Models of visual topographic map alignment in the Superior Colliculus (Tikidji-Hamburyan et al 2016)

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Accession:195658
We develop two novel computational models of visual map alignment in the SC that incorporate distinct activity-dependent components. First, a Correlational Model assumes that V1 inputs achieve alignment with established retinal inputs through simple correlative firing mechanisms. A second Integrational Model assumes that V1 inputs contribute to the firing of SC neurons during alignment. Both models accurately replicate in vivo findings in wild type, transgenic and combination mutant mouse models, suggesting either activity-dependent mechanism is plausible.
Reference:
1 . Tikidji-Hamburyan RA, El-Ghazawi TA, Triplett JW (2016) Novel Models of Visual Topographic Map Alignment in the Superior Colliculus. PLoS Comput Biol 12:e1005315 [PubMed]
Model Information (Click on a link to find other models with that property)
Model Type:
Brain Region(s)/Organism: Superior colliculus;
Cell Type(s):
Channel(s):
Gap Junctions:
Receptor(s):
Gene(s):
Transmitter(s):
Simulation Environment: Cython; Python;
Model Concept(s): Connectivity matrix; Development; Vision;
Implementer(s): Tikidji-Hamburyan, Ruben [ruben.tikidji.hamburyan at gmail.com] ; 
#! /bin/bash

#setup bigger number of step Nstep for better convergence.
#This parameter is 15000 for any simulation in the paper.
#For NSTEP=15000 each simulation takes ~ 1 day
[ -z "$NSTEP" ] && NSTEP=2000

#Setup INICATOR=True if you want see progress report.
[ -z "$INDICATOR" ] && INDICATOR=False




if [[ "$NSTEP" != '0' ]]; then
	[ -d 'local' ] || mkdir local
	python steup.py install --install-lib=local ||{ echo "Cannot compile EnergyChaser module"; exit 1; }
	
	pushd local

	#Random model ID for all runs
	[ -z "$MODELID" ] && MODELID=`python -c 'import time; from numpy import random as rnd; print time.strftime("%Y%m%d%H%M%S") + "-%03d"%rnd.randint(1000)'`
	
	#Correlational Model WT
	python EnergyModel.py /Model=1 /Gca=20.                          /Knocked=False /Apr=450 /ModelID=\"$MODELID"-CM-WT"\"   /Graphs=False /Log=False /RunDB=\"$MODELID"-CM-WT.csv"\"   /Report=False /StopRec=True /Nstep=$NSTEP /Indicator=$INDICATOR &

	#Correlational Model KI/KI
	python EnergyModel.py /Model=1 /Gca=20.     /Sca=1.              /Knocked=True  /Apr=450 /ModelID=\"$MODELID"-CM-KI"\"   /Graphs=False /Log=False /RunDB=\"$MODELID"-CM-KI.csv"\"   /Report=False /StopRec=True /Nstep=$NSTEP /Indicator=$INDICATOR &

	#Correlational Model KI/KI / B2-/-
	python EnergyModel.py /Model=1 /Gca=20./2.3 /Sca=4. /Bca=Bca*2.1 /Knocked=True  /Apr=450 /ModelID=\"$MODELID"-CM-KIB2"\" /Graphs=False /Log=False /RunDB=\"$MODELID"-CM-KIB2.csv"\" /Report=False /StopRec=True /Nstep=$NSTEP /Indicator=$INDICATOR &

	wait

	#Integrational Model WT
	python EnergyModel.py /Model=3 /Vca=15 /Rca=3. /Gca=20.                         /Knocked=False /Apr=450 /ModelID=\"$MODELID"-IM-WT"\"   /Graphs=False /Log=False /RunDB=\"$MODELID"-IM-WT.csv"\"   /Report=False /StopRec=True /Nstep=$NSTEP /Indicator=$INDICATOR &

	#Integrational Model KI/KI
	python EnergyModel.py /Model=3 /Vca=15 /Rca=3. /Gca=20.     /Sca=1.             /Knocked=True  /Apr=450 /ModelID=\"$MODELID"-IM-KI"\"   /Graphs=False /Log=False /RunDB=\"$MODELID"-IM-KI.csv"\"   /Report=False /StopRec=True /Nstep=$NSTEP /Indicator=$INDICATOR &

	#Integrational Model KI/KI / B2-/-
	python EnergyModel.py /Model=3 /Vca=15 /Rca=3. /Gca=20./2.3 /Sca=4. /Bca=Bca*2.1 /Knocked=True  /Apr=450 /ModelID=\"$MODELID"-IM-KIB2"\" /Graphs=False /Log=False /RunDB=\"$MODELID"-IM-KIB2.csv"\" /Report=False /StopRec=True /Nstep=$NSTEP /Indicator=$INDICATOR &

	wait
	cat $MODELID"-CM-WT-rec.db" $MODELID"-CM-KI-rec.db" $MODELID"-CM-KIB2-rec.db" $MODELID"-IM-WT-rec.db" $MODELID"-IM-KI-rec.db" $MODELID"-IM-KIB2-rec.db" >$MODELID"-tot.db" &&\
	gzip -9 $MODELID"-tot.db" &&\
	rm $MODELID"-CM-WT-rec.db" $MODELID"-CM-KI-rec.db" $MODELID"-CM-KIB2-rec.db" $MODELID"-IM-WT-rec.db" $MODELID"-IM-KI-rec.db" $MODELID"-IM-KIB2-rec.db"  &&\
	cat $MODELID"-CM-WT.csv" $MODELID"-CM-KI.csv" $MODELID"-CM-KIB2.csv" $MODELID"-IM-WT.csv" $MODELID"-IM-KI.csv" $MODELID"-IM-KIB2.csv" >$MODELID"-tot.csv" &&\
	rm $MODELID"-CM-WT.csv" $MODELID"-CM-KI.csv" $MODELID"-CM-KIB2.csv" $MODELID"-IM-WT.csv" $MODELID"-IM-KI.csv" $MODELID"-IM-KIB2.csv" &&\
	python ../2D-View.py        $MODELID"-tot.db.gz" /Nraaw=3 /R=4 & python ../1D-DensityView.py $MODELID"-tot.db.gz" /Nraw=3  /Sml=20 &&\
	popd
else
	[ -z "$MODELID" ] && MODELID="20160910104211-402"
	python 2D-View.py        $MODELID"-tot.db.gz"  /Nraaw=3 /R=4 & python 1D-DensityView.py $MODELID"-tot.db.gz"  /Nraw=3  /Sml=20
fi

echo 'done'

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