Model of the cerebellar granular network (Sudhakar et al 2017)

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Accession:232023
"The granular layer, which mainly consists of granule and Golgi cells, is the first stage of the cerebellar cortex and processes spatiotemporal information transmitted by mossy fiber inputs with a wide variety of firing patterns. To study its dynamics at multiple time scales in response to inputs approximating real spatiotemporal patterns, we constructed a large-scale 3D network model of the granular layer. ..."
Reference:
1 . Sudhakar SK, Hong S, Raikov I, Publio R, Lang C, Close T, Guo D, Negrello M, De Schutter E (2017) Spatiotemporal network coding of physiological mossy fiber inputs by the cerebellar granular layer. PLoS Comput Biol 13:e1005754 [PubMed]
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Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network;
Brain Region(s)/Organism: Cerebellum;
Cell Type(s): Cerebellum golgi cell;
Channel(s): I A; I Calcium; I K; I K,Ca; I Na,t; I h; I Na,p; I T low threshold;
Gap Junctions: Gap junctions;
Receptor(s): AMPA; NMDA; Gaba;
Gene(s):
Transmitter(s): Glutamate; Gaba;
Simulation Environment: NEURON;
Model Concept(s): Spatio-temporal Activity Patterns; Oscillations; Synchronization; Winner-take-all;
Implementer(s): Hong, Sungho [shhong at oist.jp]; Guo, Daqing [dqguo at uestc.edu.cn]; Raikov, Ivan [ivan.g.raikov at gmail.com]; Publio, Rodrigo [publio at oist.jp]; De Schutter, Erik [erik at oist.jp];
Search NeuronDB for information about:  AMPA; NMDA; Gaba; I Na,p; I Na,t; I T low threshold; I A; I K; I h; I K,Ca; I Calcium; Gaba; Glutamate;
#!/bin/sh
#
# Example script to compile and deploy brep
#
# Written by Ivan Raikov and Sungho Hong
# Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Japan
# Supervisor: Erik De Schutter
#
# Correspondence: Ivan Raikov (iraikov@stanford.edu)
#
# September 16, 2017

DEPLOYDIR=... # Where to install brep
CHICKENHOME=... # Where your chicken-scheme is installed
MPIHOME=... # Here specify your mpi home

mkdir -p $DEPLOYDIR

## Get bvspis.sh
curl -L -O http://www.netlib.org/toms/770.gz
gunzip 770.gz
mkdir bvspis && awk 'NR>4' 770 > bvspis/bvspis.sh && chmod u+x bvspis/bvspis.sh
rm 770
pushd bvspis && ./bvspis.sh && popd

## Install packages first
MPI_DIR=$MPIHOME $CHICKENHOME/bin/chicken-install mpi
$CHICKENHOME/bin/chicken-install matchable datatype typeclass cis kd-tree \
random-mtzig  getopt-long srfi-4-utils srfi-63 records bind srfi-42 \
srfi-4-comprehensions mathh lalr parametric-curve
BVSPIS_PATH=$PWD/bvspis $CHICKENHOME/bin/chicken-install bvsp-spline

## Install and deploy everything
MPI_DIR=$MPIHOME $CHICKENHOME/bin/chicken-install -deploy -prefix $DEPLOYDIR mpi
BVSPIS_PATH=$PWD/bvspis $CHICKENHOME/bin/chicken-install -deploy -prefix $DEPLOYDIR bvsp-spline
$CHICKENHOME/bin/chicken-install -deploy -prefix $DEPLOYDIR matchable datatype typeclass cis kd-tree \
random-mtzig  getopt-long srfi-4-utils srfi-63 records bind srfi-42 \
srfi-4-comprehensions mathh lalr parametric-curve

$CHICKENHOME/bin/csc -deploy -O3 -d0 -o $DEPLOYDIR brep.scm