Improving the Standardized Channel Template

[r-makarov]

Help us improve the ion channel MOD file template! 🧬

DendroTweaks uses a standardized template for generating voltage-dependent ion channel MOD files, making it easier to maintain consistent channel kinetics across models. We'd love your input on how to make this template even better.

We use Jinja templating to automatically generate MOD files with standardized equations. You can learn more about the standardization approach in our tutorial.

You can view our current standardized channel template here.

Here's an example of a voltage-dependent potassium channel generated from the original file using this template.

TITLE standardized stdKv channel

COMMENT
Standardized and templated by DendroTweaks.
This NMODL file defines a model for a k ion channel.
ENDCOMMENT

NEURON {
    SUFFIX stdKv
    
    USEION k READ ek WRITE ik
    
    RANGE gbar, i, vhalf_n, sigma_n, k_n, delta_n, tau0_n, gbar, q10, temp
}

UNITS {
    (mA) = (milliamp)
	(mV) = (millivolt)
	(S)  = (siemens)
	(um) = (micron)
}

PARAMETER {
    vhalf_n = 14.164 (mV)
    sigma_n = 9.0 (mV)
    k_n     = 0.123 (1/ms)
    delta_n = 0.732 (1)
    tau0_n  = 0.877 (ms)
    gbar    = 0.0 (S/cm2)
    q10     = 2.3 (1)
    temp    = 23 (degC)
}

ASSIGNED {
    v        (mV)     : membrane voltage
    i        (mA/cm2) : current density
    ik       (mA/cm2) : current density of k ion
    gk       (S/cm2)  : conductance of k ion
    ek       (mV)     : reversal potential of k ion
    
    n_inf    (1)      : steady state value of n
    tau_n    (ms)     : time constant of n
    
    tadj     (1)      : temperature adjustment factor
    celsius  (degC)   : simulation temperature in celsius
}

STATE { n }

BREAKPOINT {
    SOLVE states METHOD cnexp
    gk = tadj * gbar * n
    i = gk * (v - ek) 
    ik = i
}

DERIVATIVE states {
    rates(v)
    n' = (n_inf - n) / tau_n
    
}

INITIAL {
    tadj = q10^((celsius - temp)/10(degC))
    rates(v)
    n = n_inf
    
}


FUNCTION alpha_prime(v (mV), k (1/ms), delta (1), vhalf (mV), sigma (mV)) (1/ms) {
    alpha_prime = k * exp(delta * (v - vhalf) / sigma)
}

FUNCTION beta_prime(v (mV), k (1/ms), delta (1), vhalf (mV), sigma (mV)) (1/ms) {
    beta_prime = k * exp(-(1 - delta) * (v - vhalf) / sigma)
}                

PROCEDURE rates(v(mV)) {
    LOCAL alpha_n, beta_n

    
    n_inf = 1 / (1 + exp(-(v - vhalf_n) / sigma_n))
    alpha_n = alpha_prime(v, k_n, delta_n, vhalf_n, sigma_n)
    beta_n = beta_prime(v, k_n, delta_n, vhalf_n, sigma_n)
    tau_n = (1 / (alpha_n + beta_n) + tau0_n) / tadj
    
    
}

If you think the template could be better structured, documented, etc. please leave your feedback here.

[ramcdougal]

The first line of the units block here is invented with spaces. The rest of the lines in that block are invented with tabs. Consider doing four spaces throughout.