A 1000 cell network model for Lateral Amygdala (Kim et al. 2013)

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Accession:150288
1000 Cell Lateral Amygdala model for investigation of plasticity and memory storage during Pavlovian Conditioning.
Reference:
1 . Kim D, Pare D, Nair SS (2013) Mechanisms contributing to the induction and storage of Pavlovian fear memories in the lateral amygdala. Learn Mem 20:421-30 [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; Synapse; Dendrite;
Brain Region(s)/Organism: Amygdala;
Cell Type(s): Hippocampus CA1 pyramidal cell; Hippocampus CA3 pyramidal cell; Hodgkin-Huxley neuron;
Channel(s): I Na,t; I L high threshold; I A; I M; I Sodium; I Calcium; I Potassium; I_AHP; Ca pump;
Gap Junctions:
Receptor(s): AMPA; NMDA; Gaba; Dopaminergic Receptor;
Gene(s):
Transmitter(s): Dopamine; Norephinephrine;
Simulation Environment: NEURON;
Model Concept(s): Synaptic Plasticity; Short-term Synaptic Plasticity; Long-term Synaptic Plasticity; Learning; Neuromodulation;
Implementer(s): Kim, Dongbeom [dk258 at mail.missouri.edu];
Search NeuronDB for information about:  Hippocampus CA1 pyramidal cell; Hippocampus CA3 pyramidal cell; AMPA; NMDA; Gaba; Dopaminergic Receptor; I Na,t; I L high threshold; I A; I M; I Sodium; I Calcium; I Potassium; I_AHP; Ca pump; Dopamine; Norephinephrine;
/
KimEtAl2013
README.txt
bg2inter.mod
bg2pyr.mod
ca.mod *
cadyn.mod
cal2.mod *
capool.mod *
function_TMonitor.mod *
h.mod *
im.mod
interD2pyrD_STFD.mod
interD2pyrDDA_STFD.mod
interD2pyrDDANE_STFD.mod
interD2pyrDNE_STFD.mod
interD2pyrV_STFD.mod
interD2pyrVDA_STFD.mod
interV2pyrD_STFD.mod
interV2pyrDDA_STFD.mod
interV2pyrDDANE_STFD.mod
interV2pyrDNE_STFD.mod
interV2pyrV_STFD.mod
interV2pyrVDA_STFD.mod
kadist.mod *
kaprox.mod
kdrca1.mod
kdrca1DA.mod
kdrinter.mod *
leak.mod *
leakDA.mod *
leakinter.mod *
na3.mod
na3DA.mod
nainter.mod *
pyrD2interD_STFD.mod
pyrD2interV_STFD.mod
pyrD2pyrD_STFD.mod
pyrD2pyrDDA_STFD.mod
pyrD2pyrV_STFD.mod
pyrD2pyrVDA_STFD.mod
pyrV2interD_STFD.mod
pyrV2interV_STFD.mod
pyrV2pyrD_STFD.mod
pyrV2pyrDDA_STFD.mod
pyrV2pyrV_STFD.mod
pyrV2pyrVDA_STFD.mod
sahp.mod
sahpNE.mod
shock2interD.mod
shock2interV.mod
shock2pyrD.mod
shock2pyrV.mod
tone2interD.mod
tone2interDNE.mod
tone2interV.mod
tone2interVNE.mod
tone2pyrD.mod
tone2pyrD_LAdv.mod
tone2pyrDNE.mod
tone2pyrDNE_LAdv.mod
tone2pyrV.mod
tone2pyrV_LAdd.mod
tone2pyrVNE.mod
tone2pyrVNE_LAdd.mod
BgGen.hoc
Cell_list.txt
Cell_type.txt
function_ConnectInternal.hoc
function_ConnectTwoCells.hoc
function_NetStimOR.hoc
function_TimeMonitor.hoc
function_ToneGen.hoc
function_ToneSignalGen_Ctx.hoc
function_ToneSignalGen_Th.hoc
interneuron_template.hoc
LA_model_main_file.hoc
LAcells_template.hoc
NM.txt
shock2Idd.txt
shock2Idv.txt
shock2LAdd.txt
shock2LAdv.txt
shockcondi.hoc
Syn_Matrix.txt
tone2Idd.txt
tone2Idd2.txt
tone2Idv.txt
tone2Idv2.txt
tone2LAdd.txt
tone2LAdd2.txt
tone2LAdv.txt
tone2LAdv2.txt
                            
This is the readme for the model associated with the paper:

Kim D, Pare D, Nair SS (2013) Mechanisms contributing to the induction
and storage of pavlovian fear memories in the lateral amygdala,
Learning & Memory

This is the code that the authors used. It is written in NEURON which
is freely available at http://www.neuron.yale.edu

DATA INPUT FILES

1) Cell_list.txt: List of cells whose weight changes and Ca+
concentration will be saved.
2) Cell_type.txt: This file indicates the type of cell for the
principal cells. The types are defined in the main file. We have this
predetermined to maintain the proper distributions of cell-types (Type
A, TypeB etc).
3) NM.txt: This file indicates whether the cell has any neuromodulator
receptors present. It can be of three types, DA, NE and DANE.
4) tone2LAdd.txt: List of randomly chosen principal cell numbers in
LAdd for thalamic tone input.
5) tone2LAdd2.txt: List of randomly chosen principal cell numbers in
LAdd for cortical tone input.
6) tone2LAdv.txt: List of randomly chosen principal cell numbers in
LAdv for cortical tone input.
7) tone2LAdv2.txt: List of randomly chosen principal cell numbers in
LAdv for thalamic tone input.
8) shock2LAdd.txt: List of randomly chosen principal cell numbers in
LAdd for shock input.
9) shock2LAdv.txt: List of randomly chosen principal cell numbers in
LAdv for shock input.
10) tone2Idd.txt, tone2Idd2.txt, tone2Idv.txt, tone2Idv2.txt, etc.:
Same as above, but for interneurons
11) Syn_Matrix.txt: Synapse matrix for connections.
________________________________________

NEURON FILES

1. BgGen.hoc : File for generating background inputs.
2. function_ConnectInternal.hoc: Loads internal connectivity from
Syn_Matrix.txt and makes appropriate connections.
3. function_ConnectTwoCells.hoc: Connects two cells.
4. function_NetStimOR.hoc: Netstim template for tone and shock inputs.
5. function_TimeMonitor: indicates how much of the simulation has
completed
6. function_ToneGen.hoc: tone protocol
7. function_ToneSignalGen_Th.hoc: protocol for thalamic tone to LA
8. function_ToneSignalGen_Ctx.hoc: protocol for cortical tone to LA
9. interneuron_template.hoc: Template file for interneuron
10. LA_model_main_file: The main model file
11. LAcell_template.hoc: Template file for different LA principal cell
types.
12. shockcondi.hoc: File for generating shock protocol

NOTE: These .hoc files call several .mod files (current channels,
synapses and other functions) that are provided in the folder.

___________________________________________


OUTPUT FILES:

1) data: saves spiking time history of all cells
2) Matrix_NEW: saves internal connections with cell ids and synapse
ids for checking.
3) XXX_ca: Calcium conc. of particular synapse (with pre- and post-
cell IDs in XXX)
4) XXX_wt: weight change of particular synapse (with pre- and post-
cell IDs in XXX)

___________________________

BEFORE YOU RUN:

In the file (LA_model_main_file.hoc) set the path to save the data as
/home/yourdirectory/output for saving data correctly.

Also make sure to make an empty folder named 'output' in the directory
that has all the files. NEURON will save the output files into this
directory.