//genesis
/*************************** MS Model, Version 5.2 *********************
**************************** naP_channel.g *********************
Tom Sheehan tsheeha2@gmu.edu thsheeha@vt.edu 703-538-8361
******************************************************************************
******************************************************************************/
/* Na Persistent channel
* In the original program written by Johanes Hjorth a set of MatLab
* routines in striatum/mspn/vectMakers opened a set of text (data) files in
* striatum/mspn/tau_tables and used those to create a set of of text (data)
* files in striatum/mspn/channels/vecs.
* The product of this sequence was then opened by a set of genesis
* routines in striatum/mspn/channels to populate an approprite set of tabchannels
* An example is as follows
* striatum/mspn/vectMakers/makeNaPtable.m reads:
* striatum/mspn/tau_tables/vtau_nap.txt
* and then writes:
* striatum/mspn/channels/vecs/nap_taum.txt
* striatum/mspn/channels/vecs/nap_tauh.txt
* striatum/mspn/channels/vecs/nap_minf.txt
* striatum/mspn/channels/vecs/nap_hinf.txt
* Later in the running code control shifts to function make_NaP_channel
* (in striatum/mspn/channels/naP_channel.g). This function will read those
* same four files and use them to create the tabchannel NaP_channel
*
* In the rework by Kai_Du the MatLab files are remeoved but their product (the
* four data files noted above are retained.
*
* This revision moves the MatLab calculations to the .g file that is creating
* the tabchannel and removes the data files (four for each channel). In the example
* case given above directory vecs has been deleted which removes nap_taum.txt etc,
* and function make_NaP_channel has been modified to calculate the data in those
* files and place it directly into the appropritate tabchannel
*************** Tom Sheehan 1/10/09 703-538-8361********************************/
function make_NaP_channel
/*reversal potential of sodium */
float Erev = 0.05
str path = "NaP_channel"
float xmin = -0.1 /* minimum voltage we will see in the simulation */
float xmax = 0.05 /* maximum voltage we will see in the simulation */
int xdivs = 14 /* the number of divisions between -0.1 and 0.04 */
int xdivsFiner = 3000
int c = 0
float minf = 0
float hinf = 0
float htau = 0
float mtau = 0
/* Begin values from Hjorth: striatum/mspn/vectMakers/makeNaPtable.m */
float mvhalf = -52.6 //(mV) Magistretti 1999, Fig 4
float mslope = -4.6 //(mV) Magistretti 1999, Fig 4
float mshift = 0.0
float hvhalf = -48.8 //(mV) Magistretti 1999, Fig 4
float hslope = 10.0 //(mV) Magistretti 1999, Fig 4
float hshift = 0.0
/** End values from Hjorth: striatum/mspn/vectMakers/makeNaPtable.m **/
/****** Begin vars used to enable genesis calculations ********/
float increment = 0.05
float x = -100.00
float numerator = 0.0
float denominator = 0.0
float theta = 0.0
float exp_theta = 0.0
float neg_one = -1.0
/****** End vars used to enable genesis calculations **********/
//make the table for the activation with a range of -100mV - +40mV
//with an entry for every 10mV
create tabchannel {path}
call {path} TABCREATE X {xdivsFiner} {xmin} {xmax}
call {path} TABCREATE Y {xdivsFiner} {xmin} {xmax}
// calculate values for minf, mtau, hinf and htau. Each iteration of the for
// loop calculates those values using an x that begins with -100 and increments
// by 0.05 with each loop
for(c = 0; c < {xdivsFiner} + 1; c = c + 1)
//The equation for htau is a basic fit of the original curve from Johanes
//Matlab function found in striatum/mspn/vectMakers/makeNaPtable.m
htau = -3.4566e-008*x*x*x*x -4.7314e-007*x*x*x + 0.00025297*x*x -0.0087294*x + 0.77324
//calculate Hodgkin Huxley hinf -> 1/(1 + exp(x - mvhalf + mshift)/mslope)
numerator = x - hvhalf + hshift
theta = numerator/hslope
exp_theta = {exp {theta}}
denominator = 1.0 + exp_theta
hinf = 1.0/denominator
//calculate Hodgkin Huxley minf -> 1/(1 + exp(x - mvhalf + mshift)/mslope)
numerator = x - mvhalf + mshift
theta = numerator/mslope
exp_theta = {exp {theta}}
denominator = 1.0 + exp_theta
minf = 1.0/denominator
//The equation for mtau is an exact fit of the original curve from Johanes
//Matlab function found in striatum/mspn/vectMakers/makeNaPtable.m
if (c < 1410)
//mtau = (0.025 + 0.14*exp((x + 40.0) / 10))
numerator = x + 40.0
theta = numerator/10
exp_theta = {exp {theta}}
mtau = 0.025 + 0.14 * {exp_theta}
mtau = 1e-3 * mtau
else
//mtau = (0.02 + 0.145*exp( -(x + 40.0)) / 10))
numerator = x + 40.0
numerator = neg_one * numerator
theta = numerator/10
exp_theta = {exp {theta}}
mtau = 0.025 + 0.145 * {exp_theta}
mtau = 1e-3 * mtau
end
setfield {path} Y_A->table[{c}] {htau}
setfield {path} Y_B->table[{c}] {hinf}
setfield {path} X_A->table[{c}] {mtau}
setfield {path} X_B->table[{c}] {minf}
x = x + increment
end
//Define the powers of m and h in the Hodgkin-Huxley equation
setfield {path} Ek {Erev} Xpower 1 Ypower 1
//fill the tables with the values of A and B
//calculated from tau and n_inf
tweaktau {path} X
tweaktau {path} Y
end
| 
