Distal inhibitory control of sensory-evoked excitation (Egger, Schmitt et al. 2015)

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Accession:167499
Model of a cortical layer (L) 2 pyramidal neuron embedded in an anatomically realistic network of two barrel columns in rat vibrissal cortex. This model is used to investigate the effects of spatially and temporally specific inhibition from L1 inhibitory interneurons on the sensory-evoked subthreshold responses of the L2 pyramidal neuron, and can be used to create simulation results underlying Figures 3D, 4B, 4C and 4E from (Egger, Schmitt et al. 2015).
Reference:
1 . Egger R, Schmitt AC, Wallace DJ, Sakmann B, Oberlaender M, Kerr JN (2015) Robustness of sensory-evoked excitation is increased by inhibitory inputs to distal apical tuft dendrites. Proc Natl Acad Sci U S A 112:14072-7 [PubMed]
Citations  Citation Browser
Model Information (Click on a link to find other models with that property)
Model Type: Realistic Network; Neuron or other electrically excitable cell;
Brain Region(s)/Organism: Neocortex;
Cell Type(s): Neocortex L2/3 pyramidal GLU cell;
Channel(s):
Gap Junctions:
Receptor(s): GabaA; AMPA; NMDA;
Gene(s):
Transmitter(s): Gaba; Glutamate;
Simulation Environment: NEURON; Python;
Model Concept(s): Active Dendrites; Synaptic Integration; Sensory processing; Whisking;
Implementer(s): Egger, Robert [robert.egger at nyumc.org];
Search NeuronDB for information about:  Neocortex L2/3 pyramidal GLU cell; GabaA; AMPA; NMDA; Gaba; Glutamate;
#!/bin/bash

modeldir=$(cd $(dirname ${BASH_SOURCE[0]}) && pwd)
source $modeldir"/pythonpath.sh"
cd $modeldir"/Figure4C_2"

cellModelName=$modeldir"/../cell_model/waters_l23_ar_dend.param"

ongoingUp=$modeldir"/Figure4C_2/up_state_parameters_new_boutons.param"
ongoingDown=$modeldir"/Figure4C_2/down_state_parameters_new_boutons.param"
ongoingUpL1inact=$modeldir"/Figure4C_2/up_state_parameters_new_boutons_L1D1_inactivated.param"
ongoingDownL1inact=$modeldir"/Figure4C_2/down_state_parameters_new_boutons_L1D1_inactivated.param"

python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization00/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1526_23551.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1526_23551.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization01/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1526_23554.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1526_23554.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization02/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1526_23558.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1526_23558.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization03/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23562.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23562.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization04/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23566.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23566.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization05/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23570.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23570.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization06/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23574.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23574.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization07/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23578.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23578.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization08/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23582.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23582.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization09/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23586.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23586.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization10/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23590.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23590.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization11/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23594.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23594.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization12/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23598.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23598.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization13/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23602.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23602.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization14/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23606.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23606.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization15/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23610.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23610.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization16/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23614.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23614.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization17/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23618.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23618.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization18/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23622.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23622.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization19/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23626.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23626.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization20/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23630.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23630.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization21/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23634.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23634.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization22/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23638.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23638.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization23/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23642.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23642.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization24/control' $cellModelName $ongoingUp $ongoingDown $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_up_state_functional_map_20130326-1527_23646.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_control_down_state_functional_map_20130326-1527_23646.param'

python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization00/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1526_23551.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1526_23551.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization01/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1526_23554.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1526_23554.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization02/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1526_23558.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1526_23558.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization03/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23562.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23562.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization04/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23566.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23566.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization05/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23570.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23570.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization06/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23574.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23574.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization07/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23578.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23578.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization08/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23582.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23582.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization09/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23586.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23586.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization10/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23590.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23590.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization11/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23594.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23594.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization12/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23598.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23598.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization13/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23602.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23602.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization14/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23606.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23606.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization15/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23610.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23610.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization16/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23614.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23614.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization17/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23618.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23618.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization18/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23622.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23622.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization19/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23626.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23626.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization20/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23630.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23630.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization21/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23634.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23634.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization22/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23638.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23638.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization23/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23642.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23642.param'
python $modeldir'/evoked_activity_ex_no_variability.py' $modeldir'/Figure4C_2/results/realization24/L1inact' $cellModelName $ongoingUpL1inact $ongoingDownL1inact $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_up_state_functional_map_20130326-1527_23646.param' $modeldir'/Figure4C_2/evoked_activity_new_boutons_L1inact_down_state_functional_map_20130326-1527_23646.param'

echo "*********************"
echo "Analysis: PSP SD"
python $modeldir"/analysis/analyze_psp_std.py" $modeldir"/Figure4C_2/results" $modeldir"/Figure4C_2/results/summary_psp_std.csv" 50 1