Prosthetic electrostimulation for information flow repair in a neocortical simulation (Kerr 2012)

Accession:141505
This model is an extension of a model (<a href="http://senselab.med.yale.edu/ModelDB/ShowModel.asp?model=138379">138379</a>) recently published in Frontiers in Computational Neuroscience. This model consists of 4700 event-driven, rule-based neurons, wired according to anatomical data, and driven by both white-noise synaptic inputs and a sensory signal recorded from a rat thalamus. Its purpose is to explore the effects of cortical damage, along with the repair of this damage via a neuroprosthesis.
Reference:
1 . Kerr CC, Neymotin SA, Chadderdon GL, Fietkiewicz CT, Francis JT, Lytton WW (2012) Electrostimulation as a prosthesis for repair of information flow in a computer model of neocortex IEEE Transactions on Neural Systems & Rehabilitation Engineering 20(2):153-60 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex layer 5-6 pyramidal cell; Neocortex layer 2-3 pyramidal cell; Neocortex basket cell; Neocortex fast spiking (FS) interneuron; Neocortex spiny stellate cell;
Channel(s): I Chloride; I Sodium; I Potassium;
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Deep brain stimulation; Information transfer; Brain Rhythms;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu]; Kerr, Cliff [cliffk at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex layer 5-6 pyramidal cell; Neocortex layer 2-3 pyramidal cell; Neocortex basket cell; GabaA; AMPA; NMDA; Gaba; I Chloride; I Sodium; I Potassium; Gaba; Glutamate;
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neuroprosthesis
README
infot.mod
intf6_.mod
intfsw.mod
misc.mod
nstim.mod
staley.mod
stats.mod
vecst.mod
decvec.hoc
default.hoc
drline.hoc
filtutils.hoc
flexinput.hoc
grvec.hoc
infot.hoc
boxes.hoc
init.hoc
intfsw.hoc
col.hoc
labels.hoc
local.hoc
mosinit.hoc
network.hoc
nload.hoc
nqs.hoc
nqsnet.hoc
nrnoc.hoc
params.hoc
batch.hoc
run.hoc
setup.hoc
simctrl.hoc
spkts.hoc
staley.hoc
declist.hoc
stats.hoc
decmat.hoc
stdgui.hoc
syncode.hoc
updown.hoc
decnqs.hoc
xgetargs.hoc
comparecausality.py
runsim
comparerasters.py
bsmart.py
pyhoc.py
ratlfp.dat
misc.h
                            
This code generates the key results figures shown in

Kerr CC, Neymotin SA, Chadderdon GL, Fietkiewicz CT, Francis JT, Lytton
WW (2012). Electrostimulation as a prosthesis for repair of information
flow in a computer model of neocortex. IEEE Transactions on Neural
Systems & Rehabilitation Engineering 20(2):153–60.


This document provides brief installation and usage instructions.

INSTALLATION

Note: the code has been designed to work on Linux machines. It may work
on Macs and will definitely not work on Windows. If this is a problem,
please contact Cliff Kerr (cliffk@neurosim.downstate.edu) for assistance.

Dependencies:
1. NEURON
2. Python
3. Pylab, SciPy, NumPy, and Matplotlib.

Instructions:

1. Unzip all files (which it looks like you've already done).
2. Type "nrnivmodl *.mod" in the directory. This should create a
directory called either i686 or x86_64, depending on your computer's
architecture, and put a file called "special" in that directory.


USAGE

1. Type "runsim". Two graphs should appear, corresponding to the two
types of results figures in the paper.


OPTIONS

* To adjust cortical vs. thalamic damage, simulation time, and model
size, please adjust the hopefully-clearly-labeled parameters in runsim.

20121210 Unused packages were removed from Python scripts.