Subiculum network model with dynamic chloride/potassium homeostasis (Buchin et al 2016)

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Accession:206365
This is the code implementing the single neuron and spiking neural network dynamics. The network has the dynamic ion concentrations of extracellular potassium and intracellular chloride. The code contains multiple parameter variations to study various mechanisms of the neural excitability in the context of chloride homeostasis.
Reference:
1 . Buchin A, Chizhov A, Huberfeld G, Miles R, Gutkin BS (2016) Reduced Efficacy of the KCC2 Cotransporter Promotes Epileptic Oscillations in a Subiculum Network Model. J Neurosci 36:11619-11633 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Synapse; Extracellular; Dendrite; Realistic Network; Glia;
Brain Region(s)/Organism: Hippocampus;
Cell Type(s): Hippocampus CA1 pyramidal GLU cell; Hodgkin-Huxley neuron; Hippocampus CA1 PV+ fast-firing interneuron;
Channel(s): KCC2; I Sodium; I Potassium; Na/K pump; I Calcium; I Chloride; I Cl, leak; I M; I Na, leak; I K,leak; I_HCO3; I Na,p;
Gap Junctions:
Receptor(s): NMDA; AMPA; GabaA;
Gene(s):
Transmitter(s): Ions; Gaba; Glutamate;
Simulation Environment: MATLAB; XPPAUT;
Model Concept(s): Bursting; Epilepsy; Chloride regulation; Activity Patterns; Oscillations; Homeostasis; Potassium buffering; Brain Rhythms; Extracellular Fields;
Implementer(s): Buchin, Anatoly [anat.buchin at gmail.com];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal GLU cell; GabaA; AMPA; NMDA; I Chloride; I Na,p; I K,leak; I M; I Sodium; I Calcium; I Potassium; Na/K pump; I Cl, leak; I Na, leak; KCC2; I_HCO3; Gaba; Glutamate; Ions;
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BuchinEtAl2016KCC2
.git
hooks
applypatch-msg.sample *
commit-msg.sample *
post-update.sample *
pre-applypatch.sample *
pre-commit.sample *
prepare-commit-msg.sample *
pre-push.sample *
pre-rebase.sample *
update.sample *
                            
#!/bin/sh
#
# An example hook script to prepare the commit log message.
# Called by "git commit" with the name of the file that has the
# commit message, followed by the description of the commit
# message's source.  The hook's purpose is to edit the commit
# message file.  If the hook fails with a non-zero status,
# the commit is aborted.
#
# To enable this hook, rename this file to "prepare-commit-msg".

# This hook includes three examples.  The first comments out the
# "Conflicts:" part of a merge commit.
#
# The second includes the output of "git diff --name-status -r"
# into the message, just before the "git status" output.  It is
# commented because it doesn't cope with --amend or with squashed
# commits.
#
# The third example adds a Signed-off-by line to the message, that can
# still be edited.  This is rarely a good idea.

case "$2,$3" in
  merge,)
    /usr/bin/perl -i.bak -ne 's/^/# /, s/^# #/#/ if /^Conflicts/ .. /#/; print' "$1" ;;

# ,|template,)
#   /usr/bin/perl -i.bak -pe '
#      print "\n" . `git diff --cached --name-status -r`
#	 if /^#/ && $first++ == 0' "$1" ;;

  *) ;;
esac

# SOB=$(git var GIT_AUTHOR_IDENT | sed -n 's/^\(.*>\).*$/Signed-off-by: \1/p')
# grep -qs "^$SOB" "$1" || echo "$SOB" >> "$1"