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.