This code is associated with the paper from Trakoshiset al., "Intrinsic excitation-inhibition imbalance affects medial prefrontal cortex differently in autistic men versus women". eLife, 2020. http://doi.org/10.7554/eLife.55684

Instructions to simulate the LIF network model

Building the neuron model

Instructions to compile the neuron model in NEST are based on the tutorial about “Writing an extension module” (https://nest.github.io/nest-simulator/extension_modules).

1 - Define the environment variable 'NEST_INSTALL_DIR' to contain the path to which you have installed NEST, e.g. using bash:

export NEST_INSTALL_DIR=/Users/pablo/NEST/ins

2 - Create a build directory in the folder 'neuron_model':

cd neuron_model mkdir build cd build

3 - The configure process uses the script 'nest-config' to find out where NEST is installed, where the source code resides, and which compiler options were used for compiling NEST. If 'nest-config' is not in your path, you need to provided it explicitly like this (don't forget to add '..' at the end):

cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ..

4 - Compile:

make

make install

It might be also necessary to update the LD_LIBRARY_PATH, e.g.:

export LD_LIBRARY_PATH=${NEST_INSTALL_DIR}/lib/python2.7/site-packages/nest:$LD_LIBRARY_PATH

Running a simulation

Simulation scripts are in folder 'network/analysis'. Adjust the simulation parameters in the script and execute it using the Python interpreter, e.g.:

python save_results_1.py