Morphological model of neuron with RxD ionic diffusion. Based on NEURON.

Prerequisites

• Install requirements.txt
• Install NEURON

MOD compilation

• Before run you must compile mod files and copy compiled folder to the main folder (where run Python files are located)

nrmivmodl

• To help with compilation use compile_mods.sh (Linux only)
  • first param is folder from which to copy files fo current_mods folder
  • Don't forget to add /* at the end, eg.:

sh compile_mods.sh mods/4p_ach_da_syns/*

• If you auto-run from PyCharm - you can config to run compile_mods.sh before each run

Run

morpho_diffusion

• Shows how morphological Ca2+ diffusion with RxD and PMCA, NXC pumps works
• Shows diffusion on neuron model in real time
• pumps in this example are naively "floating", meaning - they are not attached to the membrane

python morpho_diffusion_run.py

• Example of Ca2+ diffusion from the spine head to the dendrite

membrane_flux_example

• Shows how membrane pumps works when they are "attached" to the membrane wit RxD

python membrane_flux_example.py

ebner_cell

• Shows how Ebner2019 cell works

python ebner_cell_run.py

ebner_ach_da

• Shows how Ebner2019 cell works with additional ACh and DA

python ebner_ach_da_run.py

circle_cells_run

• Shows how set position of each neurons

python circle_cells_run.py