//genesis
/******************************************************************************
** **
** PROTODEFS.G : prototype definition file, neuron builder kit. **
** **
** By U.S.Bhalla, June 1990 **
** **
** This file defines a library of prototype neuronal components. **
** It depends on the constants defined in the file 'constants.g' **
** The values set up here are derived from a variety of sources, **
** if no reference is cited the values are my informed guesses. **
** **
** The library is organised into a number of sections, (which are **
** implemented as children of suitably named 'neutral' elements). **
** This orgranisation is based on sources of data, on type of neuronal **
** module being specified, and whatever else took my fancy. To avoid **
** confusion I suggest that your additions to the library be placed in **
** new sections in a similar manner, i.e. children of a neutral with **
** a suitable name. We would be very glad to incorporate your additions **
** to the prototype library into the general distribution, so if you **
** feel like sharing your modules, send them over. **
** **
** All units are in SI (Meters Kilograms Seconds Amps). While this **
** does result in lots of powers of 10 in the parameters, it prevents **
** the chaos of interconversions when relating parameters of different **
** units. **
** **
** **
** **
******************************************************************************/
/******************************************************************************
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 :
addmsg /soma/hh_channel /soma CHANNEL Gk Ek
addmsg /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 :
addmsg /soma/channel /soma CHANNEL Gk Ek
addmsg /soma /soma/channel VOLTAGE Vm
addmsg /soma/channel/m /soma/channel {gate_type} m {Power}
(eg, addmsg Na_mitral/m Na_mitral MULTGATE m 3_
addmsg /soma /soma/channel/gate EREST Vm
*****************************************************************************/
create neutral /library
// 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
pushe /library
//========================================================================
// SYNAPTIC CHANNELS (Values guessed by Matt) (channelC2 from oldconn)
//========================================================================
create channelC2 glu
setfield glu Ek {ENA} tau1 {2.0e-3} tau2 {2.0e-3} \
gmax {DISTAL_GMAX_NA}
create channelC2 GABA
setfield GABA Ek {EK} tau1 {20.0e-3} tau2 {20.0e-3} gmax {GMAX_K}
create channelC2 inh_channel
setfield inh_channel Ek {EK} tau1 {100.0e-3} tau2 {100.0e-3} \
gmax {GMAX_K}
//========================================================================
// COMPARTMENTS
//========================================================================
create compartment compartment
setfield compartment Cm {{CM}*{SOMA_A}} Ra {{RA}*{SOMA_L}/{SOMA_XA}} \
Em {EREST_ACT} Rm {{RM}/{SOMA_A}} inject 0.0
create symcompartment symcompartment
setfield compartment Cm {{CM}*{SOMA_A}} Ra {{RA}*{SOMA_L}/{SOMA_XA}} \
Em {EREST_ACT} Rm {{RM}/{SOMA_A}} inject 0.0
//========================================================================
// Original Hodgkin-Huxley squid parameters, implemented as hh_channel elements
//========================================================================
//========================================================================
// ACTIVE SQUID NA CHANNEL
// A.L.Hodgkin and A.F.Huxley, J.Physiol(Lond) 117, pp 500-544 (1952)
//========================================================================
create hh_channel HH_Na_channel
setfield HH_Na_channel Ek {ENA_ACT} Gbar {1.2e3*{SOMA_A}} Xpower 3.0 \
Ypower 1.0 X_alpha_FORM {LINOID} X_alpha_A -0.1e6 X_alpha_B -0.010 \
X_alpha_V0 {0.025 + {EREST_ACT}} X_beta_FORM {EXPONENTIAL} \
X_beta_A 4.0e3 X_beta_B -18.0e-3 X_beta_V0 {0.0 + {EREST_ACT}} \
Y_alpha_FORM {EXPONENTIAL} Y_alpha_A 70.0 Y_alpha_B -20.0e-3 \
Y_alpha_V0 {0.0 + {EREST_ACT}} Y_beta_FORM {SIGMOID} Y_beta_A 1.0e3 \
Y_beta_B -10.0e-3 Y_beta_V0 {30.0e-3 + {EREST_ACT}}
//========================================================================
// ACTIVE K CHANNEL - SQUID
//========================================================================
create hh_channel HH_K_channel
setfield HH_K_channel Ek {EK} Gbar {360.0*{SOMA_A}} Xpower 4.0 \
Ypower 0.0 X_alpha_FORM {LINOID} X_alpha_A -10.0e3 \
X_alpha_B -10.0e-3 X_alpha_V0 {10.0e-3 + {EREST_ACT}} \
X_beta_FORM {EXPONENTIAL} X_beta_A 125.0 X_beta_B -80.0e-3 \
X_beta_V0 {0.0 + {EREST_ACT}}
//========================================================================
// Parameters used by my mitral and granule cell models for the olfactory
// bulb model. They are basically modified Traub params. These are also
// implemented as hh_channels.
//========================================================================
//========================================================================
// ACTIVE NA CHANNEL - MITRAL
//========================================================================
create hh_channel MHH_Na_channel
setfield MHH_Na_channel Ek {ENA_ACT} Gbar {1.2e3*{SOMA_A}} Xpower 3.0 \
Ypower 1.0 X_alpha_FORM {LINOID} X_alpha_A -0.32e6 X_alpha_B -0.004 \
X_alpha_V0 {0.013 + {EREST_ACT}} X_beta_FORM {LINOID} \
X_beta_A 0.28e6 X_beta_B 5.0e-3 X_beta_V0 {40.0e-3 + {EREST_ACT}} \
Y_alpha_FORM {EXPONENTIAL} Y_alpha_A 128.0 Y_alpha_B -18.0e-3 \
Y_alpha_V0 {0.017 + {EREST_ACT}} Y_beta_FORM {SIGMOID} \
Y_beta_A 4.0e3 Y_beta_B -5.0e-3 Y_beta_V0 {40.0e-3 + {EREST_ACT}}
//========================================================================
// ACTIVE NA CHANNEL - GRANULE CELL
//========================================================================
create hh_channel GHH_Na_channel
setfield GHH_Na_channel Ek {ENA_ACT} Gbar {1.2e3*{SOMA_A}} Xpower 3.0 \
Ypower 1.0 X_alpha_FORM {LINOID} X_alpha_A -0.32e6 X_alpha_B -0.004 \
X_alpha_V0 {0.013 + {EREST_ACT}} X_beta_FORM {LINOID} \
X_beta_A 0.28e6 X_beta_B 5.0e-3 X_beta_V0 {40.0e-3 + {EREST_ACT}} \
Y_alpha_FORM {EXPONENTIAL} Y_alpha_A 128.0 Y_alpha_B -18.0e-3 \
Y_alpha_V0 {0.017 + {EREST_ACT}} Y_beta_FORM {SIGMOID} \
Y_beta_A 4.0e3 Y_beta_B -5.0e-3 Y_beta_V0 {40.0e-3 + {EREST_ACT}}
//========================================================================
// ACTIVE CA CHANNEL - MITRAL
//========================================================================
create hh_channel MHH_Ca_channel
setfield MHH_Ca_channel \
Ek {ENA_ACT} \ // V
Gbar { 2.0e3 * SOMA_A } \ // S
Xpower 5.0 \
Ypower 0.0 \ // Dont want to deal with Ca conc yet.
X_alpha_FORM {LINOID} \
X_alpha_A -0.04e6 \ // 1/V-sec
X_alpha_B -0.010 \ // V
X_alpha_V0 { 0.060 + EREST_ACT } \ // V
X_beta_FORM {LINOID} \
X_beta_A 5.0e3 \ // 1/sec
X_beta_B 10.0e-3 \ // V
X_beta_V0 { 0.045 + EREST_ACT } \ // V
Y_alpha_FORM {EXPONENTIAL} \
Y_alpha_A 5e3 \ // 1/sec
Y_alpha_B 20.0e6 \ // V : we want to make Y a const here
Y_alpha_V0 { EREST_ACT } \ // V : Doesnt matter.
Y_beta_FORM {SIGMOID} \ // Messy : depends on Ca conc.
Y_beta_A 1.0e3 \ // 1/sec
Y_beta_B -10.0e-3 \ // V
Y_beta_V0 { 30.0e-3 + EREST_ACT } // V
//========================================================================
// ACTIVE K CHANNEL - MITRAL
//========================================================================
create hh_channel MHH_K_channel
setfield MHH_K_channel \
Ek {EK} \ // V
Gbar {360.0*SOMA_A} \ // S
Xpower 4.0 \
Ypower 0.0 \
X_alpha_FORM {LINOID} \
X_alpha_A -32.0e3 \ // 1/V-sec
X_alpha_B -5.0e-3 \ // V
X_alpha_V0 {0.015+EREST_ACT} \ // V
X_beta_FORM {EXPONENTIAL} \
X_beta_A 500.0 \ // 1/sec
X_beta_B -40.0e-3 \ // V
X_beta_V0 {0.010+EREST_ACT} \ // V
\ // this part cant work since Traub uses 2 exps to get the Y. So I set
\ // the Ypower to zero for now and ignore it. I need Vclamp data !
Y_alpha_FORM {EXPONENTIAL} \
Y_alpha_A 128.0 \ // 1/sec
Y_alpha_B -18.0e-3 \ // V
Y_alpha_V0 { 0.017 + EREST_ACT } \ // V
Y_beta_FORM {SIGMOID} \
Y_beta_A 4.0e3 \ // 1/sec
Y_beta_B -5.0e-3 \ // V
Y_beta_V0 { 40.0e-3 + EREST_ACT } // V
//========================================================================
// ACTIVE K CHANNEL - GRANULE CELL
//========================================================================
create hh_channel GHH_K_channel
setfield GHH_K_channel \
Ek {EK} \ // V
Gbar {360.0*SOMA_A} \ // S
Xpower 4.0 \
Ypower 0.0 \
X_alpha_FORM {LINOID} \
X_alpha_A -32.0e3 \ // 1/V-sec
X_alpha_B -5.0e-3 \ // V
X_alpha_V0 {0.015+EREST_ACT} \ // V
X_beta_FORM {EXPONENTIAL} \
X_beta_A 500.0 \ // 1/sec
X_beta_B -40.0e-3 \ // V
X_beta_V0 {0.010+EREST_ACT} \ // V
\ // this part cant work since Traub uses 2 exps to get the Y. So I set
\ // the Ypower to zero for now and ignore it. I need Vclamp data !
Y_alpha_FORM {EXPONENTIAL} \
Y_alpha_A 128.0 \ // 1/sec
Y_alpha_B -18.0e-3 \ // V
Y_alpha_V0 { 0.017 + EREST_ACT } \ // V
Y_beta_FORM {SIGMOID} \
Y_beta_A 4.0e3 \ // 1/sec
Y_beta_B -5.0e-3 \ // V
Y_beta_V0 { 40.0e-3 + EREST_ACT } // V
//========================================================================
// Miscellaneous things
//========================================================================
//========================================================================
// SPIKE DETECTOR - for use with channelC2
//========================================================================
create spike spike
setfield spike thresh -40e-3 abs_refract {10e-3} output_amp 1
//========================================================================
// Dendro-dendritic synapse
//========================================================================
create sigmoid sigmoid
setfield sigmoid \
amplitude 0.01 \ // Activation units ?
thresh -0.05 \ // V
gain 1 // dunno
//========================================================================
create graded graded
setfield graded \
baseline -0.05 \ // V
rectify 1 \ // Boolean
tmin 0.001 // Seconds
//========================================================================
create axonlink axonlink
//========================================================================
create linear linear
setfield linear \
tmin 0.001 \ // seconds
thresh -0.05 \ // V
gain 1 // dunno
//========================================================================
create diffamp diffamp
setfield diffamp plus 0.0 minus -0.07 gain 1.0 saturation 0.1
//========================================================================
// Voltage clamp circuit (from Mark Nelson, SQUID demo)
//========================================================================
create diffamp Vclamp
setfield ^ saturation 999.0 \ // unitless I hope
gain 0.002 // 1/R from the lowpass filter input
create RC Vclamp/lowpass
setfield ^ R 500.0 \ // ohms
C 0.1e-6 // Farads; for a tau of 50 us.
create PID Vclamp/PID
setfield ^ gain 1e-6 \ // 10/Rinput of cell
tau_i 20e-6 \ // seconds
tau_d 5e-6 \ // seconds
saturation 999.0 // unitless I hope
/*
addmsg dummy Vclamp/lowpass INJECT x // The voltage to clamp at
*/
addmsg Vclamp/lowpass Vclamp PLUS state
addmsg Vclamp Vclamp/PID CMD output
/*
addmsg {dend} Vclamp/PID SNS Vm // The fb from the dend
addmsg Vclamp/PID {dend} INJECT output // The current into the dend
*/
//========================================================================
/*
** dC/dt = B*I_Ca - C/tau
** Ca = Ca_base + C
*/
create Ca_concen conc
// sec
// molarity
setfield conc \
tau {SOMA_D/CA_DIFF} \ // sec
Ca_base {BASE_CA_CONC} \ // molarity
Ca \
B \
C \
activation
// Conc in moles/cubic meter, which happens to work out to mmol/L
// Number of moles of Ca per coulomb of Ca++ ions is 5.2e-6
//========================================================================
//========================================================================
// vdep_gate versions of the mitral cell channels
//========================================================================
//========================================================================
// Na Mitral cell channel
//========================================================================
create vdep_channel Na_mitral
setfield ^ Ek {ENA_ACT} gbar {1.2e3*{SOMA_A}} Ik 0 Gk 0
create vdep_gate Na_mitral/m
setfield ^ alpha_A {320e3*(0.013 + {EREST_ACT})} alpha_B -320e3 \
alpha_C -1.0 alpha_D {-1.0*(0.013 + {EREST_ACT})} \
alpha_F -0.004 beta_A {-280e3*(0.040 + {EREST_ACT})} \
beta_B 280e3 beta_C -1.0 beta_D {-1.0*(0.040 + {EREST_ACT})} \
beta_F 5.0e-3 instantaneous 0
create vdep_gate Na_mitral/h
setfield ^ alpha_A 128.0 alpha_B 0.0 alpha_C 0.0 \
alpha_D {-1.0*(0.017 + {EREST_ACT})} alpha_F 0.018 \
beta_A 4.0e3 beta_B 0.0 beta_C 1.0 \
beta_D {-1.0*(0.040 + {EREST_ACT})} beta_F -5.0e-3 \
instantaneous 0
addmsg Na_mitral/m Na_mitral MULTGATE m 3
addmsg Na_mitral/h Na_mitral MULTGATE m 1
//========================================================================
// K Mitral cell channel
//========================================================================
create vdep_channel K_mitral
setfield ^ Ek {EK} gbar {360.0*{SOMA_A}} Ik 0 Gk 0
create vdep_gate K_mitral/n
setfield ^ alpha_A {32.0e3*(0.015 + {EREST_ACT})} \
alpha_B -32.0e3 alpha_C -1.0 \
alpha_D {-1.0*(0.015 + {EREST_ACT})} alpha_F -0.005 \
beta_A 500.0 beta_B 0.0 beta_C 0.0 \
beta_D {-1.0*(0.010 + {EREST_ACT})} beta_F 40.0e-3 \
instantaneous 0
create vdep_gate K_mitral/y1
setfield ^ alpha_A 28.0 alpha_B 0.0 alpha_C 0.0 \
alpha_D {-1.0*(0.015 + {EREST_ACT})} alpha_F -0.015 \
beta_A 400.0 beta_B 0.0 beta_C 1.0 \
beta_D {-1.0*(0.040 + {EREST_ACT})} beta_F -0.01 \
instantaneous 0
create vdep_gate K_mitral/y2
setfield ^ alpha_A 2000.0 alpha_B 0.0 alpha_C 1.0 \
alpha_D {-1.0*(0.085 + {EREST_ACT})} alpha_F -0.010 \
beta_A 400.0 beta_B 0.0 beta_C 1.0 \
beta_D {-1.0*(0.040 + {EREST_ACT})} beta_F -0.01 \
instantaneous 0
addmsg K_mitral/n K_mitral MULTGATE m 4
/*
addmsg K_mitral/y1 K_mitral MULTGATE m 1
addmsg K_mitral/y2 K_mitral MULTGATE m 1
*/
//========================================================================
// Tabulated versions of the Traub set of channels
// From : R.D.Traub, Neuroscience Vol 7 No 5 pp 1233-1242 (1982)
//========================================================================
//========================================================================
// Tabulated Na Mitral cell channel
//========================================================================
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
create vdep_channel Na_t_mitral
// V
// S
// A
// S
setfield ^ Ek {ENA_ACT} gbar {1.2e3*{SOMA_A}} Ik 0 Gk 0
create tabgate Na_t_mitral/m
setup_table Na_t_mitral/m alpha 100 {320e3*(0.013 + {EREST_ACT})} -320e3 \
-1.0 {-1.0*(0.013 + {EREST_ACT})} -0.004
setup_table Na_t_mitral/m beta 100 {-280e3*(0.040 + {EREST_ACT})} 280e3 \
-1.0 {-1.0*(0.040 + {EREST_ACT})} 5.0e-3
create tabgate Na_t_mitral/h
setup_table Na_t_mitral/h alpha 100 128.0 0.0 0.0 \
{-1.0*(0.017 + {EREST_ACT})} 0.018
setup_table Na_t_mitral/h beta 100 4.0e3 0.0 1.0 \
{-1.0*(0.040 + {EREST_ACT})} -5.0e-3
addmsg Na_t_mitral/m Na_t_mitral MULTGATE m 3
addmsg Na_t_mitral/h Na_t_mitral MULTGATE m 1
//========================================================================
// Tabulated Ca Channel - mitral cell
//========================================================================
create vdep_channel Ca_t_mitral
setfield ^ Ek {ECA_ACT} gbar {1.2e3*{SOMA_A}} Ik 0 Gk 0
create tabgate Ca_t_mitral/s
setup_table Ca_t_mitral/s alpha 100 {40e3*(0.060 + {EREST_ACT})} -40e3 \
-1.0 {-1.0*(0.060 + {EREST_ACT})} -0.010
setup_table Ca_t_mitral/s beta 100 {-5e3*(0.045 + {EREST_ACT})} 5e3 -1.0 \
{-1.0*(0.045 + {EREST_ACT})} 10.0e-3
create tabgate Ca_t_mitral/r
call Ca_t_mitral/r TABCREATE alpha 1 -100 100
setfield Ca_t_mitral/r alpha->table[0] 5.0
setfield Ca_t_mitral/r alpha->table[1] 5.0
setup_table2 Ca_t_mitral/r beta 1000 -1 100 {25.0*200.0} -25.0 -1.0 \
-200.0 -20.0
create Ca_concen Ca_t_mitral/conc
setfield Ca_t_mitral/conc \
tau 0.01 \ // sec
B {5.2e-6/(SOMA_XA*SOMA_L)} \ // Current to conc
Ca_base 0.0
addmsg Ca_t_mitral/s Ca_t_mitral MULTGATE m 5
addmsg Ca_t_mitral/r Ca_t_mitral MULTGATE m 1
addmsg Ca_t_mitral/conc Ca_t_mitral/r VOLTAGE Ca
addmsg Ca_t_mitral Ca_t_mitral/conc I_Ca Ik
//========================================================================
// Tabulated K channel - Mitral cell
//========================================================================
create vdep_channel K_t_mitral
setfield ^ Ek {EK} gbar {360.0*{SOMA_A}} Ik 0 Gk 0
create tabgate K_t_mitral/n
setup_table K_t_mitral/n alpha 100 {32e3*(0.015 + {EREST_ACT})} -32e3 \
-1.0 {-1.0*(0.015 + {EREST_ACT})} -0.005
setup_table K_t_mitral/n beta 100 500.0 0.0 0.0 \
{-1.0*(0.010 + {EREST_ACT})} 40.0e-3
create table K_t_mitral/ya2
call K_t_mitral/ya2 TABCREATE 100 -0.1 0.1
setup_table3 K_t_mitral/ya2 table 100 -0.1 0.1 2000 0 1 \
{-1.0*(0.085 + {EREST_ACT})} -0.010
create tabgate K_t_mitral/y
setup_table K_t_mitral/y alpha 100 28 0 0 {-1.0*(0.015 + {EREST_ACT})} \
0.015
setup_table K_t_mitral/y beta 100 400 0 1 {-1.0*(0.040 + {EREST_ACT})} \
-0.010
addmsg K_t_mitral/n K_t_mitral MULTGATE m 4
addmsg K_t_mitral/y K_t_mitral MULTGATE m 1
addmsg K_t_mitral/ya2 K_t_mitral/y SUM_ALPHA output
//========================================================================
// Tabulated Ca dependent K - channel.
//========================================================================
create vdep_channel Kca_t_mitral
setfield ^ Ek {EK} gbar {360.0*{SOMA_A}} Ik 0 Gk 0
create table Kca_t_mitral/qv
call Kca_t_mitral/qv TABCREATE 100 -0.1 0.1
int i
float x, dx, y
x = -0.1
dx = 0.2/100.0
for (i = 0; i <= 100; i = i + 1)
y = {exp {(x - {EREST})/0.027}}
setfield Kca_t_mitral/qv table->table[{i}] {y}
x = x + dx
end
create tabgate Kca_t_mitral/qca
setup_table2 Kca_t_mitral/qca alpha 1000 -1 100 {5.0*200.0} -5.0 -1.0 \
-200.0 -20.0
call Kca_t_mitral/qca TABCREATE beta 1 -1 100
setfield Kca_t_mitral/qca beta->table[0] 2.0
setfield Kca_t_mitral/qca beta->table[1] 2.0
addmsg Kca_t_mitral/qv Kca_t_mitral/qca PRD_ALPHA output
addmsg Kca_t_mitral/qca Kca_t_mitral MULTGATE m 1
pope
//========================================================================