Motor cortex microcircuit simulation based on brain activity mapping (Chadderdon et al. 2014)

 Download zip file   Auto-launch 
Help downloading and running models
Accession:146949
"... We developed a computational model based primarily on a unified set of brain activity mapping studies of mouse M1. The simulation consisted of 775 spiking neurons of 10 cell types with detailed population-to-population connectivity. Static analysis of connectivity with graph-theoretic tools revealed that the corticostriatal population showed strong centrality, suggesting that would provide a network hub. ... By demonstrating the effectiveness of combined static and dynamic analysis, our results show how static brain maps can be related to the results of brain activity mapping."
Reference:
1 . Chadderdon GL, Mohan A, Suter BA, Neymotin SA, Kerr CC, Francis JT, Shepherd GM, Lytton WW (2014) Motor cortex microcircuit simulation based on brain activity mapping. Neural Comput 26:1239-62 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex M1 pyramidal intratelencephalic L2-5 cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Oscillations; Laminar Connectivity;
Implementer(s): Lytton, William [billl at neurosim.downstate.edu]; Neymotin, Sam [samn at neurosim.downstate.edu]; Shepherd, Gordon MG [g-shepherd at northwestern.edu]; Chadderdon, George [gchadder3 at gmail.com]; Kerr, Cliff [cliffk at neurosim.downstate.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex M1 pyramidal intratelencephalic L2-5 cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
/
src
README
infot.mod *
intf6.mod *
intfsw.mod *
matrix.mod
misc.mod *
nstim.mod *
staley.mod *
stats.mod *
vecst.mod *
boxes.hoc *
col.hoc
declist.hoc *
decmat.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
filtutils.hoc *
gcelldata.hoc
gmgs102.nqs
grvec.hoc *
infot.hoc *
init.hoc
intfsw.hoc *
labels.hoc *
load.py
local.hoc *
main.hoc
misc.h *
miscfuncs.py
network.hoc
neuroplot.py *
nload.hoc
nqs.hoc *
nqsnet.hoc
nrnoc.hoc *
params.hoc
run.hoc
samutils.hoc *
saveoutput.hoc
saveweights.hoc
setup.hoc *
simctrl.hoc *
spkts.hoc *
staley.hoc *
stats.hoc *
stdgui.hoc *
syncode.hoc *
updown.hoc *
wdmaps2.nqs
xgetargs.hoc *
                            
This code generates figures related to the model defined in

Chadderdon GL, Suter BA, Neymotin SA, Kerr CC, Shepherd GMG, 
Lytton WW (2012) Interlaminar activity propagation in a spiking 
model of primary motor cortex.  Frontiers in Neural Circuits.

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.

Instructions:

1. Unzip all files.
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

Run the simulation by typing "nrngui main.hoc" in the directory.  This
saves data for the simulation.  To look at a cell spiking raster, type
"ipython -i --pylab auto load.py" in the directory.  After this loads
the data, it will bring up a figure which corresponds to Figure 2C
from the paper.  Ctrl-D or "exit()" can be used to exit ipython from
the prompt.

To change the synchronous stimulation type and amplitude, the 
following lines (14-15 of main.hoc) should be modified before 
"nrngui main.hoc" is executed:

  grpshocktyp=1   // group shock type (0=none,1=L2/3,2=L5A,3=L5B,4=L6)
  grpshockpct=13  // group shock % cells

"ipython -i --pylab auto load.py" after this will bring up the raster
for those changes.

Examples:
* To get Fig. 2B, set up
  grpshocktyp=1  
  grpshockpct=12
* To get Fig. 3C, set up
  grpshocktyp=2  
  grpshockpct=54
* To get Fig. 5C, set up
  grpshocktyp=4  
  grpshockpct=17

20160921 Updates from the Lytton lab to allow the model to run on mac
OS X.

Loading data, please wait...