From cd98d7a282ae227237dcd265eef238989d2fee4e Mon Sep 17 00:00:00 2001 From: JustasB Date: Wed, 19 Aug 2015 16:38:20 -0700 Subject: [PATCH 01/14] XPP version of RS cell --- XPP/RS.ode | 69 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 XPP/RS.ode diff --git a/XPP/RS.ode b/XPP/RS.ode new file mode 100644 index 0000000..ecedc4f --- /dev/null +++ b/XPP/RS.ode @@ -0,0 +1,69 @@ +# Pospischil, et. al. Regular Spiking (RS) cell model + +par Cap=2.9 + +par Eleak=-70 +par Ena=50 +par Ek=-90 +par Vt=-63 + +par gleak=0.4 +par gna=50 +par gkd=5 +par gm=0.07 + +par tmax=4000 + +par Idelay=200 +par Iduration=500 +par I=5 + +# initial conditions +init V=-65 + +# Current balance +V'=(-Ileak-INa-IKd-Im+Iinput)/Cap + +# Input current +Iinput=if(t>=Idelay)then(if(t<=(Idelay+Iduration))then(I)else(0))else(0) + +# Leak current +Ileak=gleak*(V-Eleak) + +# Na current +INa=gna*m*m*m*h*(V-Ena) + +m'=am*(1-m)-bm*m +h'=ah*(1-h)-bh*h + +am=(-0.32*(V-Vt-13))/(exp(-(V-Vt-13)/4)-1) +bm=(0.28*(V-Vt-40))/(exp((V-Vt-40)/5)-1) +ah=0.128*exp(-(V-Vt-17)/18) +bh=(4)/(1+exp(-(V-Vt-40)/5)) + +# Kd current +IKd=gkd*n*n*n*n*(V-Ek) + +n'=an*(1-n)-bn*n + +an=(-0.032*(V-Vt-15))/(exp(-(V-Vt-15)/5)-1) +bn=0.5*exp(-(V-Vt-10)/40) + +# Km current +Im=gm*p*(V-Ek) + +p'=(pinf-p)/tp + +pinf=1/(1+exp(-(V+35)/10)) +tp=tmax/(3.3*exp((V+35)/20)+exp(-(V+35)/20)) + +# integrator params +@ maxstor=80000,total=1000,bound=10000,xlo=0,xhi=1000,ylo=-75,yhi=40 +@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.3 +done + + + + + + From cab81198935afa9cf0225d6649c963a5a4800fe8 Mon Sep 17 00:00:00 2001 From: JustasB Date: Wed, 19 Aug 2015 16:49:43 -0700 Subject: [PATCH 02/14] Na, Kd, Km channels matching the equations provided in the paper --- NEURON_MODIFIED/HH_traub.mod | 108 ++++++++-------------------------- NEURON_MODIFIED/IM_cortex.mod | 71 ++++++++-------------- 2 files changed, 50 insertions(+), 129 deletions(-) diff --git a/NEURON_MODIFIED/HH_traub.mod b/NEURON_MODIFIED/HH_traub.mod index 8bf017f..354d98d 100644 --- a/NEURON_MODIFIED/HH_traub.mod +++ b/NEURON_MODIFIED/HH_traub.mod @@ -20,9 +20,8 @@ NEURON { USEION na READ ena WRITE ina USEION k READ ek WRITE ik RANGE gnabar, gkbar, vtraub - RANGE m_inf, h_inf, n_inf - RANGE tau_m, tau_h, tau_n - RANGE m_exp, h_exp, n_exp + RANGE alpha_m, alpha_h, alpha_n + RANGE beta_m, beta_h, beta_n } @@ -40,7 +39,7 @@ PARAMETER { celsius = 36 (degC) dt (ms) v (mV) - vtraub = -55 (mV) : PG changed this from -63 to -55, as this is value for vtraub is used in all ModelDB examples + vtraub = -63 (mV) : PG changed this from -63 to -55, as this is value for vtraub is used in all ModelDB examples } STATE { @@ -50,101 +49,46 @@ STATE { ASSIGNED { ina (mA/cm2) ik (mA/cm2) - il (mA/cm2) - m_inf - h_inf - n_inf - tau_m - tau_h - tau_n - m_exp - h_exp - n_exp - tadj + alpha_m + alpha_h + alpha_n + beta_m + beta_h + beta_n } BREAKPOINT { - SOLVE states - ina = gnabar * m*m*m*h * (v - ena) - ik = gkbar * n*n*n*n * (v - ek) -} + SOLVE states -:DERIVATIVE states { : exact Hodgkin-Huxley equations -: evaluate_fct(v) -: m' = (m_inf - m) / tau_m -: h' = (h_inf - h) / tau_h -: n' = (n_inf - n) / tau_n -:} - -PROCEDURE states() { : exact when v held constant - evaluate_fct(v) - m = m + m_exp * (m_inf - m) - h = h + h_exp * (h_inf - h) - n = n + n_exp * (n_inf - n) - VERBATIM - return 0; - ENDVERBATIM + ina = gnabar * m*m*m*h * (v - ena) + ik = gkbar * n*n*n*n * (v - ek) } -UNITSOFF -INITIAL { - - tadj = 3.0 ^ ((celsius-36)/ 10 ) : JB - was the last line, moved - : to top as value used in evaluate_fct - evaluate_fct(v) : JB - Added here, to compute x_inf vars +DERIVATIVE states { : exact Hodgkin-Huxley equations - m = m_inf : JB - These were all 0 - h = h_inf - n = n_inf -: -: Q10 was assumed to be 3 for both currents -: -: original measurements at roomtemperature? + evaluate_fct(v) + m' = alpha_m*(1-m)-beta_m*m + h' = alpha_h*(1-h)-beta_h*h + n' = alpha_n*(1-n)-beta_n*n } -PROCEDURE evaluate_fct(v(mV)) { LOCAL a,b,v2 +UNITSOFF +PROCEDURE evaluate_fct(v(mV)) { LOCAL vt - v2 = v - vtraub : convert to traub convention + vt = vtraub -: a = 0.32 * (13-v2) / ( Exp((13-v2)/4) - 1) - a = 0.32 * vtrap(13-v2, 4) -: b = 0.28 * (v2-40) / ( Exp((v2-40)/5) - 1) - b = 0.28 * vtrap(v2-40, 5) - tau_m = 1 / (a + b) / tadj - m_inf = a / (a + b) + alpha_m = (-0.32*(v-vt-13))/(exp(-(v-vt-13)/4)-1) + beta_m = (0.28*(v-vt-40))/(exp((v-vt-40)/5)-1) - a = 0.128 * Exp((17-v2)/18) - b = 4 / ( 1 + Exp((40-v2)/5) ) - tau_h = 1 / (a + b) / tadj - h_inf = a / (a + b) + alpha_h = 0.128*exp(-(v-vt-17)/18) + beta_h = 4/(1+exp(-(v-vt-40)/5)) -: a = 0.032 * (15-v2) / ( Exp((15-v2)/5) - 1) - a = 0.032 * vtrap(15-v2, 5) - b = 0.5 * Exp((10-v2)/40) - tau_n = 1 / (a + b) / tadj - n_inf = a / (a + b) + alpha_n = (-0.032*(v-vt-15))/(exp(-(v-vt-15)/5)-1) + beta_n = 0.5*exp(-(v-vt-10)/40) - m_exp = 1 - Exp(-dt/tau_m) - h_exp = 1 - Exp(-dt/tau_h) - n_exp = 1 - Exp(-dt/tau_n) -} -FUNCTION vtrap(x,y) { - if (fabs(x/y) < 1e-6) { - vtrap = y*(1 - x/y/2) - }else{ - vtrap = x/(Exp(x/y)-1) - } } - -FUNCTION Exp(x) { - if (x < -100) { - Exp = 0 - }else{ - Exp = exp(x) - } -} diff --git a/NEURON_MODIFIED/IM_cortex.mod b/NEURON_MODIFIED/IM_cortex.mod index 0ebaaac..5b92eda 100644 --- a/NEURON_MODIFIED/IM_cortex.mod +++ b/NEURON_MODIFIED/IM_cortex.mod @@ -20,80 +20,57 @@ TITLE Cortical M current INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)} NEURON { - SUFFIX im - USEION k READ ek WRITE ik - RANGE gkbar, m_inf, tau_m - GLOBAL taumax + SUFFIX im + USEION k READ ek WRITE ik + RANGE gkbar, pinf, tp, taumax } UNITS { - (mA) = (milliamp) - (mV) = (millivolt) + (mA) = (milliamp) + (mV) = (millivolt) } PARAMETER { - v (mV) - celsius = 36 (degC) - ek (mV) - gkbar = 1e-6 (mho/cm2) - taumax = 1000 (ms) : peak value of tau + v (mV) + celsius = 36 (degC) + ek (mV) + gkbar = 1e-6 (mho/cm2) + taumax = 1000 (ms) : peak value of tau } STATE { - m + p m } ASSIGNED { - ik (mA/cm2) - m_inf - tau_m (ms) - tau_peak (ms) - tadj + ik (mA/cm2) + pinf + tp (ms) } BREAKPOINT { - SOLVE states METHOD cnexp - ik = gkbar * m * (v - ek) + SOLVE states METHOD cnexp + ik = gkbar * p * (v - ek) + m = p } -DERIVATIVE states { - evaluate_fct(v) +DERIVATIVE states { - m' = (m_inf - m) / tau_m -} - -UNITSOFF -INITIAL { - -: -: The Q10 value is assumed to be 2.3 -: - tadj = 2.3 ^ ((celsius-36)/10) - tau_peak = taumax / tadj - evaluate_fct(v) : JB - moved here from first line - : as tau_peak is used in evaluate_fct + evaluate_fct(v) - m = m_inf : JB - this was 0 + p'=(pinf-p)/tp } +UNITSOFF PROCEDURE evaluate_fct(v(mV)) { - m_inf = 1 / ( 1 + exptable(-(v+35)/10) ) - tau_m = tau_peak / ( 3.3 * exptable((v+35)/20) + exptable(-(v+35)/20) ) + pinf=1/(1+exp(-(v+35)/10)) + tp=taumax/(3.3*exp((v+35)/20)+exp(-(v+35)/20)) + } UNITSON - -FUNCTION exptable(x) { - TABLE FROM -25 TO 25 WITH 10000 - - if ((x > -25) && (x < 25)) { - exptable = exp(x) - } else { - exptable = 0. - } -} From aca2e16149c9cf7b647c5e573243c1c73a17b398 Mon Sep 17 00:00:00 2001 From: JustasB Date: Fri, 21 Aug 2015 11:36:47 -0700 Subject: [PATCH 03/14] RS cell with parameters from figure 1C and paper --- XPP/RS.ode | 69 -------------------------- XPP/RS_fromFigure.ode | 112 ++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 112 insertions(+), 69 deletions(-) delete mode 100644 XPP/RS.ode create mode 100644 XPP/RS_fromFigure.ode diff --git a/XPP/RS.ode b/XPP/RS.ode deleted file mode 100644 index ecedc4f..0000000 --- a/XPP/RS.ode +++ /dev/null @@ -1,69 +0,0 @@ -# Pospischil, et. al. Regular Spiking (RS) cell model - -par Cap=2.9 - -par Eleak=-70 -par Ena=50 -par Ek=-90 -par Vt=-63 - -par gleak=0.4 -par gna=50 -par gkd=5 -par gm=0.07 - -par tmax=4000 - -par Idelay=200 -par Iduration=500 -par I=5 - -# initial conditions -init V=-65 - -# Current balance -V'=(-Ileak-INa-IKd-Im+Iinput)/Cap - -# Input current -Iinput=if(t>=Idelay)then(if(t<=(Idelay+Iduration))then(I)else(0))else(0) - -# Leak current -Ileak=gleak*(V-Eleak) - -# Na current -INa=gna*m*m*m*h*(V-Ena) - -m'=am*(1-m)-bm*m -h'=ah*(1-h)-bh*h - -am=(-0.32*(V-Vt-13))/(exp(-(V-Vt-13)/4)-1) -bm=(0.28*(V-Vt-40))/(exp((V-Vt-40)/5)-1) -ah=0.128*exp(-(V-Vt-17)/18) -bh=(4)/(1+exp(-(V-Vt-40)/5)) - -# Kd current -IKd=gkd*n*n*n*n*(V-Ek) - -n'=an*(1-n)-bn*n - -an=(-0.032*(V-Vt-15))/(exp(-(V-Vt-15)/5)-1) -bn=0.5*exp(-(V-Vt-10)/40) - -# Km current -Im=gm*p*(V-Ek) - -p'=(pinf-p)/tp - -pinf=1/(1+exp(-(V+35)/10)) -tp=tmax/(3.3*exp((V+35)/20)+exp(-(V+35)/20)) - -# integrator params -@ maxstor=80000,total=1000,bound=10000,xlo=0,xhi=1000,ylo=-75,yhi=40 -@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.3 -done - - - - - - diff --git a/XPP/RS_fromFigure.ode b/XPP/RS_fromFigure.ode new file mode 100644 index 0000000..2015a9f --- /dev/null +++ b/XPP/RS_fromFigure.ode @@ -0,0 +1,112 @@ +# Pospischil, et. al. Regular Spiking (RS) cell model +# Figure 1c + +# ---- PARAMETERS ---- # + +# 1 nF in section 2.1 & NEURON +par Cm=1 + +# Both 96 um in figure & NEURON +par Ldiam = 0.96 + +# from figure & NEURON +par Eleak=-70 + +# from section 2.2.1 Na current & NEURON +par Ena=50 + +# -90mV in section 2.2.1 K current +# -100mV in NEURON hoc file +par Ek=-90 + +# ??? Not in paper or figure +# -63mV in NEURON mod file +# -55mV in NEURON hoc file +par Vt=-63 + +# 1e-4 S/cm2 in figure & NEURON +par gleak=0.1 + +# 0.05 S/cm2 in figure & NEURON +par gna=50 + +# 0.005 S/cm2 in figure & NEURON +par gkd=5 + +# 7e-5 S/cm2 in figure & NEURON +par gm=0.07 + +# 4000ms in section 2.2.2 +# 1000ms in NEURON hoc file +par tmax=4000 + +# Estimated by pixel count del=200, dur=500 +# In NEURON hoc del=300, dur=400 +par Idelay=200 +par Iduration=500 + +# 0.5nA in figure +# 0.75nA in NEURON hoc +par I=5 + +# No DC current in paper or NEURON +# Figure starts and stays at -65mV +# DC current of 0.516 needed to keep at -65mV +par Idc=0 + +# initial conditions +# Figure starts at -65mV +# -70mV in NEURON hoc +init V=-65 + + +# ---- EQUATIONS ---- # + +# Lateral area +area=2*PI*Ldiam/2*Ldiam + +# Total Capacitance +# 0.29 nF in figure +# 0.28953 nF in NEURON +Cap=area*Cm + +# Current balance +V'=(-Ileak-INa-IKd-Im+Iinput/area)/Cap + +# Input current with DC, delay, and duration +Iinput=if(t>=Idelay)then(if(t<=(Idelay+Iduration))then(I)else(0))else(0)+Idc + +# Leak current +Ileak=gleak*(V-Eleak) + +# Na current +INa=gna*m*m*m*h*(V-Ena) + +m'=am*(1-m)-bm*m +h'=ah*(1-h)-bh*h + +am=(-0.32*(V-Vt-13))/(exp(-(V-Vt-13)/4)-1) +bm=(0.28*(V-Vt-40))/(exp((V-Vt-40)/5)-1) +ah=0.128*exp(-(V-Vt-17)/18) +bh=(4)/(1+exp(-(V-Vt-40)/5)) + +# Kd current +IKd=gkd*n*n*n*n*(V-Ek) + +n'=an*(1-n)-bn*n + +an=(-0.032*(V-Vt-15))/(exp(-(V-Vt-15)/5)-1) +bn=0.5*exp(-(V-Vt-10)/40) + +# Km current +Im=gm*p*(V-Ek) + +p'=(pinf-p)/tp + +pinf=1/(1+exp(-(V+35)/10)) +tp=tmax/(3.3*exp((V+35)/20)+exp(-(V+35)/20)) + +# integrator params +@ maxstor=80000,total=1000,bound=10000,xlo=0,xhi=1000,ylo=-75,yhi=40 +@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.3 +done \ No newline at end of file From bd011b944c58379af46a4d827bf8cb4694b07077 Mon Sep 17 00:00:00 2001 From: JustasB Date: Fri, 21 Aug 2015 11:37:11 -0700 Subject: [PATCH 04/14] RS cell with parameters from NEURON_ORIG files --- XPP/RS_fromNEURON.ode | 112 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100644 XPP/RS_fromNEURON.ode diff --git a/XPP/RS_fromNEURON.ode b/XPP/RS_fromNEURON.ode new file mode 100644 index 0000000..fb66ab9 --- /dev/null +++ b/XPP/RS_fromNEURON.ode @@ -0,0 +1,112 @@ +# Pospischil, et. al. Regular Spiking (RS) cell model +# Figure 1c + +# ---- PARAMETERS ---- # + +# 1 nF in section 2.1 & NEURON +par Cm=1 + +# Both 96 um in figure & NEURON +par Ldiam = 0.96 + +# from figure & NEURON +par Eleak=-70 + +# from section 2.2.1 Na current & NEURON +par Ena=50 + +# -90mV in section 2.2.1 K current +# -100mV in NEURON hoc file +par Ek=-100 + +# ??? Not in paper or figure +# -63mV in NEURON mod file +# -55mV in NEURON hoc file +par Vt=-55 + +# 1e-4 S/cm2 in figure & NEURON +par gleak=0.1 + +# 0.05 S/cm2 in figure & NEURON +par gna=50 + +# 0.005 S/cm2 in figure & NEURON +par gkd=5 + +# 7e-5 S/cm2 in figure & NEURON +par gm=0.07 + +# 4000ms in section 2.2.2 +# 1000ms in NEURON hoc file +par tmax=1000 + +# Visually estimated del=200, dur=500 +# In NEURON hoc del=300, dur=400 +par Idelay=300 +par Iduration=400 + +# 0.5nA in figure +# 0.75nA in NEURON hoc +par I=7.5 + +# No DC current in paper or NEURON +# Figure starts and stays at -65mV +# DC current of 0.516 needed to keep at -65mV +par Idc=0 + +# initial conditions +# Figure starts at -65mV +# -70mV in NEURON hoc +init V=-70 + + +# ---- EQUATIONS ---- # + +# Lateral area +area=2*PI*Ldiam/2*Ldiam + +# Total Capacitance +# 0.29 nF in figure +# 0.28953 nF in NEURON +Cap=area*Cm + +# Current balance +V'=(-Ileak-INa-IKd-Im+Iinput/area)/Cap + +# Input current with DC, delay, and duration +Iinput=if(t>=Idelay)then(if(t<=(Idelay+Iduration))then(I)else(0))else(0)+Idc + +# Leak current +Ileak=gleak*(V-Eleak) + +# Na current +INa=gna*m*m*m*h*(V-Ena) + +m'=am*(1-m)-bm*m +h'=ah*(1-h)-bh*h + +am=(-0.32*(V-Vt-13))/(exp(-(V-Vt-13)/4)-1) +bm=(0.28*(V-Vt-40))/(exp((V-Vt-40)/5)-1) +ah=0.128*exp(-(V-Vt-17)/18) +bh=(4)/(1+exp(-(V-Vt-40)/5)) + +# Kd current +IKd=gkd*n*n*n*n*(V-Ek) + +n'=an*(1-n)-bn*n + +an=(-0.032*(V-Vt-15))/(exp(-(V-Vt-15)/5)-1) +bn=0.5*exp(-(V-Vt-10)/40) + +# Km current +Im=gm*p*(V-Ek) + +p'=(pinf-p)/tp + +pinf=1/(1+exp(-(V+35)/10)) +tp=tmax/(3.3*exp((V+35)/20)+exp(-(V+35)/20)) + +# integrator params +@ maxstor=80000,total=1000,bound=10000,xlo=0,xhi=1000,ylo=-75,yhi=40 +@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.3 +done \ No newline at end of file From feb296f66b76e73820d3ce9abdcc3aa8bd209116 Mon Sep 17 00:00:00 2001 From: JustasB Date: Fri, 21 Aug 2015 11:37:33 -0700 Subject: [PATCH 05/14] RS cell with parameters that best fit figure 1C --- XPP/RS_bestFit.ode | 116 +++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 116 insertions(+) create mode 100644 XPP/RS_bestFit.ode diff --git a/XPP/RS_bestFit.ode b/XPP/RS_bestFit.ode new file mode 100644 index 0000000..b4d7152 --- /dev/null +++ b/XPP/RS_bestFit.ode @@ -0,0 +1,116 @@ +# Pospischil, et. al. Regular Spiking (RS) cell model +# Figure 1c + +# ---- PARAMETERS ---- # + +# 1 nF in section 2.1 & NEURON +par Cm=1 + +# Both 96 um in figure & NEURON +par Ldiam = 0.96 + +# from figure & NEURON +par Eleak=-70 + +# from section 2.2.1 Na current & NEURON +par Ena=50 + +# -90mV in section 2.2.1 K current +# -100mV in NEURON hoc file +# -100mv best fit to figure +par Ek=-100 + +# ??? Not in paper or figure +# -63mV in NEURON mod file +# -55mV in NEURON hoc file +# -68.6mV best fit to figure +par Vt=-68.6 + +# 1e-4 S/cm2 in figure & NEURON +par gleak=0.1 + +# 0.05 S/cm2 in figure & NEURON +par gna=50 + +# 0.005 S/cm2 in figure & NEURON +par gkd=5 + +# 7e-5 S/cm2 in figure & NEURON +par gm=0.07 + +# 4000ms in section 2.2.2 +# 1000ms in NEURON hoc file +# 1000ms best fit to figure +par tmax=1000 + +# Estimated by pixel count del=200, dur=500 +# In NEURON hoc del=300, dur=400 +par Idelay=200 +par Iduration=500 + +# 0.5nA in figure +# 0.75nA in NEURON hoc +# 1.87 best fit to figure +par I=1.87 + +# No DC current in paper or NEURON +# Figure starts and stays at -65mV +# DC current of 1.12 needed to keep at -65mV +par Idc=1.12 + +# initial conditions +# Figure starts at -65mV +# -70mV in NEURON hoc +init V=-65 + + +# ---- EQUATIONS ---- # + +# Lateral area +area=2*PI*Ldiam/2*Ldiam + +# Total Capacitance +# 0.29 nF in figure +# 0.28953 nF in NEURON +Cap=area*Cm + +# Current balance +V'=(-Ileak-INa-IKd-Im+Iinput/area)/Cap + +# Input current with DC, delay, and duration +Iinput=if(t>=Idelay)then(if(t<=(Idelay+Iduration))then(I)else(0))else(0)+Idc + +# Leak current +Ileak=gleak*(V-Eleak) + +# Na current +INa=gna*m*m*m*h*(V-Ena) + +m'=am*(1-m)-bm*m +h'=ah*(1-h)-bh*h + +am=(-0.32*(V-Vt-13))/(exp(-(V-Vt-13)/4)-1) +bm=(0.28*(V-Vt-40))/(exp((V-Vt-40)/5)-1) +ah=0.128*exp(-(V-Vt-17)/18) +bh=(4)/(1+exp(-(V-Vt-40)/5)) + +# Kd current +IKd=gkd*n*n*n*n*(V-Ek) + +n'=an*(1-n)-bn*n + +an=(-0.032*(V-Vt-15))/(exp(-(V-Vt-15)/5)-1) +bn=0.5*exp(-(V-Vt-10)/40) + +# Km current +Im=gm*p*(V-Ek) + +p'=(pinf-p)/tp + +pinf=1/(1+exp(-(V+35)/10)) +tp=tmax/(3.3*exp((V+35)/20)+exp(-(V+35)/20)) + +# integrator params +@ maxstor=80000,total=1000,bound=10000,xlo=0,xhi=1000,ylo=-75,yhi=40 +@ meth=cvode,atol=0.0001,toler=0.0001,dt=0.3 +done \ No newline at end of file From 7410b939b95c2e2f76a24820669424fbc804a0bb Mon Sep 17 00:00:00 2001 From: JustasB Date: Sun, 23 Aug 2015 12:19:47 -0700 Subject: [PATCH 06/14] *** to indicate which parameters were used for best fit --- XPP/RS_bestFit.ode | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/XPP/RS_bestFit.ode b/XPP/RS_bestFit.ode index b4d7152..cf47bcf 100644 --- a/XPP/RS_bestFit.ode +++ b/XPP/RS_bestFit.ode @@ -1,5 +1,7 @@ # Pospischil, et. al. Regular Spiking (RS) cell model # Figure 1c +# Parameters that have been found to best reproduce the published figure +# *** indicates discovered parameter # ---- PARAMETERS ---- # @@ -23,7 +25,7 @@ par Ek=-100 # ??? Not in paper or figure # -63mV in NEURON mod file # -55mV in NEURON hoc file -# -68.6mV best fit to figure +# -68.6mV best fit to figure *** par Vt=-68.6 # 1e-4 S/cm2 in figure & NEURON @@ -50,12 +52,12 @@ par Iduration=500 # 0.5nA in figure # 0.75nA in NEURON hoc -# 1.87 best fit to figure +# 1.87 best fit to figure *** par I=1.87 # No DC current in paper or NEURON # Figure starts and stays at -65mV -# DC current of 1.12 needed to keep at -65mV +# DC current of 1.12 needed to keep at -65mV *** par Idc=1.12 # initial conditions From 65401a354949aed31376d571e0a1bb5ef1ccbf59 Mon Sep 17 00:00:00 2001 From: JustasB Date: Sun, 23 Aug 2015 14:56:09 -0700 Subject: [PATCH 07/14] Spiking behavior screenshots --- Frequency adaptation.png | Bin 0 -> 12829 bytes Intrinsic bursting.png | Bin 0 -> 11423 bytes Rebound.png | Bin 0 -> 11652 bytes Regular Spiking.png | Bin 0 -> 11317 bytes 4 files changed, 0 insertions(+), 0 deletions(-) create mode 100644 Frequency adaptation.png create mode 100644 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h_exp, n_exp } @@ -39,7 +40,7 @@ PARAMETER { celsius = 36 (degC) dt (ms) v (mV) - vtraub = -63 (mV) : PG changed this from -63 to -55, as this is value for vtraub is used in all ModelDB examples + vtraub = -55 (mV) : PG changed this from -63 to -55, as this is value for vtraub is used in all ModelDB examples } STATE { @@ -49,46 +50,101 @@ STATE { ASSIGNED { ina (mA/cm2) ik (mA/cm2) - alpha_m - alpha_h - alpha_n - beta_m - beta_h - beta_n + il (mA/cm2) + m_inf + h_inf + n_inf + tau_m + tau_h + tau_n + m_exp + h_exp + n_exp + tadj } BREAKPOINT { - - SOLVE states - + SOLVE states ina = gnabar * m*m*m*h * (v - ena) ik = gkbar * n*n*n*n * (v - ek) } -DERIVATIVE states { : exact Hodgkin-Huxley equations +:DERIVATIVE states { : exact Hodgkin-Huxley equations +: evaluate_fct(v) +: m' = (m_inf - m) / tau_m +: h' = (h_inf - h) / tau_h +: n' = (n_inf - n) / tau_n +:} + +PROCEDURE states() { : exact when v held constant + evaluate_fct(v) + m = m + m_exp * (m_inf - m) + h = h + h_exp * (h_inf - h) + n = n + n_exp * (n_inf - n) + VERBATIM + return 0; + ENDVERBATIM +} + +UNITSOFF +INITIAL { + + tadj = 3.0 ^ ((celsius-36)/ 10 ) : JB - was the last line, moved + : to top as value used in evaluate_fct + + evaluate_fct(v) : JB - Added here, to compute x_inf vars - evaluate_fct(v) + m = m_inf : JB - These were all 0 + h = h_inf + n = n_inf +: +: Q10 was assumed to be 3 for both currents +: +: original measurements at roomtemperature? - m' = alpha_m*(1-m)-beta_m*m - h' = alpha_h*(1-h)-beta_h*h - n' = alpha_n*(1-n)-beta_n*n } -UNITSOFF -PROCEDURE evaluate_fct(v(mV)) { LOCAL vt +PROCEDURE evaluate_fct(v(mV)) { LOCAL a,b,v2 - vt = vtraub + v2 = v - vtraub : convert to traub convention - alpha_m = (-0.32*(v-vt-13))/(exp(-(v-vt-13)/4)-1) - beta_m = (0.28*(v-vt-40))/(exp((v-vt-40)/5)-1) +: a = 0.32 * (13-v2) / ( Exp((13-v2)/4) - 1) + a = 0.32 * vtrap(13-v2, 4) +: b = 0.28 * (v2-40) / ( Exp((v2-40)/5) - 1) + b = 0.28 * vtrap(v2-40, 5) + tau_m = 1 / (a + b) / tadj + m_inf = a / (a + b) - alpha_h = 0.128*exp(-(v-vt-17)/18) - beta_h = 4/(1+exp(-(v-vt-40)/5)) + a = 0.128 * Exp((17-v2)/18) + b = 4 / ( 1 + Exp((40-v2)/5) ) + tau_h = 1 / (a + b) / tadj + h_inf = a / (a + b) - alpha_n = (-0.032*(v-vt-15))/(exp(-(v-vt-15)/5)-1) - beta_n = 0.5*exp(-(v-vt-10)/40) +: a = 0.032 * (15-v2) / ( Exp((15-v2)/5) - 1) + a = 0.032 * vtrap(15-v2, 5) + b = 0.5 * Exp((10-v2)/40) + tau_n = 1 / (a + b) / tadj + n_inf = a / (a + b) + m_exp = 1 - Exp(-dt/tau_m) + h_exp = 1 - Exp(-dt/tau_h) + n_exp = 1 - Exp(-dt/tau_n) +} +FUNCTION vtrap(x,y) { + if (fabs(x/y) < 1e-6) { + vtrap = y*(1 - x/y/2) + }else{ + vtrap = x/(Exp(x/y)-1) + } } + +FUNCTION Exp(x) { + if (x < -100) { + Exp = 0 + }else{ + Exp = exp(x) + } +} diff --git a/NEURON_MODIFIED/IM_cortex.mod b/NEURON_MODIFIED/IM_cortex.mod index 5b92eda..0ebaaac 100644 --- a/NEURON_MODIFIED/IM_cortex.mod +++ b/NEURON_MODIFIED/IM_cortex.mod @@ -20,57 +20,80 @@ TITLE Cortical M current INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)} NEURON { - SUFFIX im - USEION k READ ek WRITE ik - RANGE gkbar, pinf, tp, taumax + SUFFIX im + USEION k READ ek WRITE ik + RANGE gkbar, m_inf, tau_m + GLOBAL taumax } UNITS { - (mA) = (milliamp) - (mV) = (millivolt) + (mA) = (milliamp) + (mV) = (millivolt) } PARAMETER { - v (mV) - celsius = 36 (degC) - ek (mV) - gkbar = 1e-6 (mho/cm2) - taumax = 1000 (ms) : peak value of tau + v (mV) + celsius = 36 (degC) + ek (mV) + gkbar = 1e-6 (mho/cm2) + taumax = 1000 (ms) : peak value of tau } STATE { - p m + m } ASSIGNED { - ik (mA/cm2) - pinf - tp (ms) + ik (mA/cm2) + m_inf + tau_m (ms) + tau_peak (ms) + tadj } BREAKPOINT { - SOLVE states METHOD cnexp - ik = gkbar * p * (v - ek) - m = p + SOLVE states METHOD cnexp + ik = gkbar * m * (v - ek) } -DERIVATIVE states { +DERIVATIVE states { + evaluate_fct(v) - evaluate_fct(v) - - p'=(pinf-p)/tp + m' = (m_inf - m) / tau_m } UNITSOFF -PROCEDURE evaluate_fct(v(mV)) { +INITIAL { - pinf=1/(1+exp(-(v+35)/10)) - tp=taumax/(3.3*exp((v+35)/20)+exp(-(v+35)/20)) +: +: The Q10 value is assumed to be 2.3 +: + tadj = 2.3 ^ ((celsius-36)/10) + tau_peak = taumax / tadj + evaluate_fct(v) : JB - moved here from first line + : as tau_peak is used in evaluate_fct + m = m_inf : JB - this was 0 +} + +PROCEDURE evaluate_fct(v(mV)) { + + m_inf = 1 / ( 1 + exptable(-(v+35)/10) ) + tau_m = tau_peak / ( 3.3 * exptable((v+35)/20) + exptable(-(v+35)/20) ) } UNITSON + +FUNCTION exptable(x) { + TABLE FROM -25 TO 25 WITH 10000 + + if ((x > -25) && (x < 25)) { + exptable = exp(x) + } else { + exptable = 0. + } +} From 194d84be6884023c64dd04ea03d0e7e6d096375c Mon Sep 17 00:00:00 2001 From: JustasB Date: Sun, 23 Aug 2015 15:04:44 -0700 Subject: [PATCH 09/14] Readme update --- README.md | 83 +++++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 81 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 221bc7f..815ecab 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,86 @@ -### Minimal Hodgkin–Huxley type models for different classes of cortical and thalamic neurons +## Minimal Hodgkin–Huxley type models for four common classes of cortical and thalamic neurons -Conversion to NeuroML of cell models from: [Minimal Hodgkin–Huxley type models for different classes of cortical and thalamic neurons](http://link.springer.com/article/10.1007/s00422-008-0263-8), Martin Pospischil, Maria Toledo-Rodriguez, Cyril Monier, Zuzanna Piwkowska, Thierry Bal, Yves Frégnac, Henry Markram and Alain Destexhe, Biological Cybernetics, 2008. +[![Build Status](https://travis-ci.org/OpenSourceBrain/PospischilEtAl2008.svg?branch=master)](https://travis-ci.org/OpenSourceBrain/PospischilEtAl2008) +#### Overview of the Model +[Pospischil, et. al. (2008)](http://link.springer.com/article/10.1007/s00422-008-0263-8) contains conductance-based ([Hodgin-Huxley](https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model)) models for four different classes of [cortical](https://en.wikipedia.org/wiki/Cerebral_cortex) and [thalamic](https://en.wikipedia.org/wiki/Thalamus) neurons. The classes represented are: + +- Regular Spiking (RS) cells +- Fast Spiking (FS) cells +- Intrinsicly Bursting (IB) +- Low-Threshold Spike (LTS) cells + +All cell models are composed of [ion channel](https://en.wikipedia.org/wiki/Ion_channel) models generating the following currents: + +- INa Voltage dependent Na+ current for depolarization phase of action potentials (APs) +- IKd Delayed rectifier K+ current for hyperpolarization phase of APs +- IM Slow non-inactivating K+ current for spike-frequency adaptation +- IL High-threshold Ca2+ current for burst generation +- IT Low-threshold Ca2+ current for rebound-burst generation + +Leak and input current models are present in all cells as well. + +These models demonstrate that a wide variety of spiking behaviors can be implemented using a small number of ion channels. + +**Original Reference:** + +[Minimal Hodgkin–Huxley type models for different classes of cortical and thalamic neurons](http://link.springer.com/article/10.1007/s00422-008-0263-8), Martin Pospischil, Maria Toledo-Rodriguez, Cyril Monier, Zuzanna Piwkowska, Thierry Bal, Yves Frégnac, Henry Markram and Alain Destexhe, *Biological Cybernetics*, 2008. + +#### Demonstrated Physiological Properties + +Specifically, these models demonstrate the following properties: + +**Regular Spiking** +The use of INa and IKd currents and applying a constant input current is sufficient to generate a train of spikes with constant frequency. + + + +**Frequency Adaptation** +In addition to INa and IKd currents, including the IM current will result in a train of spikes where the inter-spike interval increases (and frequency decreases) with each spike in the train. + +**Intrinsic Bursting** + +When a calcium-dependent IL current is added to a cell with INa, IKd, and IM currents, the cell membrane potential will display an initial high-frequency burst of spikes and then settle onto a regular, frequency-adapting spiking behavior. The IL current makes use of variable Ca2+ reversal potential which is computed from the [Nernst equation](https://en.wikipedia.org/wiki/Nernst_equation) by tracking changes in the intracellular Ca2+ concentration. + +**Rebound Bursting** + +Similarly, using the calcium-dependent IT current instead of IL results in a cell that will fire a series of high-frequency spikes after a negative (hyperpolarizing) current is withdrawn from cell. + + +Figure produced with NEURON_ORIG LTS Cell with gcabar_it = 0.0012 and input current -0.1 amp + +### Model Versions + +#### Why Convert to NeuroML? + +The original models were implemented for the [NEURON simulator](https://www.neuron.yale.edu/neuron/). We have converted the model to NeuroML. The modular, XML nature of NeuroML allows to quickly re-use this model in network simulations and our tools allow [automated conversion to other supported simulator formats](https://neuroml.org/mappings). + +#### NeuroML Version + +All five cells have been implemented in NeuroML and match the output produced by the cells provided in the [original NEURON code](http://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=123623). + +#### XPP Version + +The Regular Spiking (RS) cell was also implemented in [XPP simulator](http://www.math.pitt.edu/~bard/xpp/xpp.html) to enable rapid debugging of parameter and other issues with the original models. + + +### Installation Instructions + +1. [Download the Model Files](archive/master.zip), or clone the repository using git: + +git clone https://github.com/OpenSourceBrain/PospischilEtAl2008.git + +2. [Follow instructions to Install jNeuroML](https://github.com/NeuroML/jNeuroML) for the **jnml** executable. On Windows, you may also need [SVN](https://subversion.apache.org/packages.html#windows). Alternatively install [PyNeuroML](https://github.com/NeuroML/pyNeuroML) for the **pynml** executable. +3. Set the $PATH and $JNML_HOME variables as described in [#2](https://github.com/NeuroML/jNeuroML) +4. Extract the model files to a folder. +5. For Figure 1: Change to NeuroML2/Figure1 folder. Type `jnml LEMS_Figure1C.xml` or `pynml LEMS_Figure1C.xml`. +6. For RS (and other cells): Change to NeuroML2/cells/RS (or other) folder. Type `jnml LEMS_RS.xml` or `pynml LEMS_RS.xml`. +7. Windows with the plotted figures should show up as can be seen below. + + +### Issues + +See Issues Tab for reported issues with the original model and the conversion. From bcb2eaf0ea2fc85ce47acc407aa7e981a9cd3429 Mon Sep 17 00:00:00 2001 From: Justas Birgiolas Date: Sun, 23 Aug 2015 15:10:59 -0700 Subject: [PATCH 10/14] Update README.md --- README.md | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 815ecab..4b52018 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@ #### Overview of the Model -[Pospischil, et. al. (2008)](http://link.springer.com/article/10.1007/s00422-008-0263-8) contains conductance-based ([Hodgin-Huxley](https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model)) models for four different classes of [cortical](https://en.wikipedia.org/wiki/Cerebral_cortex) and [thalamic](https://en.wikipedia.org/wiki/Thalamus) neurons. The classes represented are: +[Pospischil, et. al. (2008)](http://link.springer.com/article/10.1007/s00422-008-0263-8) describes conductance-based ([Hodgin-Huxley](https://en.wikipedia.org/wiki/Hodgkin%E2%80%93Huxley_model)) models of four different classes of [cortical](https://en.wikipedia.org/wiki/Cerebral_cortex) and [thalamic](https://en.wikipedia.org/wiki/Thalamus) neurons. The classes represented are: - Regular Spiking (RS) cells - Fast Spiking (FS) cells @@ -34,19 +34,24 @@ Specifically, these models demonstrate the following properties: **Regular Spiking** The use of INa and IKd currents and applying a constant input current is sufficient to generate a train of spikes with constant frequency. - +![RS](Regular Spiking.png) **Frequency Adaptation** In addition to INa and IKd currents, including the IM current will result in a train of spikes where the inter-spike interval increases (and frequency decreases) with each spike in the train. +![FA](Frequency adaptation.png) + **Intrinsic Bursting** When a calcium-dependent IL current is added to a cell with INa, IKd, and IM currents, the cell membrane potential will display an initial high-frequency burst of spikes and then settle onto a regular, frequency-adapting spiking behavior. The IL current makes use of variable Ca2+ reversal potential which is computed from the [Nernst equation](https://en.wikipedia.org/wiki/Nernst_equation) by tracking changes in the intracellular Ca2+ concentration. +![IB](Intrinsic bursting.png) + **Rebound Bursting** Similarly, using the calcium-dependent IT current instead of IL results in a cell that will fire a series of high-frequency spikes after a negative (hyperpolarizing) current is withdrawn from cell. +![Rebound](Rebound.png) Figure produced with NEURON_ORIG LTS Cell with gcabar_it = 0.0012 and input current -0.1 amp @@ -81,6 +86,6 @@ git clone https://github.com/OpenSourceBrain/PospischilEtAl2008.git ### Issues -See Issues Tab for reported issues with the original model and the conversion. +See [Issues Tab](issues) for reported issues with the original model and the conversion. From 19fbf2a06ccbd39c5d4b1e6385c573a3ba556937 Mon Sep 17 00:00:00 2001 From: Justas Birgiolas Date: Sun, 23 Aug 2015 15:12:09 -0700 Subject: [PATCH 11/14] Update README.md --- README.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/README.md b/README.md index 4b52018..e2a39d2 100644 --- a/README.md +++ b/README.md @@ -72,10 +72,7 @@ The Regular Spiking (RS) cell was also implemented in [XPP simulator](http://www ### Installation Instructions -1. [Download the Model Files](archive/master.zip), or clone the repository using git: - -git clone https://github.com/OpenSourceBrain/PospischilEtAl2008.git - +1. [Download the Model Files](archive/master.zip), or clone the repository using git: `git clone https://github.com/OpenSourceBrain/PospischilEtAl2008.git` 2. [Follow instructions to Install jNeuroML](https://github.com/NeuroML/jNeuroML) for the **jnml** executable. On Windows, you may also need [SVN](https://subversion.apache.org/packages.html#windows). Alternatively install [PyNeuroML](https://github.com/NeuroML/pyNeuroML) for the **pynml** executable. 3. Set the $PATH and $JNML_HOME variables as described in [#2](https://github.com/NeuroML/jNeuroML) 4. Extract the model files to a folder. From 4a89a040cc7c04e1cd62ab582e8625c289058617 Mon Sep 17 00:00:00 2001 From: JustasB Date: Sun, 23 Aug 2015 15:40:16 -0700 Subject: [PATCH 12/14] Folder Documentation --- NeuroML2/README.md | 7 +++++++ XPP/README.md | 5 +++++ 2 files changed, 12 insertions(+) create mode 100644 NeuroML2/README.md create mode 100644 XPP/README.md diff --git a/NeuroML2/README.md b/NeuroML2/README.md new file mode 100644 index 0000000..2c194d1 --- /dev/null +++ b/NeuroML2/README.md @@ -0,0 +1,7 @@ +This folder contains the NeuroML2 versions of the models. The folders contain the following: + +- cells: The 5 cells that were provided with the original NEURON code, implemented in NeuroML2 +- channels: All the ion channels used by the 5 cells +- figures: Figures from the paper that have been reproduced + +To run any of these models, find the LEMS_XYZ.xml files and run them via `jnml LEMS_XYZ.xml`. See [Installation Instructions](..) for more details. \ No newline at end of file diff --git a/XPP/README.md b/XPP/README.md new file mode 100644 index 0000000..b54ca66 --- /dev/null +++ b/XPP/README.md @@ -0,0 +1,5 @@ +This folder contains the XPP version of the RS (Regular Spiking) cell implementing Figure 1C from the paper. There are files for: + + - _fromFigure: This is the model that is using the parameters for Figure 1C as **described in the paper figure** + - _fromNEURON: Parameters as **described in the original NEURON code** + - _bestFit: A combination of parameters from paper, NEURON, **and as discovered through parameter search to find the best fit to the published figure** \ No newline at end of file From 4d6778c7c9698dc86b311194c3621d3059ed1578 Mon Sep 17 00:00:00 2001 From: Justas Birgiolas Date: Sun, 23 Aug 2015 15:43:20 -0700 Subject: [PATCH 13/14] Update README.md --- NeuroML2/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NeuroML2/README.md b/NeuroML2/README.md index 2c194d1..c4f92c1 100644 --- a/NeuroML2/README.md +++ b/NeuroML2/README.md @@ -4,4 +4,4 @@ This folder contains the NeuroML2 versions of the models. The folders contain th - channels: All the ion channels used by the 5 cells - figures: Figures from the paper that have been reproduced -To run any of these models, find the LEMS_XYZ.xml files and run them via `jnml LEMS_XYZ.xml`. See [Installation Instructions](..) for more details. \ No newline at end of file +To run any of these models, find the LEMS_XYZ.xml files and run them via `jnml LEMS_XYZ.xml`. See [Installation Instructions](https://github.com/OpenSourceBrain/PospischilEtAl2008) for more details. From 5bcc5add70ae1c2390c92082dccd4676a5bbf9c1 Mon Sep 17 00:00:00 2001 From: Justas Birgiolas Date: Sun, 23 Aug 2015 15:44:51 -0700 Subject: [PATCH 14/14] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index e2a39d2..8596081 100644 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ Similarly, using the calcium-dependent IT current instead of IL< ![Rebound](Rebound.png) -Figure produced with NEURON_ORIG LTS Cell with gcabar_it = 0.0012 and input current -0.1 amp +Figure produced with NEURON_ORIG LTS Cell with gcabar_it = 0.0012 and input current = -0.1 ### Model Versions