Tutorial 2: Spike Input Simulation

Overview

This tutorial describes how to perform spike input to biophysical neurons.

Warning

bionetlite currently does not support input via Virtual cells. This tutorial confirms that the population information file for biophysical neurons is generated.

See also

Corresponding BMTK tutorial: Tutorial: Single Cell Simulation with External Feedforward Input

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

Code Example

from bionetlite import NeuliteBuilder as NetworkBuilder

# Create network
net = NetworkBuilder('mcortex')

# Add biophysical neurons
net.add_nodes(
    N=1,
    pop_name='Scnn1a',
    model_type='biophysical',
    model_template='ctdb:Biophys1.hoc',
    dynamics_params='472363762_fit.json',
    morphology='Scnn1a_473845048_m.swc'
)

# Add Virtual cells for input
# Note: bionetlite ignores Virtual cells
net.add_nodes(
    N=10,
    pop_name='input',
    model_type='virtual'
)

# Build network
net.build()

# Save to files
net.save_nodes(output_dir='sim_ch02/network')

Generated Files

In this simulation, only the population file for biophysical neurons is generated. Information about Virtual cells is not included.

mcortex_population.csv

Contains information for biophysical neuron(s) (1 neuron). The column structure is as follows:

#n_cell,n_comp,name,swc_file,ion_file
1,3682,Scnn1a_100,data/Scnn1a_473845048_m.swc,data/472363762_fit.csv

  • #n_cell: Number of cells

  • n_comp: Number of compartments

  • name: Population name

  • swc_file: Path to SWC morphology file

  • ion_file: Path to ion channel parameter file

Note

Since Virtual cells are not output, mcortex_mcortex_connection.csv becomes a file with only the header.

Limitations

bionetlite and Neulite support the following input methods:

  • ✅ Steady-state current injection

  • ❌ Spike train input from file (currently not supported)

  • ❌ Input via Virtual cell (currently not supported)

Note

If spike input functionality is required, implementation on the Neulite side is needed.

Next Steps