Model of peripheral nerve with ephaptic coupling (Capllonch-Juan & Sepulveda 2020)

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Accession:263988
We built a computational model of a peripheral nerve trunk in which the interstitial space between the fibers and the tissues is modelled using a resistor network, thus enabling distance-dependent ephaptic coupling between myelinated axons and between fascicles as well. We used the model to simulate a) the stimulation of a nerve trunk model with a cuff electrode, and b) the propagation of action potentials along the axons. Results were used to investigate the effect of ephaptic interactions on recruitment and selectivity stemming from artificial (i.e., neural implant) stimulation and on the relative timing between action potentials during propagation.
Reference:
1 . Capllonch-Juan M, Sepulveda F (2020) Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves. PLoS Comput Biol 16:e1007826 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Extracellular; Axon;
Brain Region(s)/Organism:
Cell Type(s): Myelinated neuron;
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: NEURON; Python;
Model Concept(s): Ephaptic coupling; Stimulus selectivity;
Implementer(s):
/
publication_data
dataset_04__eph_stim_vs_dist
fig9b
code
data
models
settings
src
x86_64
AXNODE.mod *
aaa_info_dataset
algebra.py *
analysis.py *
anatomy.py *
biophysics.py *
circlepacker.py *
contourhandler.py *
electrodes.py *
fill_nerve.py *
geometry.py *
get_extstim.py *
read_results.py *
sim_launcher.py *
simcontrol.py *
tessellations.py *
tools.py *
visualisation.py *
vm_vs_t.py
workspace.py *
                            
"""
This is just a module containing handy tools for lists, dictionaries, etc.
"""

import os
import numpy as np

import workspace as ws



def flattenlist(l):
	""" Flatten a list of lists """
	return [item for sublist in l for item in sublist]

def list_to_number(l):
	""" Given a list or a list of lists with ONLY ONE NUMBER INSIDE, 
	retrieve that number.
	If there's more than one number, yield an error and quit """


	# Check if it's a list or a number
	try:
		ll = len(l)
	except TypeError:
		# It's probably a number, so just return it as it is
		return float(l)

	l = np.array(l).flatten()
	if len(l) != 1:
		msg = 'ERROR: tools.list_to_number got a list with more than one number'
		ws.log(msg)
		ws.terminate()

	return float(l[0])

def append_items(d, k, items):
	""" Append a list of items to a list which is a value of a dictionary 
	entry and create the entry if it does not exist yet """
	try:
		d[k].append(items[0])
	except KeyError:
		# Create entry
		d[k] = items[:]
	else:
		d[k] = d[k] + items[1:]
	return d

def arrtonum(x):
	""" Meant only for arrays with one size 1. 
	Return the element as a float """
	try:
		a = x.mean()
	except AttributeError:
		a = x
	return a

def str2bool(s):
	""" Very simple tool to parse the strings 'True' or 'False' into
	their corresponding booleans """
	str2booldict = {
		"True": True, 
		"False": False
	}
	try:
		return str2booldict[s]
	except KeyError:
		return s

def explore_folder(path):
	""" List all the items of a folder and return its sub-folders """
	items = []
	dirs = []
	for item in os.listdir(path):
		items.append(item)
		if os.path.isdir(item):
			dirs.append(item)
	return items, dirs

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