FullSimulation

This is the folder where the core simulation is built and run.

Files

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. Created during the build step by SimulationBuilder.save_groups

NetParams.json

Contains parameters for the simulation that SimulationBuilder uses.

Structure:

• “lengths”: total lengths of different types of segments (um)
  • “basal_dist”: basal dendrites more than 50 um from the soma,
  • “basal_prox”: basal dendrites less than 50 um from the soma,
  • “apic”: apical dendrites
• “syn_density”: number of synapses per um
  • “exc”: excitatory synapses,
  • “inh”: inhibitory synapses
• “n_soma_syns”: number of (PV+) synapses on the soma,
• “divergence”: distributions of connections per cell pairing
  • “exc”: uniform with {“min”, “max”} counts,
  • “peri_inh”: normal with {“m”: mean, “s”: standard deviation, “min”:floor, “max”:cap},
  • “basal_inh”: normal with {“m”: mean, “s”: standard deviation, “min”:floor, “max”:cap},
  • “apic_inh”: normal with {“m”: mean, “s”: standard deviation, “min”:floor, “max”:cap},
• “groups”: properties of functional groups
  • “cells_per_group”: number of cells per functional group,
  • “cluster_radius”: radius of the sphere that clusters are constrained to,
  • “group_radius”: radius of the sphere that groups are constrained to
• “inh_frs”: inhibitory firing rates
  • “proximal”: PV+, normal with {“m”:mean, “s”:standard deviation},
  • “distal”: SOM+, normal with {“m”:mean, “s”:standard deviation}
• “time”: {“start”:when input should start (ms),”stop”:simulation run time (ms)},
• “dL”: target length of each segment,
• “dt”: time (ms) between each simulation step,
• “inh_shift”: how many ms the average excitation trace is shifted to make the inhibition noise trace

Segments.csv

Contains information about every segment in the morphology. Each segment is approximately 1 um in length.

Columns:

• BMTK ID: the ID that bmtk associates with the segments’s section
• X: standardized (0 to 1) distance along the segment’s section
• Type: whether the segment is soma, apic, dend (basal), or axon
• Sec ID: the ID of the segments’s section within the morphology
• Distance: length (um) of closest path to soma
• Coord X: x coordinate (um) of the segment
• Coord Y: y coordinate (um) of the segment
• Coord Z: z coordinate (um) of the segment