LCNhm_main

It is the main script, the core module of the LCN-HippoModel project.

Its function is to:

1. Load the parameters from the LCNhm_configurationfile
2. Create the pyramidal cell according to the configuration parameters through the LCNhm_class
3. Run the simulation
4. Save the specified physical magnitudes inside DIR_LOCATION/LCNhm-results/FolderName

The FolderName is define by one of the LCNhm_functions, and looks like:

< D(ate)YearMonthDay _ T(ime)HourMinute _ OPT_FOLDER_NAME >

Eg.: ./ LCNhm-results / D20190730_T1030_First_Test

It will add suffixes if the folder already exists:

Eg.: ./ LCNhm-results / D20190730_T1030_First_Test_001

Eg.: ./ LCNhm-results / D20190730_T1030_First_Test_002

Eg.: ./ LCNhm-results / D20190730_T1030_First_Test_003

Eg.: ./ LCNhm-results / D20190730_T1031_First_Test

Eg.: ./ LCNhm-results / D20190730_T1031_First_Test_001

It will contain:

• TimeSpikes.txt: Time of spikes. If there are no spikes, it will write NaN
• Recordings_Vmem.txt: Recordings of the membrane potential (if specified in the LCNhm_configurationfile)
• Recordings_Imem.txt: Recordings of the membrane current (if specified in the LCNhm_configurationfile)
• Recordings_Pos.txt: Spatial positions (if specified in the LCNhm_configurationfile)

Membrane potentials (Vmem) and membrane currents (Imem) along time of each recording site is saved in different rows. Position is saved in different rows for each recording SIMPROP_TEMPERATURE

Functions and descriptions

LCNhm_main.CurrentFactors = [[0.0], [0.0], [0.0], ['SomaList0'], [0.0]]

List of properties for all desired current pulses, packed to be a one of the LCNhm_class.neuron_class’s inputs

• LCNhm_configurationfile.CURRENT_DURATION : List of durations of each current pulse in milliseconds
• LCNhm_configurationfile.CURRENT_DELAY: List of delays of each current pulse in milliseconds
• LCNhm_configurationfile.CURRENT_AMPLITUDES: List of amplitudes of each current pulse in nanoampers (nA)
• LCNhm_configurationfile.CURRENT_SECTION: List of sections of each current pulse
• LCNhm_configurationfile.CURRENT_LOCATION: List of location along the defined LCNhm_configurationfile.CURRENT_SECTION of each current pulse

Their length must be the same, the number of different current clamps

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LCNhm_main.FolderName = '/home/andrea/Projects/HippoModel/LCNhippomodel/LCNhm-results/D20200219_T1338_test'

String – Full name of folder where results will be saved

LCNhm_main.IntrinsicFactors = [['iNas', 'iA', 'iAHPs', 'iC', 'iCaL', 'iCaT', 'iKDR', 'iM', 'iHCN', 'iL'], [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], 2]

List – List of all intrinsic properties, packed to be a one of the LCNhm_class.neuron_class’s inputs

• LCNhm_configurationfile.CELLPROP_INTRINSIC_IONCHS: Ion channels to include in the cell
• LCNhm_configurationfile.CELLPROP_INTRINSIC_EXPERIMENT: Additional factor multiplying the following maximum conductances and axial resistance
• LCNhm_configurationfile.CELLPROP_INDIVIDUAL: Number of the intrinsic genetic-algorithm individual

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LCNhm_main.Pyramidal = <LCNhm_class.neuron_class object>

Object – Pyramidal from LCNhm_class.neuron_class

LCNhm_main.Recordings = {'Vmem': {'ApicList0_020': Vector[5], 'SomaList0_000': Vector[4], 'ApicList0_060': Vector[6]}, 'Pos': {'ApicList0_020': [15.890000343322754, -45.37799835205078, 172.83999633789062, 0.9200000166893005], 'SomaList0_000': [-0.3199999928474426, -32.43199920654297, -0.550000011920929, 8.430000305175781], 'ApicList0_060': [-76.08000183105469, -15.107999801635742, 464.25, 0.7799999713897705]}, 'Time': Vector[3]}

Dictionary – Ouput from LCNhm_function.recordings() with recordings of the LCNhm_class.neuron_class Pyramidal

LCNhm_main.SynapticFactors = [['CA3', 'CA2', 'EC3', 'EC2', 'Axo', 'Bis', 'CCK', 'Ivy', 'NGF', 'OLM', 'PV', 'SCA'], [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0], True, 166.0, 0, 1660.0, 0.025, 0]

List – List of all synaptic properties, packed to be a one of the LCNhm_class.neuron_class’s inputs * LCNhm_configurationfile.CELLPROP_SYNAPTIC_INPUTS : Synaptic inputs to include in the cell

• LCNhm_configurationfile.CELLPROP_SYNAPTIC_EXPERIMENT : Additional factor multiplying the following maximum conductances
• LCNhm_configurationfile.SIMPROP_THETA_MODE : Set theta (True) or not (False)
• LCNhm_configurationfile.SIMPROP_THETA_PERIOD : Theta period in milliseconds
• LCNhm_configurationfile.SIMPROP_START_TIME : Lapse of time before starting the simulation in milliseconds
• LCNhm_configurationfile.SIMPROP_END_TIME : Total duration of the simulation in milliseconds (LCNhm_configurationfile.SIMPROP_START_TIME + LCNhm_configurationfile.SIMPROP_SIM_TIME)

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