Cerebellar granular layer (Maex and De Schutter 1998)

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Accession:227363
Circuit model of the granular layer representing a one-dimensional array of single-compartmental granule cells (grcs) and Golgi cells (Gocs). This paper examines the effects of feedback inhibition (grc -> Goc -> grc) versus feedforward inhibition (mossy fibre -> Goc -> grc) on synchronization and oscillatory behaviour.
Reference:
1 . Maex R, De Schutter E (1998) Synchronization of golgi and granule cell firing in a detailed network model of the cerebellar granule cell layer. J Neurophysiol 80:2521-37 [PubMed]
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 interneuron granule GLU cell; Cerebellum golgi cell;
Channel(s): I Na,t; I A; I h; I K,Ca; I L high threshold; I_KD;
Gap Junctions:
Receptor(s): AMPA; GabaA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: GENESIS;
Model Concept(s): Synchronization; Oscillations;
Implementer(s): Maex, Reinoud [reinoud at bbf.uia.ac.be];
Search NeuronDB for information about:  Cerebellum interneuron granule GLU cell; GabaA; AMPA; NMDA; I Na,t; I L high threshold; I A; I h; I K,Ca; I_KD; Gaba; Glutamate;
This directory contains the scripts used for building a
one-dimensional array of mossy fibers (MFs), granule cells (grcs) and
Golgi cells (Gocs). The Goc and grc responses are computed with random
MF input. The single-neuron models of the grcs and Gocs are
implemented in the ../Granule_cell and ../Golgi_cell directories.

The main script is Gran_layer_hines.g and can be run by the command
>genesis Gran_layer_hines.


Output can be produced on disk, through asc_file and spikehistory
objects, or on the screen, through xgraph and xview objects. The
former, especially the output produced with spikehistory objects, is
intended to be used when large networks are simulated, while the
latter, especially the graph output, can be used for the visual
inspection and fine-tuning of small networks (e.g. a network of 6 MFs,
2 Gocs and 15 grcs).  You can select the desidered output stream by
uncommenting the corresponding include statement in the main
script.

All parameters of the network (numbers of neurons, connection
probabilities, synaptic strengths and delays, randomization intervals,
MF input) are described in Gran_layer_const.g. Only the name of the
file written by a spikehistory element must be specified in
Gran_layer_spike_history_hines.g (Gran_layer_spike_history_exp.g).

Here is an overview of the scripts :

// network construction

Granule_cell.g : function make_granule_cell_array makes a prototype
grc in the library, creates with readcell a more realistic grc and
creates with createmap a 1D array of grcs.

Golgi_cell.g : function make_Golgi_cell_array : same but for Gocs.

Mossy_fiber.g : function make_mossy_fiber_array implements MFs as
randomspike elements giving input to spikegen elements; creates a 1D
array of MFs.

Gran_layer_setup.g : connects the Gocs, grcs and MFs through synapses,
as specified in Gran_layer_const.g; positions each grc at the center
of its afferent MFs.

Gran_layer_randomize_hines.g, Gran_layer_randomize_exp.g : randomizes
the reversal potentials of the neurons' leak currents, randomizes the
gmax of the synchan elements and the weights of the afferents.

// network output

Gran_layer_spike_history_hines.g :
creates spikehistory elements for the arrays of MFs, grcs and Gocs.

Gran_layer_ascii_hines.g : creates asc_file
elements for the arrays of MFs, grcs and Gocs.

Gran_layer_view_hines.g : creates xview
elements for the arrays of MFs, grcs and Gocs (not used ordinarily).

Gran_layer_graph_hines.g : creates xgraph
elements for the arrays of MFs, grcs and Gocs.


// main script

Gran_layer_hines.g


(Some scripts refer already to Stellate cells, the Stellate_cell.g
script however is not yet included.)



The spike trains produced as files with extension .history 
can be visualized as rasterplots with the xplot-program 
written by M. Wilson, which is now part of the Genesis2.2.1 release. 

You can download genesis2.2.1
from http://www.genesis-sim.org/GENESIS or via http://www.neuroinf.org.
The xplot program can then be found in directory 
src/Release2-2.1-Linux/contrib/xplot
and can be compiled by just typing 'make'. 

The command 
xplot <history file name>   
gives a line diagram; change it to a raster diagram by typing
/scatter
in the window.

Probably you wish to have time on the horizontal axis, which can be done
with a shell script that changes the order of the columns. E.g.
make a file rasterplot containing

cut -c12- $1 > temp1
cut -c-6 $1 > temp2
paste temp1 temp2 | xplot  &
sleep 5
rm temp1
rm temp2

The command 
rasterplot <history file name> 
then plots time on the x-axis (you still need to type /scatter).

For more questions, e-mail us at reinoud.maex@uantwerpen.be.


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