# Full Simulation Folder This is the folder where the core simulation is run. ## Files batch_comet_build.sh/batch_comet_run.sh - scripts used to build and run the simulation remotely. build_network.py - Contains the class SimulationBuilder which performs the build step of the simulation. This uses BMTK to create files that are then loaded in for the simulation step. Connections.csv - Contains information for each synapse in the simulation. Created during the run step. Columns: - Node ID: the integer id of the presynaptic node within its population (exc, prox_inh, dist_inh) - Distance: float representing the distance (um) from the synapse to the soma - Conductance: the weight of the synapse (already scaled by distance) - Type: what part of the cell the synapse is on (soma, dend, apic) - Name: the full string that NEURON associates with the postsynaptic segment. - Source Population: the node population that the presynaptic node is a member of (exc, prox_inh, dist_inh) - Release Probability: release probability for the synapse FunctionalGroups.csv - contains the functional group id for each excitatory presynaptic node NetParams.json - contains parameters for the simulation that SimulationBuilder uses output_FRs.txt - contains firing rate for various combinations of synaptic weight distributions **REMOVE** run_network.py - runs the simulation and save Connections.csv Segments.csv - contains information about every segment in the morphology show_results - used to plot and print various aspects of the simulation **CAN REMOVE IF NOT NEEDED** synapses.py- used to set the correct parameters for the synapses during the run step