This is a tutorial how to use the CompressEM program. This program uses NEURON. This is the code for the paper Simulating Extracted Connectomes.
To first start the simulation, first install the following programs
After following the directions in the NEURON installation documentation, then clone the github repository for FlyEM Simulation Construction. NOTE: Installation instructions for em_neuron is only for x86-linux systems.
To start the program installation process, run the following commands:
cd CompressEM
nrnivmodl mod
python installationdir.py
The command nrnivmodl mod will compile the special mods that were created for the FlyEM model. The python installationdir.py command is for saving the directory structure of where files are in the program.
To run an example of the network simulation:
export PYTHONHOME=/usr
python savedata.py #to convert data for CompressEM to use
python graphconvert.py #this is to graph what neuron connects to what
python columncreate.py #this is to grab cells in the column dataset
python columndata.py #this is to create a dataset for column simulations
./x86_64/special -python nodetest.py 0 #this is to run the simulation of node network with stimuli right to left