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//genesis - this file is obsolete
/***********************************************************************
LIBRARY.G : library definition file, neuron builder kit.
By U.S.Bhalla, Nov 1990
************************************************************************
Some conventions in using the HH_CHANNELS and the VDEP_GATES
HH_CONVENTIONS
==============
Activation state variable is called x for all channels
Inactivation state variable is called y for all channels
In the traditional hh notations: x=m, y=h for Na channel; x=n for K_channel
There are three functional forms for alpha and beta for each state variable:
FORM 1: alpha(v) = A exp((v-V0)/B) (EXPONENTIAL)
FORM 2: alpha(v) = A / (exp((v-V0)/B) + 1) (SIGMOID)
FORM 3: alpha(v) = A (v-V0) / (exp((v-V0)/B) - 1) (LINOID)
The same functional forms are used for beta.
In the simulator, the FORM, A, B and V0 are designated by:
X_alpha_FORM, X_alpha_A, X_alpha_B, X_alpha_V0 alpha function for state var x
X_beta_FORM, X_beta_A, X_beta_B, X_beta_V0 beta function for state var x
Y_alpha_FORM, Y_alpha_A, Y_alpha_B, Y_alpha_V0 alpha function for state var y
Y_beta_FORM, Y_beta_A, Y_beta_B, Y_beta_V0 beta function for state var y
The conductance is calculated as g = Gbar*x^Xpower * y^Ypower
For a squid axon Na channel: Xpower = 3, Ypower = 1 (m^3 h)
K channel: Xpower = 4, Ypower = 0 (n^4)
These are linked to the soma by two messages :
sendmsg /soma/hh_channel /soma CHANNEL Gk Ek
sendmsg /soma /soma/hh_channel VOLTAGE Vm
----------------------------------------------------------------------
For the VDEP Gates, the form of each gate is
alpha = (A+B*V)/(C+exp((V+D)/F))
This is related to the above forms as follows :
EXPONENTIAL :
gate variables Value of gate variable in terms of hh-channel variables
A A
B 0
C 0
D -V0
F -B
SIGMOID :
Gate in terms of hh-ch variables
A A
B 0
C 1
D -V0
F B
LINOID :
A -A * V0
B A
C -1
D -V0
F B
These are linked to the soma and the channel proper as follows :
sendmsg /soma/channel /soma CHANNEL Gk Ek
sendmsg /soma /soma/channel VOLTAGE Vm
sendmsg /soma/channel/m /soma/channel {gate_type} m {Power}
(eg, senndmsg Na_mitral/m Na_mitral MULTGATE m 3_
sendmsg /soma /soma/channel/gate EREST Vm
********************************************************************* ******/
/*
** VARIABLES USED BY ACTIVE COMPONENTS
*/
int EXPONENTIAL = 1
int SIGMOID = 2
int LINOID = 3
/*
** VARIABLES ASSUMED DEFINED BY CELL_PARSER
*/
// Farads/m^2
float CM = 0.01
// Ohms m
float RA = 0.5
// Ohms m^2
float RM = 0.2
// Volts
float EREST_ACT = -0.070
/*********************************************************************** \
******/
if (!({exists /library}))
create neutral /library
end
// We dont want the library to try to calculate anything,
// so we disable it
disable /library
// To ensure that all subsequent elements are made in the library
ce /library
// The only 'permanent' element in the library needs to be the compartment
if (!({exists compartment}))
create compartment compartment
end
// F
// ohm
// V
// ohm
setfield compartment Cm {CM*1e-9} Ra {RA*1e5} Em {EREST_ACT} \
Rm {RM/1e-9} inject 0.0
function setup_table3(gate, table, xdivs, xmin, xmax, A, B, C, D, F)
str gate, table
int xdivs
float xmin, xmax, A, B, C, D, F
int i
float x, dx, y
dx = xdivs
dx = (xmax - xmin)/dx
x = xmin
for (i = 0; i <= (xdivs); i = i + 1)
y = (A + B*x)/(C + ({exp {(x + D)/F}}))
setfield {gate} {table}->table[{i}] {y}
x = x + dx
end
end
function setup_table2(gate, table, xdivs, xmin, xmax, A, B, C, D, F)
str gate, table
int xdivs
float xmin, xmax, A, B, C, D, F
if (xdivs <= 9)
echo must have at least 9, preferably over 100 elements \
in table
return
end
call {gate} TABCREATE {table} {xdivs} {xmin} {xmax}
setup_table3 {gate} {table} {xdivs} {xmin} {xmax} {A} {B} {C} \
{D} {F}
end
function setup_table(gate, table, xdivs, A, B, C, D, F)
str gate, table
int xdivs
float A, B, C, D, F
setup_table2 {gate} {table} {xdivs} -0.1 0.1 {A} {B} {C} {D} {F}
end
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