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

 Download zip file   Auto-launch 
Help downloading and running models
"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. ..."
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]
Citations  Citation Browser
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;
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]; Guo, Daqing [dqguo at]; Raikov, Ivan [ivan.g.raikov at]; Publio, Rodrigo [publio at]; De Schutter, Erik [erik at];
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;
# Script for initializing cell populations in the SLURM system
# Written by Shyam Kumar Sudhakar, Ivan Raikov, Tom Close, Rodrigo Publio, Daqing Guo, and Sungho Hong
# Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Japan
# Supervisor: Erik De Schutter
# Correspondence: Sungho Hong (
# September 16, 2017

## Some parameters for running a SLURM job
#SBATCH --tasks=10
#SBATCH --cpus-per-task=2
#SBATCH --job-name=GL_POP
#SBATCH --mem-per-cpu=20g
#SBATCH --error=population_init.err.log
#SBATCH --output=population_init.out.log


echo "==============Starting population init==============="
cd SHAREDDIR/model

export PATH=... # Set paths for python, etc. here
export PATH=$NEURONHOME/nrn/x86_64/bin:$NEURONHOME/iv/x86_64/bin:$PATH
export LD_LIBRARY_PATH=$NEURONHOME/nrn/x86_64/lib:$NEURONHOME/iv/x86_64/lib:$LD_LIBRARY_PATH


## Initialize cell populations first
mpirun nrniv -mpi -python --initpop

echo "==============Population init has ended==============="