An electrophysiological model of GABAergic double bouquet cells (Chrysanthidis et al. 2019)

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We present an electrophysiological model of double bouquet cells (DBCs) and integrate them into an established cortical columnar microcircuit model that implements a BCPNN (Bayesian Confidence Propagation Neural Network) learning rule. The proposed architecture effectively solves the problem of duplexed learning of inhibition and excitation by replacing recurrent inhibition between pyramidal cells in functional columns of different stimulus selectivity with a plastic disynaptic pathway. The introduction of DBCs improves the biological plausibility of our model, without affecting the model's spiking activity, basic operation, and learning abilities.
1 . Chrysanthidis N, Fiebig F, Lansner A (2019) Introducing double bouquet cells into a modular cortical associative memory model Journal of Computational Neuroscience
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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:
Cell Type(s): Neocortex U1 interneuron basket PV GABA cell; Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Abstract integrate-and-fire adaptive exponential (AdEx) neuron; Neocortex layer 2-3 interneuron; Neocortex bitufted interneuron;
Gap Junctions:
Simulation Environment: NEST;
Model Concept(s): Learning;
Implementer(s): Chrysanthidis, Nikolaos [nchr at]; Fiebig, Florian [fiebig at]; Lansner, Anders [ala at];
Search NeuronDB for information about:  Neocortex U1 L2/6 pyramidal intratelencephalic GLU cell; Neocortex U1 interneuron basket PV GABA cell;
#Input: Take module-DATE as input

# on the cluster:
# compile with the GNU compiler
#module swap PrgEnv-cray PrgEnv-gnu

#For the correct directory
echo "current dir: $CURR"

#Start time watch
START=$(date +%s)

#Get number of processors on the system
noProcs=$(grep -c 'model name' /proc/cpuinfo) 

#Source directory

#Bootstrap directory, used temoprally. Removed at end of script.

#Build directory

echo "Source dir: $srcDir"
echo $bootstrapDir
echo "Build dir: $buildDir"

#Copy source to bootstrap directory
cp -r $srcDir $bootstrapDir

echo $(pwd)
#Go into bootstrap dir and run bootstrap
cd $bootstrapDir

#Move out
cd ..

#Remove old build
echo "Removing previous build directory" 
rm -r "$CURR/build*"

#Make new build directory, configure and run make, make install and make installcheck
mkdir $buildDir
echo "Entering $buildDir"
cd $buildDir

export NEST_INSTALL_DIR=/home/fiebig/Programs/nest-2.4.2-build
#export NEST_INSTALL_DIR=/home/bernhard/Downloads/nest-2.4.2-build/
#export NEST_INSTALL_DIR=/pdc/vol/nest/2.2.2/
#$bootstrapDir"configure" --with-nest=${NEST_INSTALL_DIR}/bin/nest-config --prefix=${NEST_INSTALL_DIR}/ 2>&1 | tee "$CURR/mymodule-configure.log"
$bootstrapDir"configure" --with-nest=${NEST_INSTALL_DIR}/bin/nest-config --prefix=$CURR/ 2>&1 | tee "$CURR/mymodule-configure.log"
make -j $noProcs 2>&1 | tee "$CURR/mymodule-make.log"
make -j $noProcs install  

#Stop time watch
END=$(date +%s)
DIFF=$(( $END - $START ))

# Move out
cd ..

#ln -s /home/bernhard/workspace/BCPNN-Module/share/nest/sli/pt_module.sli share/nest/sli/pt_module.sli
ln -s $CURR/share/nest/sli/pt_module.sli $NEST_INSTALL_DIR/share/nest/sli/pt_module.sli

#sudo ln -s $buildDir/pt_module /usr/bin/pt_module

#Display script execution time
echo "It took $DIFF seconds"