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setParameters.hoc
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///////////////////////////////////////////////////////////////////////////////
// setParameters.hoc: sets all the user adjustable parameters for the model
///////////////////////////////////////////////////////////////////////////////
//-----------------------------------------------------------------------------
// global parameters
// built in parameters
v_init = -70 // mV
tstop = 40500 // ms FOR PLASTICITY INDUCTION PROTOCOL OF 20s
dt = 0.025 // ms
celsius = 36 // C degrees
// custom parameters from makeIons.hoc
ki0_k_ion = 140 // mM (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
ko0_k_ion = 5 // mM (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
nai0_na_ion = 10 // mM (range 5-15) (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
nao0_na_ion = 145 // mM (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
cli0_cl_ion = 4 // mM (range 4-30) (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
clo0_cl_ion = 110 // mM (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
cai0_ca_ion = 1e-4// mM (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
cao0_ca_ion = 1.5 // mM (as given in "Neuroscience" 2e, Sinauer- ISBN 9780878937424)
hco3i0_hco3_ion = 15 // 24 // mM (as given in Kaila et al. Review 1994, p 510)
hco3o0_hco3_ion = 25 // mM (as given in Kaila et al. Review 1994, p 510)
//-----------------------------------------------------------------------------
// morphological parameters to makeGeometry.hoc
proximal_limit = 100 // um (limit of "proximal" distances in apical dendrites)
middle_limit = 600 // um (limit of "middle" distances in apical dendrites)
//-----------------------------------------------------------------------------
// biophysical parameters from makeGeometry.hoc - proc biophys()
// somatic section
cm_soma = 1 // uF/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
Ra_soma = 34.5 // Ohm*cm (NEURON defaults)
// proximal dendritic section
cm_prox = 1 // uF/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
Ra_prox = 34.5 // Ohm*cm (NEURON defaults)
// middle dendritic section
cm_mid = 1 // uF/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
Ra_mid = 34.5 // Ohm*cm (NEURON defaults)
// distal dendritic section
cm_dist = 1 // uF/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
Ra_dist = 34.5 // Ohm*cm (NEURON defaults)
//-----------------------------------------------------------------------------
// ion parameters from .mod files {kleak, naleak, KCC2} to makeIons.hoc, makeTransporters.hoc
// somatic section
// leak parameters
gl_soma = 0.04 // S/cm^2
el_soma = -70 // mV
// chloride parameters
axD_soma = 2 // um^2/ms (http://www.nature.com/articles/srep23196; Kuner & Augustine Neuron 2000)
// proximal dendritic section
// leak parameters
gl_prox = 0.04 // S/cm^2
el_prox = -70 // mV
// chloride parameters
axD_prox = 2 // um^2/ms
// middle dendritic section
// leak parameters
gl_mid = 0.04 // S/cm^2
el_mid = -70 // mV
// chloride parameters
axD_mid = 2 // um^2/ms
// distal dendritic section
// leak parameters
gl_dist = 0.04 // S/cm^2
el_dist = -70 // mV
// chloride parameters
axD_dist = 2 // um^2/ms
//-----------------------------------------------------------------------------
// active ion channel parameters from .mod files {HH, cat, calL, calH} to makeActiveChannels.hoc
// somatic section
// Hodgkin-Huxley Na & K currents
hh_soma = 1 // Boolean: 0 = no HH in soma, 1 = HH in soma
gnabar_soma = 1.120 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
gkbar_soma = 0.05 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
vtraub_soma = -60 // mV
// Calcium Currents (as given in Poirazi et al., 2003, Neuron)
vgcc_soma = 1 // Boolean: 0 = no VGCC in soma, 1 = VGCC in soma
gcatbar_soma = 3.8e-3 // mho/cm^2
gcalbar_soma = 7.6e-3 // mho/cm^2 Low activation threshold L-type channel
// proximal dendritic section
// Hodgkin-Huxley Na & K currents
hh_prox = 1 // Boolean: 0 = no HH in prox, 1 = HH in prox
gnabar_prox = 1.120 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
gkbar_prox = 0.05 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
vtraub_prox = -60 // mV
// Calcium Currents (as given in Poirazi et al., 2003, Neuron)
vgcc_prox = 1 // Boolean: 0 = no VGCC in prox, 1 = VGCC in prox
gcatbar_prox = 0 // mho/cm^2
gcalbar_prox = 0.0316e-3 // mho/cm^2 Low activation threshold L-type channel
// middle dendritic section
// Hodgkin-Huxley Na & K currents
hh_mid = 1 // Boolean: 0 = no HH in mid, 1 = HH in mid
gnabar_mid = 1.120 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
gkbar_mid = 0.05 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
vtraub_mid = -60 // mV
// Calcium Currents (as given in Poirazi et al., 2003, Neuron)
vgcc_mid = 1 // Boolean: 0 = no VGCC in mid, 1 = VGCC in mid
gcatbar_mid = 0.514e-3 // mho/cm^2
gcalbar_mid = 1.4536e-3 // mho/cm^2 Low activation threshold L-type channel
// distal dendritic section
// Hodgkin-Huxley Na & K currents
hh_dist = 1 // Boolean: 0 = no HH in dist, 1 = HH in dist
gnabar_dist = 1.120 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
gkbar_dist = 0.05 // S/cm^2 (as given in Saraga et al. 2008, J Neurosci.)
vtraub_dist = -60 // mV
// Calcium Currents (as given in Poirazi et al., 2003, Neuron)
vgcc_dist = 1 // Boolean: 0 = no VGCC in dist, 1 = VGCC in dist from cat.mod, calL.mod
gcatbar_dist = 1.029e-3 // mho/cm^2
gcalbar_dist = 1.4536e-3 // mho/cm^2 High activation threshold L-type channel
//-----------------------------------------------------------------------------
// transporter parameters from .mod files {KCC2_Trans} to makeTransporters.hoc
// somatic section
// KCC2 Potassium-Chloride Cotransporter
KCC2_soma = 1 // Boolean: 0 = no KCC2 in soma, 1 = KCC2 in soma
Michaelis_soma = 29.8 // (mM) < 0, 1e9 > : Michaelis constant for KCC2 ion transport
transp_soma = 5.07 // (/s) < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
// proximal dendritic section
// KCC2 Potassium-Chloride Cotransporter
KCC2_prox = 1 // Boolean: 0 = no KCC2 in prox, 1 = KCC2 in prox
Michaelis_prox = 29.8 // (mM) < 0, 1e9 > : Michaelis constant for KCC2 ion transport
transp_prox = 5.07 // (/s) < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
// middle dendritic section
// KCC2 Potassium-Chloride Cotransporter
KCC2_mid = 1 // Boolean: 0 = no KCC2 in mid, 1 = KCC2 in mid
Michaelis_mid = 29.8 // (mM) < 0, 1e9 > : Michaelis constant for KCC2 ion transport
transp_mid = 5.07 // (/s) < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
// distal dendritic section
// KCC2 Potassium-Chloride Cotransporter
KCC2_dist = 1 // Boolean: 0 = no KCC2 in dist, 1 = KCC2 in dist
Michaelis_dist = 29.8 // (mM)< 0, 1e9 > : Michaelis constant for KCC2 ion transport
transp_dist = 5.07 // (/s) < 0, 1e9 > : rate of transport of KCC2-bound ions across the membrane
//-----------------------------------------------------------------------------
// kinase/phosphatase parameters from .mod files {KCC2} to makeTransporters.hoc
// somatic section
alpha_soma = 0.2533 // (/s) < 0, 1e9 > alpha
beta_soma = 1.4776 // (/s) < 0, 1e9 > beta
R_m_soma = 1 // (/s) < 0, 1e9 > R_M
R_mp_soma = 0.0969760285 // (/s) < 0, 1e9 > R_Mp
R_k_soma = 2.37e-3 // (mM) < 0, 1e9 > R_k (From Kohout 2002)
R_p_soma = 7.943e-4 // (mM) < 0, 1e9 > R_p ([***] Need reference)
maxK_soma = 390 // (/s) < 0, 1e9 > V_ak (From Kohout 2002)
maxP_soma = 74 // (/s) < 0, 1e9 > V_ap (hand tuned parameter from plot3dkapa.py)
HillK_soma = 1.5 // (1) < 0, 1e9 > h_k (From Kohout 2002)
HillP_soma = 2.9 // (1) < 0, 1e9 > h_p (From Stemmer & Klee 1994)
inactK_soma = 32.1 // (/s) < 0, 1e9 > v_ik (From Kohout 2002)
inactP_soma = 10 // (/s) < 0, 1e9 > v_ip (hand tuned parameter from plot3dkapa.py)
// proximal dendritic section
alpha_prox = 0.2533 // (/s) < 0, 1e9 > alpha
beta_prox = 1.4776 // (/s) < 0, 1e9 > beta
R_m_prox = 1 // (/s) < 0, 1e9 > R_M
R_mp_prox = 0.0969760285 // (/s) < 0, 1e9 > R_Mp
R_k_prox = 2.37e-3 // (mM) < 0, 1e9 > R_k (From Kohout 2002)
R_p_prox = 7.943e-4 // (mM) < 0, 1e9 > R_p ([***] Need reference)
maxK_prox = 390 // (/s) < 0, 1e9 > V_ak (From Kohout 2002)
maxP_prox = 74 // (/s) < 0, 1e9 > V_ap (hand tuned parameter from plot3dkapa.py)
HillK_prox = 1.5 // (1) < 0, 1e9 > h_k (From Kohout 2002)
HillP_prox = 2.9 // (1) < 0, 1e9 > h_p (From Stemmer & Klee 1994)
inactK_prox = 32.1 // (/s) < 0, 1e9 > v_ik (From Kohout 2002)
inactP_prox = 10 // (/s) < 0, 1e9 > v_ip (hand tuned parameter from plot3dkapa.py)
// middle dendritic section
alpha_mid = 0.2533 // (/s) < 0, 1e9 > alpha
beta_mid = 1.4776 // (/s) < 0, 1e9 > beta
R_m_mid = 1 // (/s) < 0, 1e9 > R_M
R_mp_mid = 0.0969760285 // (/s) < 0, 1e9 > R_Mp
R_k_mid = 2.37e-3 // (mM) < 0, 1e9 > R_k (From Kohout 2002)
R_p_mid = 7.943e-4 // (mM) < 0, 1e9 > R_p ([***] Need reference)
maxK_mid = 390 // (/s) < 0, 1e9 > V_ak (From Kohout 2002)
maxP_mid = 74 // (/s) < 0, 1e9 > V_ap (hand tuned parameter from plot3dkapa.py)
HillK_mid = 1.5 // (1) < 0, 1e9 > h_k (From Kohout 2002)
HillP_mid = 2.9 // (1) < 0, 1e9 > h_p (From Stemmer & Klee 1994)
inactK_mid = 32.1 // (/s) < 0, 1e9 > v_ik (From Kohout 2002)
inactP_mid = 10 // (/s) < 0, 1e9 > v_ip (hand tuned parameter from plot3dkapa.py)
// distal dendritic section
alpha_dist = 0.2533 // (/s) < 0, 1e9 > alpha
beta_dist = 1.4776 // (/s) < 0, 1e9 > beta
R_m_dist = 1 // (/s) < 0, 1e9 > R_M
R_mp_dist = 0.0969760285 // (/s) < 0, 1e9 > R_Mp
R_k_dist = 2.37e-3 // (mM) < 0, 1e9 > R_k (From Kohout 2002)
R_p_dist = 7.943e-4 // (mM) < 0, 1e9 > R_p ([***] Need reference)
maxK_dist = 390 // (/s) < 0, 1e9 > V_ak (From Kohout 2002)
maxP_dist = 74 // (/s) < 0, 1e9 > V_ap (hand tuned parameter from plot3dkapa.py)
HillK_dist = 1.5 // (1) < 0, 1e9 > h_k (From Kohout 2002)
HillP_dist = 2.9 // (1) < 0, 1e9 > h_p (From Stemmer & Klee 1994)
inactK_dist = 32.1 // (/s) < 0, 1e9 > v_ik (From Kohout 2002)
inactP_dist = 10 // (/s) < 0, 1e9 > v_ip (hand tuned parameter from plot3dkapa.py)
//-----------------------------------------------------------------------------
//synaptic parameters from makePairedUnpaired.hoc; "foo_prompt" set in promptWindow.hoc
// paired synapses
location_paired = location_paired_prompt // soma = 0, prox = 1, mid = 2, dist = 3
interval_paired = interval_paired_prompt // ms/spike
number_paired = number_paired_prompt // total number of spikes
start_paired = start_paired_prompt // ms
noise_paired = noise_paired_prompt // Boolean: 0 = noiseless, 1 = Poisson
//GABAa maximal conductance
gmax_paired_soma = 0.00053 // (uS) (as given in http://www.ncbi.nlm.nih.gov/pubmed/9214504)
gmax_paired_prox = 0.00053 // (uS) (as given in http://www.ncbi.nlm.nih.gov/pubmed/9214504)
gmax_paired_mid = 0.00053 // (uS) (as given in http://www.ncbi.nlm.nih.gov/pubmed/9214504)
gmax_paired_dist = 0.00053 // (uS) (as given in http://www.ncbi.nlm.nih.gov/pubmed/9214504)
// unpaired synapses
location_unpaired = location_paired_prompt // soma = 0, prox = 1, mid = 2, dist = 3
interval_unpaired = interval_unpaired_prompt // ms/spike
number_unpaired = number_unpaired_prompt // total number of spikes
start_unpaired = start_unpaired_prompt // ms
noise_unpaired = noise_unpaired_prompt // Boolean: 0 = noiseless, 1 = Poisson
//GABAa maximal conductance
gmax_unpaired_soma = 0.025 // (uS) (as given in Macaferri et al. 2000, J physiol.)
gmax_unpaired_prox = 0.025 // (uS) (as given in Macaferri et al. 2000, J physiol.)
gmax_unpaired_mid = 0.025 // (uS) (as given in Macaferri et al. 2000, J physiol.)
gmax_unpaired_dist = 0.025 // (uS) (as given in Macaferri et al. 2000, J physiol.)
//-----------------------------------------------------------------------------
// synaptic densities from makePairedUnpaired.hoc; "foo_prompt" set in promptWindow.hoc
density_paired = density_paired_prompt //number of synapses / um^2 of membrane
density_unpaired = density_unpaired_prompt //number of synapses / um^2 of membrane
//-----------------------------------------------------------------------------
// clamp parameters from makeClamp.hoc
clamp_amp = clamp_amp_prompt // (nA)
clamp_dur = clamp_dur_prompt // (ms)
clamp_interval = clamp_int_prompt // (ms) time between current injections
clamp_number = clamp_num_prompt // total number of current injections
//clamp_start = start_paired + 1 // (ms)
//print "Clamp Start (setParamters) = ", clamp_start
clamp_noise = clamp_noise_prompt // Boolean: 0 = noiseless, 1 = Poisson