computational-model

Computational model for Padamsey et al.

Neuron model: Hodgkin-Huxley type, single compartment.

Numerical simulations were performed using the NEURON simulation environment interfaced with Python:

https://www.neuron.yale.edu/neuron/

Analysis was done in Python, channel calibration in MATLAB.

Simulation notebooks

We ran the simulations and visualised results with jupyter notebooks (.ipynb files). The notebooks are in the folder neuron-model. Note that clicking on the .ipynb files via GitHub gives a preview of the simulation results.

File	Description
simu_toy_model_passive.ipynb	Toy model (Figure 3/ H-K) Passive components only, no voltage-gated channels
simu_deterministic_model.ipynb	Input/Output and tuning curves (Figure 5/ C-F) - Deterministic channels model - Simulate synaptic input trial-trial variability
simu_stochastic_model.ipynb	Input/Output and tuning curves (Figure 5/ I-L) - Stochastic channels model - Voltage-dependent membrane noise
simu_trace_detchannels.ipynb	Temporal traces (Figure 5/ B) - Deterministic channels model - Simulate synaptic input trial-trial variability
simu_trace_stochannels.ipynb	Temporal traces (Figure 5/ H) - Stochastic channels model - Voltage-dependent membrane noise

Python scripts

Custom modules imported in the simulation jupyter notebooks. The .py files are in the folder neuron-model.

File	Description
custommodel.py	Define neuron model parameters and synaptic input parameters
modelsetup.py	Setup neuron model and synaptic input
deterministicfunc.py	Functions to run the simulations for the deterministic model (I/O, tuning curves, traces)
stochasticfunc.py	Functions to run the simulations for the stochastic model (I/O, tuning curves, traces)

Ion channels models

Custom scripts were written in MATLAB to adjust the parameters of the voltage-gated channels (Na and Kdr). They can be found in the folder matlab-calibrate-channels. The main scripts for calibration are main_voltage_step_channels.m and main_input_current_trace.m.

The custom ion channels were then defined using NEURON's Channel Builder:

https://www.neuron.yale.edu/neuron/static/docs/chanlbild/main.html

All channels are saved in a single session file, and can be found in the folder neuron-model.

File	Description
ch_carter_subtchan.ses	Deterministic channels
stch_carter_subtchan.ses	Stochastic channels