src_python

Biophysical Simulations in Herrera et al. 2023

Codes for replicating simulations in Herrera et al. 2023.

Note: mod files must be compiled before running simulation scripts.

Description

• cell_models: cells model files.
• Data: data files.
• generate_tone_times.py: run to generate the tone times for each simulated trial.
• hayetalmodel_active_declarations.py: biophysics of the Hay et al. 2011 model (ModelDB, accession #139653, “cell #1”).
• make_fig5_data_*.py: run to generate the data for creating Fig. 5.
• make_synapses.py: functions package to insert synapses into the L3 and L5 PC models.
• modhayetalmodel_active_declarations.py: biophysics of the Hay et al. 2011 model, incorporating the modifications of voltage-gated calcium channel densities as in Shai et al. (2015) and Ih channel density distribution as in Labarrera et al. (2018) (Leleo and Segev 2021).
• params_synapses.py: synaptic models parameters, and number of synapses per region per cell type.
• PopulationL3PCsEyal.py and PopulationL5PCsHay.py: Python classes to create populations of N (unconnected) L3 and L5 PCs discribed by Eyal et al. (2018) and Hay et al. (2011) model, respectively.
• run_*_sim_Go.py: run to simulate the L3 or L5 PCs population for correct (Go) trials. Check the script for the input parameters.
• run_*_sim_NC.py: run to simulate the L3 or L5 PCs population for error (NC) trials. Check the script for the input parameters.
• utils: util functions.

Dependencies

• NEURON simulator (release 8.0, http://www.neuron.yale.edu/neuron)
• Python 3.8
• LFPy 2.2.2 (https://github.com/LFPy/LFPy)
• Elephant (https://elephant.readthedocs.io/en/latest/)
• Neo (https://neo.readthedocs.io/en/latest/)