Ca+/HCN channel-dependent persistent activity in multiscale model of neocortex (Neymotin et al 2016)

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Accession:185858
"Neuronal persistent activity has been primarily assessed in terms of electrical mechanisms, without attention to the complex array of molecular events that also control cell excitability. We developed a multiscale neocortical model proceeding from the molecular to the network level to assess the contributions of calcium regulation of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels in providing additional and complementary support of continuing activation in the network. ..."
Reference:
1 . Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW (2016) Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex Neuroscience 316:344-366 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell; Synapse; Channel/Receptor; Molecular Network;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; Neocortex fast spiking (FS) interneuron; Neocortex spiking regular (RS) neuron; Neocortex spiking low threshold (LTS) neuron; Neocortex layer 2-3 interneuron; Neocortex layer 5 interneuron; Neocortex layer 6a interneuron;
Channel(s): I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I CAN; I Calcium; I_AHP; I_KD; Ca pump;
Gap Junctions:
Receptor(s): mGluR1; GabaA; GabaB; AMPA; NMDA; mGluR; Glutamate; Gaba; IP3;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON;
Model Concept(s): Activity Patterns; Ion Channel Kinetics; Oscillations; Spatio-temporal Activity Patterns; Signaling pathways; Working memory; Attractor Neural Network; Calcium dynamics; Laminar Connectivity; G-protein coupled; Rebound firing; Brain Rhythms; Dendritic Bistability; Reaction-diffusion; Beta oscillations; Persistent activity; Multiscale;
Implementer(s): Neymotin, Sam [samn at neurosim.downstate.edu]; McDougal, Robert [robert.mcdougal at yale.edu];
Search NeuronDB for information about:  Neocortex V1 pyramidal corticothalamic L6 cell; Neocortex V1 pyramidal intratelencephalic L2-5 cell; Neocortex V1 interneuron basket PV cell; mGluR1; GabaA; GabaB; AMPA; NMDA; mGluR; Glutamate; Gaba; IP3; I Na,t; I L high threshold; I T low threshold; I A; I K; I M; I h; I K,Ca; I CAN; I Calcium; I_AHP; I_KD; Ca pump; Gaba; Glutamate;
  
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CaHDemo
readme.txt
cagk.mod
cal.mod *
calts.mod *
can.mod *
cat.mod *
gabab.mod
IC.mod *
icalts.mod *
Ih.mod
ihlts.mod *
IKM.mod *
kap.mod
kcalts.mod *
kdmc.mod
kdr.mod
kdrbwb.mod
km.mod *
mglur.mod *
misc.mod *
MyExp2SynBB.mod *
MyExp2SynNMDABB.mod
nafbwb.mod
nax.mod
stats.mod *
vecst.mod *
aux_fun.inc *
conf.py
declist.hoc *
decnqs.hoc *
decvec.hoc *
default.hoc *
drline.hoc *
geom.py
ghk.inc *
grvec.hoc *
init.hoc
labels.hoc
labels.py *
local.hoc *
misc.h *
mpisim.py
netcfg.cfg
nqs.hoc
nqs.py
nrnoc.hoc *
onepyr.cfg
onepyr.py
pyinit.py *
python.hoc *
pywrap.hoc *
simctrl.hoc *
simdat.py
syncode.hoc *
xgetargs.hoc *
                            
These simulations were used in the following article:
  Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW.
  Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex.
  Neuroscience 2016 (in press).
  http://www.sciencedirect.com/science/article/pii/S0306452215011367

The code in this folder generates Fig. 4 (isolated pyramidal neuron persistent activity) and 
Fig. 5 (network persistent activity).

The simulations were tested/developed on LINUX systems, but may run on Microsoft Windows or Mac OS.

To run the demo, you will need the NEURON simulator (version 7.4 and up; available at http://www.neuron.yale.edu)
compiled with python and MPI enabled. You will need Matplotlib to draw the output ( http://matplotlib.org/ ).

Instructions to setup the model:
  unzip the file
  cd CaHDemo
  nrnivmodl 

The nrnivmodl command will produce an architecture-dependent folder with a script called special.
On 64 bit systems the folder is x86_64.

-----------------------------------------------------------------------------------------------------
Simulation of isolated pyramidal cell persistent activity (Figure 4).
Run the following code in a terminal from within the directory containing the model files: 
python -i onepyr.py onepyr.cfg
This simulation takes ~35 seconds on Linux with Intel(R) Core(TM) i7-4940MX CPU @ 3.10GHz
-----------------------------------------------------------------------------------------------------
Run network simulation from a terminal with:
mpiexec -np 8 nrniv -python -mpi mpisim.py netcfg.cfg

The network simulation uses MPI for parallelization. The simulation can take a long time to run,
depending on your hardware setup. This simulation saves output data to the data subdirectory. 
simdat.py loads the data and draws the output.

To plot the output from this simulation, run the following:
python -i simdat.py

Note: The -np 8 above specifies that mpiexec should use 8 cores. This number should change depending
on your hardware setup. If changing 8 to 24 cores (-np 24), make sure to update the defnCPU
parameter on line 38 of simdat.py; this is because mpisim.py saves 1 output file per core.
The simulation takes ~28 minutes on Linux with 8 cores (Intel(R) Core(TM) i7-4940MX CPU @ 3.10GHz)
and runs in ~11 minutes on Linux with 24  cores (Intel(R) Xeon(R) CPU E5-4610 0 @ 2.40GHz).
-----------------------------------------------------------------------------------------------------

For questions/comments email:  
  samn at neurosim dot downstate dot edu
   or
  robert dot mcdougal at yale dot edu

20160915 This updated version from the Lytton lab allows their models
which contain misc.mod and misc.h to compile on the mac.

Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW (2016) Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex Neuroscience 316:344-366[PubMed]

References and models cited by this paper

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