Files Involved in a Circuit

Introduction

The BBP-style circuit and simulation is composed of many different files with different purposes. Generally, their location is based off of keys in the BlueConfig.

Locations

For each heading, the value in the BlueConfig/CircuitConfig is used to resolve the file name.

Ex:

Run Default
{
    CircuitPath /some/path/           <--- Corresponds to Run.CircuitPath
}

Means that Run.CircuitConfig:circuit.mvd2 would exist in /some/path/circuit.mvd2

Note

Essential: Yes means that the file cannot be derived from another source and is a generated by the Generated by step. If it can be generated, how it can be generated is mentioned.

Run.CircuitPath

circuit.mvd2

  • Description:

  • Format Documentation: MVD version 2

  • Generated by: BlueBuilder Phase 1

  • Essential: Yes

  • Deprecated: 2016: In the process of being moved to MVD3

blueBinaryMicrocircuity.bin

  • Description: Conversion of mvd2 to binary format (?)

  • Format Documentation: To be documented

  • Generated by: BlueBuilder Phase 1

  • Essential: Yes

  • Deprecated: 2016: Not needed w/ touchdetector that uses MVD3

circuit_mvd2.sqlite

  • Description: Conversion of MVD2 file to sqlite DB

  • Format Documentation: sqlite tables follow MVD2 exactly

  • Generated by: Created by hand using BluePy or other script

  • Essential: No, can be generated from circuit.mvd2 using BluePy

  • Deprecated: 2016: In the process of being moved to MVD3

SEGMENT(_index.dat|_index.idx|_payload.dat)

  • Description:

  • Format Documentation: To be documented

  • Generated by:

  • Essential: Unknown

  • Deprecated:

SOMA(_index.dat|_index.idx|_payload.dat)

  • Description:

  • Format Documentation: To be documented

  • Generated by:

  • Essential: Unknown

  • Deprecated:

SYNAPSE(_index.dat|_index.idx|_payload.dat)

  • Description:

  • Format Documentation: To be documented

  • Generated by:

  • Essential: Unknown

  • Deprecated: should be relative to Run.nrnPath

Run.nrnPath

start.target

  • Description: ASCII file defining the Cell/Compartment/Section targets

  • Format Documentation:

  • Generated by:

  • Essential:

  • Deprecated: No

nrn.h5

  • Description: List of Synapses in an HDF5 file

  • Format Documentation: 1 HDF5 Group per cell, with 1 row per cell with 19 columns of parameters per synapse. (To be documented)

  • Generated by:

  • Essential: Yes.

  • Deprecated: No

nrn_efferent.h5

  • Description:

  • Format Documentation:

  • Generated by:

  • Essential: No, can be generated from nrn.h5

  • Deprecated:

nrn_positions_efferent.h5

  • Description:

  • Format Documentation:

  • Generated by:

  • Essential: No, can be generated from nrn.h5

  • Deprecated:

nrn_positions.h5

  • Description:

  • Format Documentation:

  • Generated by:

  • Essential: No, can be generated from nrn.h5

  • Deprecated:

nrn_summary.h5

  • Description:

  • Format Documentation:

  • Generated by:

  • Essential: No, can be generated from nrn.h5

  • Deprecated:

start.ncs

  • Description: ASCII simulation input file with information on the template parameters, This is used by the simulation to get gid/metype associations.

  • Format Documentation: To be documented

  • Generated by:

  • Essential:

  • Deprecated: No

SYNAPSE(_index.dat|_index.idx|_payload.dat)

  • Description:

  • Format Documentation: To be documented

  • Generated by:

  • Essential:

  • Deprecated:

Run.OutputRoot

out.dat

  • Description:

  • Format Documentation: To be documented

  • Generated by:

  • Essential:

  • Deprecated:

soma.bbp

  • Description:

  • Format Documentation: To be documented

  • Generated by: Simulation, if there is a report

  • Essential:

  • Deprecated:

soma.h5

  • Description:

  • Format Documentation: To be documented

  • Generated by:

  • Essential: Generated from soma.bbp

  • Deprecated: