//genesis
function create_CaT
str path = "CaT_channel"
float xmin = -0.10 /* minimum voltage we will see in the simulation */ // V
float xmax = 0.05 /* maximum voltage we will see in the simulation */ // V
int xdivsFiner = 3000
int c = 0
float gMax = 1.0 // random number, but to be modified later
/****** Begin vars used to enable genesis calculations ********/
float increment = (xmax - xmin)*1e3/xdivsFiner // mV
echo "naF: increment" {increment} "mV"
float x = -100.00 // mV
float minf = 0
float hinf = 0
/*************************a1G*********************************************************/
float mvhalf = -59.0 // mV, McRory JE, et,al. 2001, Note: fixed with m^2
float mslope = 7.74 // mV, McRory JE, et,al. 2001
float hvhalf = -87.6 // mV, Hoehn,et,al 1993
float hslope = 6.1 // 6mV, Hoehn,et,al 1993
/*****************************************************************************************************/
/*******************************a1I*****************************************************/
//float mvhalf = -70.02 // mV, McRory JE, et,al. 2001, Note: fixed with m^2
// float mslope = 9.98 // mV, McRory JE, et,al. 2001
// float hvhalf = -93.2 // mV,
// float hslope = 4.7 // 6mV,
/******************************************************************************************************/
/************************************a1H************************************************/
// float mvhalf = -49.7 // mV, McRory JE, et,al. 2001, Note: fixed with m^2
// float mslope = 6.35 // mV, McRory JE, et,al. 2001
// float hvhalf = -73.6 // mV, a1H
// float hslope = 2.76 // a1H
/*********************************************************************************************************/
float mshift = 0.0 // mV
float hshift = 0.0 // mV
float taum = 0 // ms
float tauh = 0 // ms
/****** End vars used to enable genesis calculations **********/
pushe /library
create tabchannel {path}
call {path} TABCREATE X {xdivsFiner} {xmin} {xmax} // activation gate
call {path} TABCREATE Y {xdivsFiner} {xmin} {xmax} // inactivation gate
/* Defines the powers of m Hodgkin-Huxley equationref: Katja Hoehn, et,al. 1993 */
setfield {path} Ek {Erev} Xpower 2 Ypower 1
/********************* taken from Wolf's model************************************/
// set tau_m table
float qfactor = 3.0 // experiment was done in room temperature
create table CaT_taum // ms
call CaT_taum TABCREATE 30 {xmin} {xmax}
//the table corresponds to -100 mV to 50 mV
setfield CaT_taum table->table[0] 24.1 \
table->table[1] 24.1 \
table->table[2] 24.1 \
table->table[3] 24.1 \
table->table[4] 24.1 \
table->table[5] 24.1 \
table->table[6] 24.1 \
table->table[7] 24.1 \
table->table[8] 24.1 \
table->table[9] 13.1 \
table->table[10] 8.7 \
table->table[11] 6.8 \
table->table[12] 5.6 \
table->table[13] 4.4 \
table->table[14] 3.8 \
table->table[15] 3.6 \
table->table[16] 3.3 \
table->table[17] 3.6 \
table->table[18] 3.6 \
table->table[19] 3.3 \
table->table[20] 3.3 \
table->table[21] 3.3 \
table->table[22] 3.3 \
table->table[23] 3.3 \
table->table[24] 3.3 \
table->table[25] 3.3 \
table->table[26] 3.3 \
table->table[27] 3.3 \
table->table[28] 3.3 \
table->table[29] 3.3 \
table->table[30] 3.3
create table CaT_tauh
call CaT_tauh TABCREATE 30 {xmin} {xmax}
//the table corresponds to -100 mV to 50 mV
setfield CaT_tauh table->table[0] 382 \
table->table[1] 382 \
table->table[2] 382 \
table->table[3] 382 \
table->table[4] 382 \
table->table[5] 382 \
table->table[6] 382 \
table->table[7] 382 \
table->table[8] 208 \
table->table[9] 162 \
table->table[10] 129 \
table->table[11] 119 \
table->table[12] 107 \
table->table[13] 107 \
table->table[14] 107 \
table->table[15] 108 \
table->table[16] 109 \
table->table[17] 109 \
table->table[18] 110 \
table->table[19] 110 \
table->table[20] 110 \
table->table[21] 110 \
table->table[22] 110 \
table->table[23] 110 \
table->table[24] 110 \
table->table[25] 110 \
table->table[26] 110 \
table->table[27] 110 \
table->table[28] 110 \
table->table[29] 110 \
table->table[30] 110
call CaT_taum TABFILL {xdivsFiner} 2
call CaT_tauh TABFILL {xdivsFiner} 2
for(c = 0; c < {xdivsFiner} + 1; c = c + 1)
minf = 1/(1 + {exp {-(x - mvhalf + mshift)/mslope}})
hinf = 1/(1 + {exp {(x - hvhalf + hshift)/hslope}})
taum = {getfield CaT_taum table->table[{c}]}/qfactor
tauh = {getfield CaT_tauh table->table[{c}]}/qfactor
setfield {path} X_A->table[{c}] {2*taum*1e-3} // use m^2, the taum should X2, ref: Katja Hoehn, et,al. 1993
setfield {path} X_B->table[{c}] {minf}
setfield {path} Y_A->table[{c}] {tauh*1e-3}
setfield {path} Y_B->table[{c}] {hinf}
x = x + increment
end
/* fill the tables with the values of tau and minf/hinf
* calculated from tau and minf/hinf
*/
tweaktau {path} X
tweaktau {path} Y
create ghk {path}GHK
setfield {path}GHK Cout 2 // Carter & Sabatini 2004 uses 2mM,
// Wolf 5mM
setfield {path}GHK valency 2.0
setfield {path}GHK T {TEMPERATURE}
setfield {path} Gbar {gMax}
addmsg {path} {path}GHK PERMEABILITY Gk
end
/**************************************************************************************************
******************************* a1I subnuit******************************************
***************************************************************************************************
Ref: Molecular and Functional Characterization of a Family of Rat Brain T-type Calcium Channels
****************************************************by Kai DU, kaidu828@gmail.com****
***************************************************************************************************/
function create_CaV33
str path = "CaT33_channel"
int usingSingleGate = 0
float xmin = -0.10 /* minimum voltage we will see in the simulation */ // V
float xmax = 0.05 /* maximum voltage we will see in the simulation */ // V
int xdivsFiner = 3000
int c = 0
float gMax = 1.0 // random number, but to be modified later
/****** Begin vars used to enable genesis calculations ********/
float increment = (xmax - xmin)*1e3/xdivsFiner // mV
echo "naF: increment" {increment} "mV"
float x = -100.00 // mV
float minf = 0
float hinf = 0
float qfactor = 1 // experiment was done in room temperature
if({TEMPERATURE}>30)
qfactor = 3
end
/*******************************a1I*****************************************************/
if ({usingSingleGate}==1)
float mvhalf = -72.9 // mV, IFTINCA, et,al. 2006
float mslope = 4.6 // mV,
else
float mvhalf = -78.01 // mV, IFTINCA, et,al. 2006, Note: fixed with m^2
float mslope = 5.472 // mV,
end
float hvhalf = -78.3 // mV, IFTINCA, et,al. 2006
float hslope = 6.5 // 6mV,
/******************************************************************************************************/
// set tau_m table
create table CaV33_taum // ms
call CaV33_taum TABCREATE 15 {xmin} {xmax}
//the table corresponds to -100 mV to 50 mV
/*****************************************************/
// Mcrory,et,al.2001
// setfield CaV33_taum table->table[0] 24.1 \
// table->table[1] 24.1 \
// table->table[2] 24.1 \
// table->table[3] 24.1 \
// table->table[4] 24.1 \
// table->table[5] 24.1 \
// table->table[6] 24.1 \
// table->table[7] 24.1 \
// table->table[8] 24.1 \
// table->table[9] 13.1 \
// table->table[10] 8.7 \
// table->table[11] 6.8 \
// table->table[12] 5.6 \
// table->table[13] 4.4 \
// table->table[14] 3.8 \
// table->table[15] 3.6 \
// table->table[16] 3.3 \
// table->table[17] 3.6 \
// table->table[18] 3.6 \
// table->table[19] 3.3 \
// table->table[20] 3.3 \
// table->table[21] 3.3 \
// table->table[22] 3.3 \
// table->table[23] 3.3 \
// table->table[24] 3.3 \
// table->table[25] 3.3 \
// table->table[26] 3.3 \
// table->table[27] 3.3 \
// table->table[28] 3.3 \
// table->table[29] 3.3 \
// table->table[30] 3.3
setfield CaV33_taum table->table[0] 19.8 \
table->table[1] 19.8 \
table->table[2] 19.8 \
table->table[3] 19.8 \
table->table[4] 10.3 \
table->table[5] 7.66 \
table->table[6] 5.42 \
table->table[7] 4.36 \
table->table[8] 3.83 \
table->table[9] 3.4 \
table->table[10] 2.98 \
table->table[11] 2.13 \
table->table[12] 2.65 \
table->table[13] 2.65 \
table->table[14] 2.65 \
table->table[15] 2.65
create table CaV33_tauh
call CaV33_tauh TABCREATE 15 {xmin} {xmax}
//the table corresponds to -100 mV to 50 mV
// setfield CaV33_tauh table->table[0] 382 \
// table->table[1] 382 \
// table->table[2] 382 \
// table->table[3] 382 \
// table->table[4] 382 \
// table->table[5] 382 \
// table->table[6] 382 \
// table->table[7] 382 \
// table->table[8] 208 \
// table->table[9] 162 \
// table->table[10] 129 \
// table->table[11] 119 \
// table->table[12] 107 \
// table->table[13] 107 \
// table->table[14] 107 \
// table->table[15] 108 \
// table->table[16] 109 \
// table->table[17] 109 \
// table->table[18] 110 \
// table->table[19] 110 \
// table->table[20] 110 \
// table->table[21] 110 \
// table->table[22] 110 \
// table->table[23] 110 \
// table->table[24] 110 \
// table->table[25] 110 \
// table->table[26] 110 \
// table->table[27] 110 \
// table->table[28] 110 \
// table->table[29] 110 \
// table->table[30] 110
setfield CaV33_tauh table->table[0] 268.4 \
table->table[1] 268.4 \
table->table[2] 268.4 \
table->table[3] 268.4 \
table->table[4] 188.9 \
table->table[5] 145.6 \
table->table[6] 147.4 \
table->table[7] 141.8 \
table->table[8] 139.1 \
table->table[9] 142.27 \
table->table[10] 129.48 \
table->table[11] 119.57 \
table->table[12] 115.46 \
table->table[13] 115.46 \
table->table[14] 115.46 \
table->table[15] 115.46
call CaV33_taum TABFILL {xdivsFiner} 2
call CaV33_tauh TABFILL {xdivsFiner} 2
float mshift = 0 // mV
float hshift = 0 // mV
float taum = 0 // ms
float tauh = 0 // ms
/****** End vars used to enable genesis calculations **********/
pushe /library
create tabchannel {path}
call {path} TABCREATE X {xdivsFiner} {xmin} {xmax} // activation gate
call {path} TABCREATE Y {xdivsFiner} {xmin} {xmax} // inactivation gate
/* Defines the powers of m Hodgkin-Huxley equationref: Katja Hoehn, et,al. 1993 */
if ({usingSingleGate}==1)
setfield {path} Xpower 1 Ypower 1
else
setfield {path} Xpower 2 Ypower 1
end
/********************* taken from Wolf's model************************************/
// set tau_m table
for(c = 0; c < {xdivsFiner} + 1; c = c + 1)
minf = 1/(1 + {exp {-(x - mvhalf + mshift)/mslope}})
hinf = 1/(1 + {exp {(x - hvhalf + hshift)/hslope}})
taum = {getfield CaV33_taum table->table[{c}]}/qfactor
tauh = {getfield CaV33_tauh table->table[{c}]}/qfactor
if ({usingSingleGate}==1)
setfield {path} X_A->table[{c}] {taum*1e-3}
else
setfield {path} X_A->table[{c}] {2*taum*1e-3} // use m^2, the taum should X2, ref: Katja Hoehn, et,al. 1993
end
setfield {path} X_B->table[{c}] {minf}
setfield {path} Y_A->table[{c}] {tauh*1e-3}
setfield {path} Y_B->table[{c}] {hinf}
x = x + increment
end
/* fill the tables with the values of tau and minf/hinf
* calculated from tau and minf/hinf
*/
tweaktau {path} X
tweaktau {path} Y
create ghk {path}GHK
setfield {path}GHK Cin 0 Cout {Cout} // Carter & Sabatini 2004 uses 2mM,
// Wolf 5mM
setfield {path}GHK valency 2.0
setfield {path}GHK T {TEMPERATURE}
setfield {path} Gbar {gMax}
addmsg {path} {path}GHK PERMEABILITY Gk
end
/**************************************************************************************************
******************************* a1G subnuit******************************************
***************************************************************************************************
Ref: TEMPERATURE DEPENDENCE OF T-TYPE CALCIUM CHANNEL GATING, M. IFTINCA, et.al. 2006
****************************************************by Kai DU, kaidu828@gmail.com****
***************************************************************************************************/
function create_CaV32
int usingSingleGate = 1
str path = "CaT32_channel"
float xmin = -0.10 /* minimum voltage we will see in the simulation */ // V
float xmax = 0.05 /* maximum voltage we will see in the simulation */ // V
int xdivsFiner = 3000
int c = 0
float gMax = 0.0 // random number, but to be modified later
/****** Begin vars used to enable genesis calculations ********/
float increment = (xmax - xmin)*1e3/xdivsFiner // mV
echo "naF: increment" {increment} "mV"
float x = -100.00 // mV
float minf = 0
float hinf = 0
float qfactor = 1 // experiment was done in room temperature
if({TEMPERATURE}>30)
qfactor = 3
end
/*************************a1G*********************************************************/
if ({usingSingleGate}==1)
float mvhalf = -42.9 // mV,
float mslope = 6.2 // mV,
else
float mvhalf = -59.0 // mV, M. IFTINCA, et.al. 2006, Note: fixed with m^2
float mslope = 7.74 // mV, M. IFTINCA, et.al. 2006
end
float hvhalf = -64.2 // mV,
float hslope = 8.8 // 6mV,
float mshift = 5.0 // mV
float hshift = 5.0 // mV
float taum = 0 // ms
float tauh = 0 // ms
/*****************************************************************************************************/
/******************************************************************************************************/
pushe /library
create tabchannel {path}
call {path} TABCREATE X {xdivsFiner} {xmin} {xmax} // activation gate
call {path} TABCREATE Y {xdivsFiner} {xmin} {xmax} // inactivation gate
/* Defines the powers of m Hodgkin-Huxley equationref: Katja Hoehn, et,al. 1993 */
// setfield {path} Ek {Erev} Xpower 2 Ypower 1
// set tau_m table
create table CaV32_taum // ms
call CaV32_taum TABCREATE 15 {xmin} {xmax}
//the table corresponds to -100 mV to 50 mV
setfield CaV32_taum table->table[0] 24.1 \
table->table[1] 24.1 \
table->table[2] 24.1 \
table->table[3] 24.1 \
table->table[4] 12.76 \
table->table[5] 6.89 \
table->table[6] 3.95 \
table->table[7] 3.57 \
table->table[8] 2.04 \
table->table[9] 1.53 \
table->table[10] 1.53 \
table->table[11] 2.1 \
table->table[12] 2.04 \
table->table[13] 2.04 \
table->table[14] 2.04 \
table->table[15] 2.04
create table CaV32_tauh
call CaV32_tauh TABCREATE 15 {xmin} {xmax}
//the table corresponds to -100 mV to 50 mV
setfield CaV32_tauh table->table[0] 294 \
table->table[1] 294 \
table->table[2] 294 \
table->table[3] 294 \
table->table[4] 294 \
table->table[5] 104 \
table->table[6] 66.4 \
table->table[7] 60.08 \
table->table[8] 50.3 \
table->table[9] 40.4 \
table->table[10] 34.1 \
table->table[11] 32.9 \
table->table[12] 31.8 \
table->table[13] 31.8 \
table->table[14] 31.8 \
table->table[15] 31.8
call CaV32_taum TABFILL {xdivsFiner} 2
call CaV32_tauh TABFILL {xdivsFiner} 2
if ({usingSingleGate}==1)
setfield {path} Xpower 1 Ypower 1
else
setfield {path} Xpower 2 Ypower 1
end
/********************* taken from Wolf's model************************************/
// set tau_m table
for(c = 0; c < {xdivsFiner} + 1; c = c + 1)
minf = 1/(1 + {exp {-(x - mvhalf + mshift)/mslope}})
hinf = 1/(1 + {exp {(x - hvhalf + hshift)/hslope}})
taum = {getfield CaV32_taum table->table[{c}]}/qfactor
tauh = {getfield CaV32_tauh table->table[{c}]}/qfactor
if ({usingSingleGate}==1)
setfield {path} X_A->table[{c}] {taum*1e-3}
else
setfield {path} X_A->table[{c}] {2*taum*1e-3} // use m^2, the taum should X2, ref: Katja Hoehn, et,al. 1993
end
setfield {path} X_B->table[{c}] {minf}
setfield {path} Y_A->table[{c}] {tauh*1e-3}
setfield {path} Y_B->table[{c}] {hinf}
x = x + increment
end
/* fill the tables with the values of tau and minf/hinf
* calculated from tau and minf/hinf
*/
tweaktau {path} X
tweaktau {path} Y
create ghk {path}GHK
setfield {path}GHK Cout {Cout} // Carter & Sabatini 2004 uses 2mM,
// Wolf 5mM
setfield {path}GHK valency 2.0
setfield {path}GHK T {TEMPERATURE}
setfield {path} Gbar {gMax}
addmsg {path} {path}GHK PERMEABILITY Gk
end
