LCNhm_configurationfile

The only script thought to be modified. It contains all the simulation parameters:

  • DIR_LOCATION Directory location where all the model is (eg.: /home/acnavasolive/Projects/LCNhippomodel)
  • OPT_FOLDER_NAME Optional name for the folder in which results are going to be saved (eg.: testing_decreasing_CA3)
  • SIMPROP_X Simulation properties, such the SIMPROP_START_TIME or the SIMPROP_TEMPERATURE.
  • CELLPROP_X Artificial cell properties, such CELLPROP_MORPHOLOGY or CELLPROP_SYNAPTIC_INPUTS`
  • CURRENT_X Current clamp properties, such the CURRENT_DURATION or CURRENT_AMPLITUDE.
  • RECORDING_X Physical magnitudes to be measured and recorded, such RECORDING_MAGNITUDE or RECORDING_LOCATION.

The script in the in format:

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DIR_LOCATION = '/home/Projects/LCNhippomodel'
OPT_FOLDER_NAME = 'test'
SIMPROP_THETA_MODE = True
SIMPROP_THETA_PERIOD = 166.
# ...
CELLPROP_INTRINSIC = 0
CELLPROP_INTRINSIC_IONCHS = ['iNas','iA','iAHPs','iC','iCaL','iCaT','iKDR','iM','iHCN','iL']
# ...

so in order to change the parameters it’s just writing over the default values.

It’s convenient to read the specifications in the documentation, because error may arise if the format is not the adequate. For instance, if you want to read more about the possible magnitudes that can be recorded, you can to go Search Page, and type “RECORDING_MAGNITUDE”.

Parameters and descriptions

LCNhm_configurationfile.CELLPROP_INTRINSIC = 2

Int –

Number of the intrinsic-genetic algorithm individual

Choose between 0, 1, 2, …, 12

Individuals are defined as factors multiplying the following maximum conductances and axial resistance:

gNas, gA, gAHPs, gC, gKDR, gM, gCaL, gCaT, gHCN, gL (all in S/cm2), and Ra (Ohm*cm)

Note

Not all combinations of intrinsic and synaptic individuals are validated Please use one the following combinations:

  • CELLPROP_INTRINSIC = 1: CELLPROP_SYNAPTIC from {1}
  • CELLPROP_INTRINSIC = 2: CELLPROP_SYNAPTIC from {1, 3}
  • CELLPROP_INTRINSIC = 3: CELLPROP_SYNAPTIC from {0, 1}
  • CELLPROP_INTRINSIC = 4: CELLPROP_SYNAPTIC from {1, 3}
  • CELLPROP_INTRINSIC = 5: CELLPROP_SYNAPTIC from {3}
  • CELLPROP_INTRINSIC = 6: CELLPROP_SYNAPTIC from {0}
  • CELLPROP_INTRINSIC = 7: CELLPROP_SYNAPTIC from {0, 3}
  • CELLPROP_INTRINSIC = 8: CELLPROP_SYNAPTIC from {3}
  • CELLPROP_INTRINSIC = 9: CELLPROP_SYNAPTIC from {0, 1}
  • CELLPROP_INTRINSIC = 10: CELLPROP_SYNAPTIC from {0, 1, 3}
  • CELLPROP_INTRINSIC = 11: CELLPROP_SYNAPTIC from {1}
  • CELLPROP_INTRINSIC = 12: CELLPROP_SYNAPTIC from {0, 1}
LCNhm_configurationfile.CELLPROP_INTRINSIC_EXPERIMENT = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]

List of Floats –

Additional factor multiplying the following maximum conductances and axial resistance

gNas, gA, gAHPs, gC, gKDR, gM, gCaL, gCaT, gHCN, gL (all in S/cm2), and Ra (Ohm*cm)

Default, all factors equal 1. To experiment increasing/decreasing intrinsic properties, change the appropiate element of the list

Eg.: Decrease Nas conductance to zero

>>> CELLPROP_INTRINSIC_EXPERIMENT = [ 0., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1. ]

Eg.: Increase axial resistance and HCN conductance x2

>>> CELLPROP_INTRINSIC_EXPERIMENT = [ 1., 1., 1., 1., 1., 1., 1., 1., 2., 1., 2. ]
LCNhm_configurationfile.CELLPROP_INTRINSIC_IONCHS = ['iNas', 'iA', 'iAHPs', 'iC', 'iCaL', 'iCaT', 'iKDR', 'iM', 'iHCN', 'iL']

List of Strings – Ion channels to include in the cell.

Default (All) - iA, iAHPs, iC, iCaL, iCaT, iHCN, iKDR, iL, iM, iNas

  • iA - A-type K+ clannels (Cutsuridis2015)
  • iAHPs - CA2+ dependent slow AHP K+ conductance (Cutsuridis2015)
  • iC - Short-duration [Ca]- and voltage-dependent current (Cutsuridis2015)
  • iCaL - L-type calcium channel with low threshold for activation (Muellner2015)
  • iCaT - Somatic L-type calcium channel with low threshold for activation (Muellner2015)
  • iHCN - Hyperpolarization-activated cyclic nucleotide-gated channels (Sinha2015)
  • iKDR - Delay rectifier current (Cutsuridis2015)
  • iL - Leak channels (default)
  • iM - Slowly activating voltage-dependent potassium current (Migliore2006)
  • iNas - Slow sodium channels (Jaslove1992)
LCNhm_configurationfile.CELLPROP_MORPHOLOGY = 'n128'

String – Morphology name, choose between n128, sup1 or n409

LCNhm_configurationfile.CELLPROP_SYNAPTIC = 0

String –

Number of the synaptic-genetic algorithm individual

Choose between 0, 1, 2, 3

Note

Not all combinations of synaptic and intrinsic individuals are validated Please use one the following combinations:

  • CELLPROP_SYNAPTIC = 0: CELLPROP_INTRINSIC from {3, 6, 7, 9, 10, 12}
  • CELLPROP_SYNAPTIC = 1: CELLPROP_INTRINSIC from {1, 2, 3, 4, 9, 10, 11, 12}
  • CELLPROP_SYNAPTIC = 3: CELLPROP_INTRINSIC from {2, 4, 5, 7, 8, 10}
LCNhm_configurationfile.CELLPROP_SYNAPTIC_EXPERIMENT = [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]

List of Floats –

Additional factor multiplying the following maximum conductances

gCA3, gCA2, gEC3, gEC2, gAxo, gBis, gCCK, gIvy, gNGF, gOLM, gPV, gSCA (uS)

Default, all factors equal 1. To experiment increasing/decreasing synaptic properties, change the appropiate element of the list.

Eg.: Superficial pyramidal

>>> CELLPROP_SYNAPTIC_EXPERIMENT = [ 1., 1., 1., 1., 1., 1., 1., 1., 1., 0.3, 1. ]

Eg.: Deep pyramidal

>>> CELLPROP_SYNAPTIC_EXPERIMENT = [ 1., 1., 1., 1., 1., 1., 0.3, 1., 1., 1., 1. ]

Eg.: Just excitation

>>> CELLPROP_SYNAPTIC_EXPERIMENT = [ 1., 1., 1., 1., 0., 0., 0., 0., 0., 0., 0. ]
LCNhm_configurationfile.CELLPROP_SYNAPTIC_INPUTS = ['CA3', 'CA2', 'EC3', 'EC2', 'Axo', 'Bis', 'CCK', 'Ivy', 'NGF', 'OLM', 'PV', 'SCA']

List of Strings – Synaptic inputs to include in the cell (Bezaire2016)

Default (All) - CA3, CA2, EC3, EC2, Axo, Bis, CCK, Ivy, NGF, OLM, PV, SCA

LCNhm_configurationfile.CURRENT_AMPLITUDES = [0.0]

List of Floats –

Amplitudes of each current pulse in nanoampers (nA)

Eg.: Three pulses of 0.1, 0.2 and 0.3 nA

>>> CURRENT_AMPLITUDES = [0.1, 0.2, 0.3]

Eg.: No pulse

>>> CURRENT_AMPLITUDES = [0.]

Length of CURRENT_AMPLITUDES must be the same to CURRENT_DELAY, CURRENT_DURATION, CURRENT_SECTION and CURRENT_LOCATION

LCNhm_configurationfile.CURRENT_DELAY = [0.0]

List of Floats –

Delays of each current pulse in milliseconds

Eg.: Three pulses starting after 500ms of the simulation start, separated 100ms

>>> CURRENT_DELAY = [500., 600., 700.]

Eg.: No pulse

>>> CURRENT_DELAY = [0.]

Length of CURRENT_DELAY must be the same to CURRENT_AMPLITUDES, CURRENT_DURATION, CURRENT_SECTION and CURRENT_LOCATION

LCNhm_configurationfile.CURRENT_DURATION = [0.0]

List of Floats –

Durations of each current pulse in milliseconds

Eg.: Three pulses during 50, 100 and 150ms

>>> CURRENT_DURATION = [50., 100., 150.]

Eg.: No pulse

>>> CURRENT_DURATION = [0.]

Length of CURRENT_DURATION must be the same to CURRENT_AMPLITUDES, CURRENT_DELAY, CURRENT_SECTION and CURRENT_LOCATION

LCNhm_configurationfile.CURRENT_LOCATION = [0.0]

List of str – Location along the defined CURRENT_SECTION of each current pulse.

Location is defined between 0 and 1, being 0 the beginning on the Section, and 1 the end.

Eg.: Two pulses of 0.1nA at the beginning and the middle of ApicList0

>>> CURRENT_LOCATION = [0.0, 0.5]
>>> CURRENT_SECTION = [ApicList0, ApicList0]
>>> CURRENT_AMPLITUDES = [0.1, 0.1]
>>> CURRENT_DELAY = [0., 0.]
>>> CURRENT_DURATION = [100, 100]

Eg.: No pulse (anything)

>>> CURRENT_LOCATION = [0.]

Length of CURRENT_LOCATION must be the same to CURRENT_DELAY, CURRENT_DURATION, CURRENT_SECTION and CURRENT_AMPLITUDES

LCNhm_configurationfile.CURRENT_SECTION = ['SomaList0']

List of str – Sections of each current pulse. Choose between –

  • n128
    • Soma: SomaList0, …, SomaList3
    • Axon: AxonList0
    • Basal dendrites: DendList0, …, DendList30
    • Apical dendrites: ApicList0, …, ApicList67
    • Somato-apical dendrites: ApicList0
  • sup1
    • Soma: SomaList0
    • Axon: AxonList0, AxonList1
    • Basal dendrites: DendList0, …, DendList46
    • Apical dendrites: ApicList0, …, ApicList48
    • Somato-apical dendrites: ApicList4
  • n409
    • Soma: SomaList0, SomaList1
    • Axon: AxonList0
    • Basal dendrites: DendList0, …, DendList41
    • Apical dendrites: ApicList0, …, ApicList40
    • Somato-apical dendrites: ApicList0
  • n127
    • Soma: SomaList0, …, SomaList4
    • Axon: AxonList0
    • Basal dendrites: DendList0, …, DendList22
    • Apical dendrites: ApicList0, …, ApicList44
    • Somato-apical dendrites: ApicList0

    Eg.: Three pulses of 0.1nA, in the middle of SomaList0, ApicList20 and DendList10, simultaneouly

    >>> CURRENT_SECTION = [SomaList0, ApicList20, DendList10]
>>> CURRENT_LOCATION = [0.5, 0.5, 0.5]
>>> CURRENT_AMPLITUDES = [0.1, 0.1, 0.1]
>>> CURRENT_DELAY = [0., 0., 0.]
>>> CURRENT_DURATION = [100, 100, 100]

    Eg.: No pulse (anything)

    >>> CURRENT_SECTION = [SomaList0]

Length of CURRENT_SECTION must be the same to CURRENT_DELAY, CURRENT_DURATION, CURRENT_AMPLITUDES and CURRENT_LOCATION

LCNhm_configurationfile.DIR_LOCATION = '/home/andrea/Projects/HippoModel/LCNhippomodel'

String – Precise location of the main directory.

Eg.: /home/acnavasolive/Projects/LCNhippomodel

LCNhm_configurationfile.OPT_FOLDER_NAME = 'test'

OPT_FOLDER_NAME – String Optional folder name: additional description of the simulation.

Defined in LCNhm_configurationfile.OPT_FOLDER_NAME

Eg.: first_test, high_CA3, inhibition_suppression

LCNhm_configurationfile.RECORDING_LOCATION = [0.0, 0.2, 0.6]

List of Floats – Location along the defined RECORDING_SECTION to be measured and recorded

Location is defined between 0 and 1, being 0 the beginning on the Section, and 1 the end.

Eg.: Save only membrane potential at soma and at the beginning, middle and end of somato-apical trunk

>>> RECORDING_MAGNITUDE = ['Vmem']
>>> RECORDING_SECTION = ['SomaList0','ApicList0','ApicList0','ApicList0']
>>> RECORDING_LOCATION = [     0.0,        0.0,        0.5,        1.0  ]

Eg.: Save membrane potential, current and position at some basal dendrites

>>> RECORDING_MAGNITUDE = ['Vmem','Imem','Pos']
>>> RECORDING_SECTION = ['DendList0','DendList3','DendList5','DendList10']
>>> RECORDING_LOCATION = [     0.3,        0.3,        0.3,         0.3  ]

Lengths of RECORDING_SECTION and RECORDING_LOCATION must be the same

LCNhm_configurationfile.RECORDING_MAGNITUDE = ['Vmem', 'Pos']

List of str – Physical magnitudes to be measured and recorded. Options are:

  • Time: Simulation time (ms)

  • Vmem: Membrane potential (mV)

  • Imem: Membrane current (mA/cm2)

  • Pos: Position by three spatial coordinates (us), being z-axis the radial axis

    Eg.: Save only membrane potential at soma and some points at the somato-apical trunk

    >>> RECORDING_MAGNITUDE = ['Vmem']
>>> RECORDING_SITE = ['SomaList0','SomApicList1','SomApicList3','SomApicList5']

    Eg.: Save membrane potential, current and position at soma

    >>> RECORDING_MAGNITUDE = ['Vmem','Imem','Pos']
>>> RECORDING_SITE = ['SomaList0']
LCNhm_configurationfile.RECORDING_SECTION = ['SomaList0', 'ApicList0', 'ApicList0']

List of str – Sites/Sections to be measured and recorded. Options are:

  • n128
    • Soma: SomaList0, …, SomaList3
    • Axon: AxonList0
    • Basal dendrites: DendList0, …, DendList30
    • Apical dendrites: ApicList0, …, ApicList67
    • Somato-apical dendrites: ApicList0
  • sup1
    • Soma: SomaList0
    • Axon: AxonList0, AxonList1
    • Basal dendrites: DendList0, …, DendList46
    • Apical dendrites: ApicList0, …, ApicList48
    • Somato-apical dendrites: ApicList4
  • n409
    • Soma: SomaList0, SomaList1
    • Axon: AxonList0
    • Basal dendrites: DendList0, …, DendList41
    • Apical dendrites: ApicList0, …, ApicList40
    • Somato-apical dendrites: ApicList0
  • n127
    • Soma: SomaList0, …, SomaList4
    • Axon: AxonList0
    • Basal dendrites: DendList0, …, DendList22
    • Apical dendrites: ApicList0, …, ApicList44
    • Somato-apical dendrites: ApicList0

    Eg.: Save only membrane potential at soma and somato-apical trunk

    >>> RECORDING_MAGNITUDE = ['Vmem']
>>> RECORDING_SITE = ['SomaList0','ApicList0']

    Eg.: Save membrane potential, current and position at soma

    >>> RECORDING_MAGNITUDE = ['Vmem','Imem','Pos']
>>> RECORDING_SECTION = ['SomaList0']

Lengths of RECORDING_SECTION and RECORDING_LOCATION must be the same

LCNhm_configurationfile.SIMPROP_DT = 0.025

Float – Time step in milliseconds

Default is 0.025 ms

LCNhm_configurationfile.SIMPROP_END_TIME = 1660.0

Float – Total duration of the simulation in milliseconds (SIMPROP_START_TIME + SIMPROP_SIM_TIME)

LCNhm_configurationfile.SIMPROP_SIM_TIME = 1660.0

Float – Duration of the simulation in milliseconds

LCNhm_configurationfile.SIMPROP_START_TIME = 0

Float – Lapse of time before starting the simulation in milliseconds.

Warning

SIMPROP_SIM_TIME must be greater or equal to 1.5 * SIMPROP_THETA_PERIOD, if SIMPROP_THETA_MODE is True

LCNhm_configurationfile.SIMPROP_TEMPERATURE = 34.0

Float – Temperature of simulation (celsius)

LCNhm_configurationfile.SIMPROP_THETA_MODE = True

Boolean – Statement for setting theta state

LCNhm_configurationfile.SIMPROP_THETA_PERIOD = 166.0

Float – Theta period in milliseconds