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Merge pull request #339 from BlueBrain/update-example
Update outdated example notebooks
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@@ -21,3 +21,4 @@ bin | |
*.ipynb_checkpoints | ||
lib | ||
fllog.txt | ||
*.DS_Store |
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TITLE Cerebellum Granule Cell Model | ||
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COMMENT | ||
Reference: Theta-Frequency Bursting and Resonance in Cerebellar Granule Cells:Experimental | ||
Evidence and Modeling of a Slow K+-Dependent Mechanism | ||
Egidio D'Angelo,Thierry Nieus,Arianna Maffei,Simona Armano,Paola Rossi,Vanni Taglietti, | ||
Andrea Fontana and Giovanni Naldi | ||
ENDCOMMENT | ||
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NEURON { | ||
SUFFIX GrC_KCa | ||
USEION k READ ek WRITE ik | ||
USEION ca READ cai | ||
RANGE gkbar, ik, ica, g, alpha_c, beta_c | ||
RANGE Aalpha_c, Balpha_c, Kalpha_c | ||
RANGE Abeta_c, Bbeta_c, Kbeta_c | ||
RANGE c_inf, tau_c | ||
} | ||
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UNITS { | ||
(mA) = (milliamp) | ||
(mV) = (millivolt) | ||
(molar) = (1/liter) | ||
(mM) = (millimolar) | ||
} | ||
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PARAMETER { | ||
Aalpha_c = 2.5 (/ms) | ||
Balpha_c = 1.5e-3 (mM) | ||
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:Kalpha_c = -0.085 (/mV) | ||
Kalpha_c = -11.765 (mV) | ||
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Abeta_c = 1.5 (/ms) | ||
Bbeta_c = 0.15e-3 (mM) | ||
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:Kbeta_c = -0.085 (/mV) | ||
Kbeta_c = -11.765 (mV) | ||
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v (mV) | ||
cai (mM) | ||
gkbar= 0.004 (mho/cm2) | ||
ek = -84.69 (mV) | ||
celsius = 30 (degC) | ||
} | ||
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STATE { | ||
c | ||
} | ||
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ASSIGNED { | ||
ik (mA/cm2) | ||
ica (mA/cm2) | ||
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c_inf | ||
tau_c (ms) | ||
g (mho/cm2) | ||
alpha_c (/ms) | ||
beta_c (/ms) | ||
} | ||
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INITIAL { | ||
rate(v) | ||
c = c_inf | ||
} | ||
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BREAKPOINT { | ||
SOLVE states METHOD derivimplicit | ||
g = gkbar*c | ||
ik = g*(v - ek) | ||
alpha_c = alp_c(v) | ||
beta_c = bet_c(v) | ||
} | ||
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DERIVATIVE states { | ||
rate(v) | ||
c' =(c_inf - c)/tau_c | ||
} | ||
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FUNCTION alp_c(v(mV))(/ms) { LOCAL Q10 | ||
Q10 = 3^((celsius-30(degC))/10(degC)) | ||
alp_c = Q10*Aalpha_c/(1+(Balpha_c*exp(v/Kalpha_c)/cai)) | ||
} | ||
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FUNCTION bet_c(v(mV))(/ms) { LOCAL Q10 | ||
Q10 = 3^((celsius-30(degC))/10(degC)) | ||
bet_c = Q10*Abeta_c/(1+cai/(Bbeta_c*exp(v/Kbeta_c))) | ||
} | ||
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PROCEDURE rate(v (mV)) {LOCAL a_c, b_c | ||
TABLE c_inf, tau_c | ||
DEPEND Aalpha_c, Balpha_c, Kalpha_c, | ||
Abeta_c, Bbeta_c, Kbeta_c, celsius FROM -100 TO 100 WITH 200 | ||
a_c = alp_c(v) | ||
b_c = bet_c(v) | ||
tau_c = 1/(a_c + b_c) | ||
c_inf = a_c/(a_c + b_c) | ||
} | ||
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@@ -0,0 +1,36 @@ | ||
TITLE Cerebellum Granule Cell Model | ||
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||
COMMENT | ||
Reference: Theta-Frequency Bursting and Resonance in Cerebellar Granule Cells:Experimental | ||
Evidence and Modeling of a Slow K+-Dependent Mechanism | ||
Egidio D'Angelo,Thierry Nieus,Arianna Maffei,Simona Armano,Paola Rossi,Vanni Taglietti, | ||
Andrea Fontana and Giovanni Naldi | ||
ENDCOMMENT | ||
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NEURON { | ||
SUFFIX GrC_Lkg2 | ||
NONSPECIFIC_CURRENT il | ||
RANGE egaba, ggaba , i | ||
} | ||
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UNITS { | ||
(mA) = (milliamp) | ||
(mV) = (millivolt) | ||
} | ||
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PARAMETER { | ||
v (mV) | ||
ggaba = 2.17e-5 (mho/cm2) | ||
celsius = 30 (degC) | ||
egaba = -65 (mV) | ||
} | ||
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ASSIGNED { | ||
il (mA/cm2) | ||
i (mA/cm2) | ||
} | ||
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BREAKPOINT { | ||
il = ggaba*(v - egaba) | ||
i =il | ||
} |
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@@ -0,0 +1,97 @@ | ||
TITLE Cerebellum Granule Cell Model | ||
|
||
COMMENT | ||
Reference: Theta-Frequency Bursting and Resonance in Cerebellar Granule Cells:Experimental | ||
Evidence and Modeling of a Slow K+-Dependent Mechanism | ||
Egidio D'Angelo,Thierry Nieus,Arianna Maffei,Simona Armano,Paola Rossi,Vanni Taglietti, | ||
Andrea Fontana and Giovanni Naldi | ||
ENDCOMMENT | ||
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||
NEURON { | ||
SUFFIX GrG_KV | ||
USEION k READ ek WRITE ik | ||
RANGE gkbar, ik, g, alpha_n, beta_n | ||
RANGE Aalpha_n, Kalpha_n, V0alpha_n | ||
RANGE Abeta_n, Kbeta_n, V0beta_n | ||
RANGE n_inf, tau_n | ||
} | ||
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UNITS { | ||
(mA) = (milliamp) | ||
(mV) = (millivolt) | ||
} | ||
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PARAMETER { | ||
:Kbeta_n = -0.0125 (/mV) | ||
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Aalpha_n = -0.01 (/ms-mV) | ||
Kalpha_n = -10 (mV) | ||
V0alpha_n = -25 (mV) | ||
Abeta_n = 0.125 (/ms) | ||
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Kbeta_n = -80 (mV) | ||
V0beta_n = -35 (mV) | ||
v (mV) | ||
gkbar= 0.003 (mho/cm2) | ||
ek = -84.69 (mV) | ||
celsius = 30 (degC) | ||
} | ||
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STATE { | ||
n | ||
} | ||
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ASSIGNED { | ||
ik (mA/cm2) | ||
n_inf | ||
tau_n (ms) | ||
g (mho/cm2) | ||
alpha_n (/ms) | ||
beta_n (/ms) | ||
} | ||
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INITIAL { | ||
rate(v) | ||
n = n_inf | ||
} | ||
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BREAKPOINT { | ||
SOLVE states METHOD derivimplicit | ||
g = gkbar*n*n*n*n | ||
ik = g*(v - ek) | ||
alpha_n = alp_n(v) | ||
beta_n = bet_n(v) | ||
} | ||
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DERIVATIVE states { | ||
rate(v) | ||
n' =(n_inf - n)/tau_n | ||
} | ||
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FUNCTION alp_n(v(mV))(/ms) { LOCAL Q10 | ||
Q10 = 3^((celsius-6.3(degC))/10(degC)) | ||
alp_n = Q10*Aalpha_n*linoid(v-V0alpha_n, Kalpha_n) | ||
} | ||
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FUNCTION bet_n(v(mV))(/ms) { LOCAL Q10 | ||
Q10 = 3^((celsius-6.3(degC))/10(degC)) | ||
bet_n = Q10*Abeta_n*exp((v-V0beta_n)/Kbeta_n) | ||
} | ||
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PROCEDURE rate(v (mV)) {LOCAL a_n, b_n | ||
TABLE n_inf, tau_n | ||
DEPEND Aalpha_n, Kalpha_n, V0alpha_n, | ||
Abeta_n, Kbeta_n, V0beta_n, celsius FROM -100 TO 100 WITH 200 | ||
a_n = alp_n(v) | ||
b_n = bet_n(v) | ||
tau_n = 1/(a_n + b_n) | ||
n_inf = a_n/(a_n + b_n) | ||
} | ||
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FUNCTION linoid(x (mV),y (mV)) (mV) { | ||
if (fabs(x/y) < 1e-6) { | ||
linoid = y*(1 - x/y/2) | ||
}else{ | ||
linoid = x/(exp(x/y) - 1) | ||
} | ||
} |
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