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A 1000 cell network model for Lateral Amygdala (Kim et al. 2013)
Home Page: https://modeldb.yale.edu/150288
This project forked from modeldbrepository/150288
A 1000 cell network model for Lateral Amygdala (Kim et al. 2013)
Home Page: https://modeldb.yale.edu/150288
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.
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