wormsim 0.0.1__py3-none-any.whl

wormsim/components/mechanism/modfile/neuron_to_neuron_inh_syn.mod

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+COMMENT
+Based on NMODL code for neuron_to_neuron_exc_syn
+
+Code and comments have been normalized--that is,
+they are now of the usual form employed in 
+NMODL-specified synaptic mechanisms.
+
+Oddities that save neither storage nor time, 
+or preclude use with adaptive integration, 
+or deliberately introduce errors in an attempt
+to save a few CPU cycles, have been removed.
+
+Unused variables and parameters have also been removed.
+
+vpre is now a POINTER.
+
+In the INITIAL block, the completely unnecessary repeat
+execution of procedure rates() has been removed, 
+and the state variable s is now set to the correct 
+initial value.
+
+The value of the current i is now calculated in the
+BREAKPOINT block, instead of being calculated as a 
+side-effect of calling rates().
+ENDCOMMENT
+
+TITLE excitatory to excitatory synapse
+
+NEURON {
+    POINT_PROCESS neuron_to_neuron_inh_syn
+    POINTER vpre
+    NONSPECIFIC_CURRENT i
+    RANGE weight, conductance
+    RANGE delta, k, Vth, erev
+}
+
+UNITS {
+    (nA) = (nanoamp)
+    (uA) = (microamp)
+    (mA) = (milliamp)
+    (A) = (amp)
+    (mV) = (millivolt)
+    (mS) = (millisiemens)
+    (uS) = (microsiemens)
+    (molar) = (1/liter)
+    (kHz) = (kilohertz)
+    (mM) = (millimolar)
+    (um) = (micrometer)
+    (umol) = (micromole)
+    (S) = (siemens)
+}
+
+PARAMETER {
+    weight = 1
+    conductance = 2.0E-4 (uS)
+    delta = 5 (mV)
+    k = 0.015000001 (kHz)
+    Vth = -20 (mV)
+    erev = -70 (mV)
+}
+
+ASSIGNED {
+    v (mV)
+    vpre (mV)
+    inf
+    tau (ms)
+    i (nA)
+}
+
+STATE {
+    s  
+}
+
+INITIAL {
+    rates()
+    s = inf : NTC original code did not properly initialize s
+}
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    i = weight * conductance * s * (v - erev)
+}
+
+DERIVATIVE states {
+    rates()
+    s' = (inf - s)/tau
+}
+
+PROCEDURE rates() {
+    inf = 1/( 1 + exp((Vth - vpre)/delta) )
+    tau = (1 - inf)/k
+}

wormsim/components/mechanism/modfile/shk1.mod

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+TITLE shk1 current for C. elegans neuron model
+
+
+COMMENT
+channel type: voltage-gated potassium channel
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX shk1
+    USEION k READ ek WRITE ik
+    RANGE gbshk1, minf, hinf, tm, th, m, h
+}
+
+
+PARAMETER {
+    gbshk1 = 1 (nS/um2)
+    vhm = 20.4 (mV)
+    ka = 7.7 (mV)
+    vhh = -7.0 (mV)
+    ki = 5.8 (mV)
+    atm = 26.6 (ms)
+    btm = -33.7 (mV)
+    ctm = 15.8 (mV)
+    dtm = -33.7 (mV)
+    etm = 15.4 (mV)
+    ftm = 2.0 (ms)
+    ath = 1400 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    hinf
+    tm (ms)
+    th (ms)
+}
+
+
+STATE {
+    m
+    h
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ik = gbshk1 * m * h * (v - ek)
+    ik = gbshk1 * m * h * (v + 80) : ek=-80
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+    h = hinf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / tm
+    h' = (hinf - h) / th
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp(-(v - vhm) / ka))
+    hinf = 1 / (1 + exp((v - vhh) / ki))
+    tm = atm / (exp(- (v - btm) / ctm) + exp((v - dtm) / etm)) + ftm
+    th = ath
+} 

wormsim/components/mechanism/modfile/shl1.mod

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+TITLE shl1 current for C. elegans neuron model
+
+
+COMMENT
+channel type: voltage-gated potassium channel
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    :(mA) = (milliamp)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX shl1
+    USEION k READ ek WRITE ik
+    RANGE gbshl1, minf, hfinf, hsinf, tm, thf, ths, m, hf, hs
+}
+
+
+PARAMETER {
+    gbshl1 = 1 (nS/um2)
+    vhm = 11.2 (mV)
+    ka = 14.1 (mV)
+    vhh = -33.1 (mV)
+    ki = 8.3 (mV)
+    atm = 13.8 (ms)
+    btm = -17.5 (mV)
+    ctm = 12.9 (mV)
+    dtm = -3.7 (mV)
+    etm = 6.5 (mV)
+    ftm = 1.9 (ms)
+    athf = 539.2 (ms)
+    bthf = -28.2 (mV)
+    cthf = 4.9 (mV)
+    dthf = 27.3 (ms)
+    aths = 8422.0 (ms)
+    bths = -37.7 (mV)
+    cths = 6.4 (mV)
+    dths = 118.9 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2) :(mA/cm2)
+    minf
+    hfinf
+    hsinf
+    tm (ms)
+    thf (ms)
+    ths (ms)
+}
+
+
+STATE {
+    m
+    hf
+    hs
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ik = gbshl1 * m * m * m * (0.7 * hf + 0.3 * hs) * (v - ek)
+    ik = gbshl1 * m * m * m * (0.7 * hf + 0.3 * hs) * (v + 80) : ek = -80
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+    hf = hfinf
+    hs = hsinf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / (tm*0.4)
+    hf' = (hfinf - hf) / (thf*0.08)
+    hs' = (hsinf - hs) / (ths*0.3)
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp(-(v - vhm) / ka))
+    hfinf = 1 / (1 + exp((v - vhh) / ki))
+    hsinf = 1 / (1 + exp((v - vhh) / ki))
+    tm = atm / (exp(-(v - btm) / ctm) + exp((v - dtm) / etm)) + ftm
+    thf = athf / (1 + exp((v - bthf) / cthf)) + dthf
+    ths = aths / (1 + exp((v - bths) / cths)) + dths
+} 

wormsim/components/mechanism/modfile/slo1_egl19.mod

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+TITLE slo1 current for C. elegans neuron model (suppose to interact with egl19)
+
+
+COMMENT
+channel type: calcium-related potassium channel
+
+slo1-egl19 1:1 stoichiometry
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+    (molar) = (1/liter)  : moles do not appear in units
+    (uM) = (micromolar)
+}
+
+
+NEURON {
+    SUFFIX slo1_egl19
+    USEION k READ ek WRITE ik
+    RANGE gbslo1, minf, tm, mcavinf, tmcav, hcavinf, thcav, m, hcav, mcav
+}
+
+
+PARAMETER {
+    : slo1
+    gbslo1 = 1 (nS/um2)
+    wyx = 0.013 (1/mV)
+    wxy = -0.028 (1/mV)
+    wom = 3.15 (1/ms)
+    wop = 0.16 (1/ms)
+    kxy = 55.73 (uM/um2)
+    nxy = 1.30
+    kyx = 34.34 (uM/um2)
+    nyx = 0.0001
+    canci = 0.05 (uM/um2) : calcium concentration When the calcium channel is closed
+
+    : egl19
+    vhm = 5.6 (mV)
+    ka = 7.5 (mV)
+    vhh = 24.9 (mV)
+    ki = 12.0 (mV)
+    vhhb = -20.5 (mV)
+    kib = 8.1 (mV)
+    ahinf = 1.43
+    bhinf = 0.14
+    chinf = 5.96
+    dhinf = 0.60
+    atm = 2.9 (ms)
+    btm = 5.2 (mV)
+    ctm = 6.0 (mV)
+    dtm = 1.9 (ms)
+    etm = 1.4 (mV)
+    ftm = 30.0 (mV)
+    gtm = 2.3 (ms)
+    ath = 0.4
+    bth = 44.6 (ms)
+    cth = -23.0 (mV)
+    dth = 5.0 (mV)
+    eth = 36.4 (ms)
+    fth = 28.7 (mV)
+    gth = 3.7 (mV)
+    hth = 43.1 (ms)
+
+    : cain
+    FARADAY = 96485 (coul) : moles do not appear in units
+	gsc = 0.04 (nS)   : single channel conductance, assumed equal to 40 pS for both L-type and P/Qtype calcium channels
+    r = 0.013 (um)       : radius of the nanodomain
+    dca = 250 (um2/s) : calcium diffusion coefficient
+    kb = 500 (1/uM/s) : intracellular buffer rate constant
+    btot = 30 (uM)    : total intracellular buffer concentration
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    tm (ms)
+    mcavinf
+    tmcav (ms)
+    hcavinf
+    thcav (ms)
+}
+
+
+STATE {
+    m
+    hcav
+    mcav
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    ik = gbslo1 * m * hcav * (v + 80) : ek=-80
+}
+
+
+INITIAL {
+    setparames(v)
+    hcav = hcavinf
+    mcav = mcavinf
+    m = 0
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    mcav' = (mcavinf - mcav) / tmcav
+    hcav' = (hcavinf - hcav) / thcav
+    m' = (minf - m) / tm    
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    LOCAL alpha, beta, wm, wp, fm, fp, kom, kop, kcm, cain
+    : egl19 model
+    mcavinf = 1 / (1 + exp(-(v - vhm) / ka))
+    hcavinf = (ahinf / (1 + exp(-(v - vhh) / ki)) + bhinf) * (chinf / (1 + exp((v - vhhb) / kib)) + dhinf)
+    tmcav = atm * exp(-((v - btm) / ctm) ^ 2) + dtm * exp(-((v - etm) / ftm) ^ 2) + gtm
+    thcav = ath * ((bth / (1 + exp((v - cth) / dth))) + (eth / (1 + exp((v - fth) / gth))) + hth)
+    : cain
+    if (v < 60) {
+        cain = -gsc * (v - 60) * 10^9 / (8 * 3.1415926 * r * dca * FARADAY) * exp (-r / sqrt(dca / (kb * btot)))
+    } else {
+        cain = 0.0001
+    }
+    : slo1-egl19 model
+    alpha = mcavinf / tmcav
+    beta = 1 / tmcav - alpha
+    wm = wom * exp(-wyx * v)
+    wp = wop * exp(-wxy * v)
+    fm = 1 / (1 + (cain / kyx) ^ nyx)
+    fp = 1 / (1 + (kxy / cain) ^ nxy)
+    kom = wm * fm
+    kop = wp * fp
+    kcm = wm * 1 / (1 + (canci / kyx) ^ nyx)
+    minf = mcav * kop * (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+    tm = (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+}

wormsim/components/mechanism/modfile/slo1_unc2.mod

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+TITLE slo1 current for C. elegans neuron model (suppose to interact with unc2)
+
+
+COMMENT
+channel type: calcium-related potassium channel
+
+slo1-unc2 1:1 stoichiometry
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+    (molar) = (1/liter)  : moles do not appear in units
+    (uM) = (micromolar)
+}
+
+
+NEURON {
+    SUFFIX slo1_unc2
+    USEION k READ ek WRITE ik
+    RANGE gbslo1, minf, tm, mcavinf, tmcav, hcavinf, thcav, m, hcav, mcav
+}
+
+
+PARAMETER {
+    : slo1
+    gbslo1 = 1 (nS/um2)
+    wyx = 0.013 (1/mV)
+    wxy = -0.028 (1/mV)
+    wom = 3.15 (1/ms)
+    wop = 0.16 (1/ms)
+    kxy = 55.73 (uM/um3)
+    nxy = 1.30
+    kyx = 34.34 (uM/um3)
+    nyx = 0.0001
+    canci = 0.05 (uM/um2) : calcium concentration When the calcium channel is closed
+
+    : unc2
+    vhm = -12.2 (mV)
+    ka = 4.0 (mV)
+    vhh = -52.5 (mV)
+    ki = 5.6 (mV)
+    atm = 1.5 (ms)
+    btm = -8.2 (mV)
+    ctm = 9.1 (mV)
+    dtm = 15.4 (mV)
+    etm = 0.1 (ms)
+    ath = 83.8 (ms)
+    bth = 52.9 (mV)
+    cth = -3.5 (mV)
+    dth = 72.1 (ms)
+    eth = 23.9 (mV)
+    fth = -3.6 (mV)
+
+    : cain
+    FARADAY = 96485 (coul) : moles do not appear in units
+	gsc = 0.04 (nS)   : single channel conductance, assumed equal to 40 pS for both L-type and P/Qtype calcium channels
+    r = 0.013 (um)       : radius of the nanodomain
+    dca = 250 (um2/s) : calcium diffusion coefficient
+    kb = 500 (1/uM/s) : intracellular buffer rate constant
+    btot = 30 (uM)    : total intracellular buffer concentration
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    tm (ms)
+    mcavinf
+    tmcav (ms)
+    hcavinf
+    thcav (ms)
+}
+
+
+STATE {
+    m
+    hcav
+    mcav
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    ik = gbslo1 * m * hcav * (v + 80) : ek=-80
+}
+
+
+INITIAL {
+    setparames(v)
+    hcav = hcavinf
+    mcav = mcavinf
+    m = 0
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    mcav' = (mcavinf - mcav) / tmcav
+    hcav' = (hcavinf - hcav) / thcav
+    m' = (minf - m) / tm    
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    LOCAL alpha, beta, wm, wp, fm, fp, kom, kop, kcm, cain
+    : unc2 model
+    mcavinf = 1 / (1 + exp(-(v - vhm) / ka))
+    hcavinf = 1 / (1 + exp((v - vhh) / ki))
+    tmcav = atm / (exp(-(v - btm) / ctm) + exp((v - btm) / dtm)) + etm
+    thcav = ath / (1 + exp(-(v - bth) / cth)) + dth / (1 + exp((v - eth) / fth))
+    : cain
+    cain = -gsc * (v - 60) * 10^9 / (8 * 3.1415926 * r * dca * FARADAY) * exp (-r / sqrt(dca / (kb * btot)))
+    if (v < 60) {
+        cain = -gsc * (v - 60) * 10^9 / (8 * 3.1415926 * r * dca * FARADAY) * exp (-r / sqrt(dca / (kb * btot)))
+    } else {
+        cain = 0.0001
+    }
+    : slo1-unc2 model
+    alpha = mcavinf / tmcav
+    beta = 1 / tmcav - alpha
+    wm = wom * exp(-wyx * v)
+    wp = wop * exp(-wxy * v)
+    fm = 1 / (1 + (cain / kyx) ^ nyx)
+    fp = 1 / (1 + (kxy / cain) ^ nxy)
+    kom = wm * fm
+    kop = wp * fp
+    kcm = wm * 1 / (1 + (canci / kyx) ^ nyx)
+    minf = mcav * kop * (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+    tm = (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+}

wormsim/components/mechanism/modfile/slo2_egl19.mod

@@ -0,0 +1,148 @@
+TITLE slo2 current for C. elegans neuron model (suppose to interact with egl19)
+
+
+COMMENT
+channel type: calcium-related potassium channel
+
+slo2-egl19 1:1 stoichiometry
+
+model and parameters from:
+Nicoletti, M., et al. (2019). "Biophysical modeling of C. elegans neurons: Single ion currents and whole-cell dynamics of AWCon and RMD." PLoS One 14(7): e0218738.
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+    (molar) = (1/liter)  : moles do not appear in units
+    (uM) = (micromolar)
+}
+
+
+NEURON {
+    SUFFIX slo2_egl19
+    USEION k READ ek WRITE ik
+    RANGE gbslo2, minf, tm, mcavinf, tmcav, hcavinf, thcav, m, hcav, mcav
+}
+
+
+PARAMETER {
+    : slo2
+    gbslo2 = 1 (nS/um2)
+    wyx = 0.019 (1/mV)
+    wxy = -0.024 (1/mV)
+    wom = 0.90 (1/ms)
+    wop = 0.027 (1/ms)
+    kxy = 93.45 (uM/um2)
+    nxy = 1.84
+    kyx = 3294.55 (uM/um2)
+    nyx = 0.00001
+    canci = 0.05 (uM/um2) : calcium concentration When the calcium channel is closed
+
+    : egl19
+    vhm = 5.6 (mV)
+    ka = 7.5 (mV)
+    vhh = 24.9 (mV)
+    ki = 12.0 (mV)
+    vhhb = -20.5 (mV)
+    kib = 8.1 (mV)
+    ahinf = 1.43
+    bhinf = 0.14
+    chinf = 5.96
+    dhinf = 0.60
+    atm = 2.9 (ms)
+    btm = 5.2 (mV)
+    ctm = 6.0 (mV)
+    dtm = 1.9 (ms)
+    etm = 1.4 (mV)
+    ftm = 30.0 (mV)
+    gtm = 2.3 (ms)
+    ath = 0.4
+    bth = 44.6 (ms)
+    cth = -23.0 (mV)
+    dth = 5.0 (mV)
+    eth = 36.4 (ms)
+    fth = 28.7 (mV)
+    gth = 3.7 (mV)
+    hth = 43.1 (ms)
+
+    : cain
+    FARADAY = 96485 (coul) : moles do not appear in units
+	gsc = 0.04 (nS)   : single channel conductance, assumed equal to 40 pS for both L-type and P/Qtype calcium channels
+    r = 0.013 (um)       : radius of the nanodomain
+    dca = 250 (um2/s) : calcium diffusion coefficient
+    kb = 500 (1/uM/s) : intracellular buffer rate constant
+    btot = 30 (uM)    : total intracellular buffer concentration
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    tm (ms)
+    mcavinf
+    tmcav (ms)
+    hcavinf
+    thcav (ms)
+}
+
+
+STATE {
+    m
+    hcav
+    mcav
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    ik = gbslo2 * m * hcav * (v + 80) : ek=-80
+}
+
+
+INITIAL {
+    setparames(v)
+    hcav = hcavinf
+    mcav = mcavinf
+    m = minf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    mcav' = (mcavinf - mcav) / tmcav
+    hcav' = (hcavinf - hcav) / thcav
+    m' = (minf - m) / tm    
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    LOCAL alpha, beta, wm, wp, fm, fp, kom, kop, kcm, cain
+    : egl19 model
+    mcavinf = 1 / (1 + exp(-(v - vhm) / ka))
+    hcavinf = (ahinf / (1 + exp(-(v - vhh) / ki)) + bhinf) * (chinf / (1 + exp((v - vhhb) / kib)) + dhinf)
+    tmcav = atm * exp(-((v - btm) / ctm) ^ 2) + dtm * exp(-((v - etm) / ftm) ^ 2) + gtm
+    thcav = ath * ((bth / (1 + exp((v - cth) / dth))) + (eth / (1 + exp((v - fth) / gth))) + hth)
+    : cain
+    if (v < 60) {
+        cain = -gsc * (v - 60) * 10^9 / (8 * 3.1415926 * r * dca * FARADAY) * exp (-r / sqrt(dca / (kb * btot)))
+    } else {
+        cain = 0.0001
+    }
+    : slo2-egl19 model
+    alpha = mcavinf / tmcav
+    beta = 1 / tmcav - alpha
+    wm = wom * exp(-wyx * v)
+    wp = wop * exp(-wxy * v)
+    fm = 1 / (1 + (cain / kyx) ^ nyx)
+    fp = 1 / (1 + (kxy / cain) ^ nxy)
+    kom = wm * fm
+    kop = wp * fp
+    kcm = wm * 1 / (1 + (canci / kyx) ^ nyx)
+    minf = mcav * kop * (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+    tm = (alpha + beta + kcm) / ((kop + kom) * (kcm + alpha) + beta * kcm)
+}