3 (libfftw3-3 package in ubuntu)
• gsl (libgsl2 package in ubuntu)

Create python modules from c libraries

In the top level do:

make -Bf Makefile_fasthazard

This is a modification of the original pseudocode implementation in the paper by using a lookup table for calculating the hazard function. This yields slightly better performance. For the original implementation w/o lookup table use

make -Bf Makefile_orig

Examples

• For running a simulation of an excitatory-inhibitory network (both microscopic and mesoscopic, as in Fig.5 of the paper), change to EI_net_py/ and run

python ei_net_N000_p0.2.py

• For running a simulaion of a population of adapting neurons, change to uncoupled_py/ and run

python lif_adap.py