Tutorial 3: Single Population Network

Overview

This tutorial demonstrates simulation of a single population consisting of multiple neurons.

Warning

bionetlite currently does not support spike input from external files. This tutorial confirms that population files and synaptic connection information files for biophysical neurons are generated.

See also

Corresponding BMTK tutorial: Tutorial: Multi-Cell, Single Population Network

Changes from BMTK to bionetlite

Only the import statement needs to be changed. All other code remains exactly the same.

Before (BMTK):

from bmtk.builder.networks import NetworkBuilder

After (bionetlite):

from bionetlite import NeuliteBuilder as NetworkBuilder

Generated Files

bionetlite generates files in the following directory:

  • If base_dir is set in the script: {base_dir}_nl/

  • If base_dir is not set: neulite/

Directory Structure

neulite/  (または {base_dir}_nl/)
├── mcortex_population.csv
├── mcortex_mcortex_connection.csv
├── kernel/
│   └── config.h
└── data/
    ├── Scnn1a_473845048_m.swc
    └── 472363762_fit.csv

mcortex_population.csv

Contains information for 100 neurons. The column structure is as follows:

#n_cell,n_comp,name,swc_file,ion_file
100,3682,Scnn1a_100,data/Scnn1a_473845048_m.swc,data/472363762_fit.csv

  • #n_cell: Number of cells (100)

  • n_comp: Number of compartments

  • name: Population name

  • swc_file: Path to SWC morphology file

  • ion_file: Path to ion channel parameter file

mcortex_mcortex_connection.csv

Contains synaptic connection information. bionetlite applies the connection rules defined by bionet and determines specific connection locations (post cid).

#pre nid,post nid,post cid,weight,tau_decay,tau_rise,erev,delay,e/i
0,5,1523,0.00005,1.7,0.1,0.0,2,e
0,12,892,0.00005,1.7,0.1,0.0,2,e
...

  • #pre nid: Presynaptic neuron ID

  • post nid: Postsynaptic neuron ID

  • post cid: Postsynaptic compartment ID

  • weight: Synaptic weight

  • tau_decay: Decay time constant (ms)

  • tau_rise: Rise time constant (ms)

  • erev: Reversal potential (mV)

  • delay: Synaptic delay (ms)

  • e/i: Excitatory (e) or inhibitory (i)

Specification

bionetlite determines synaptic connection locations at the time save_edges() is called. This is normally a process performed at runtime by bionet.simulator. Connections are randomly created from compartments following predefined connection rules.

Next Steps