wormsim 0.0.1__py3-none-any.whl

wormsim/components/mechanism/modfile/gapjunction.mod

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+TITLE Gap junction current for parallel computation
+
+COMMENT
+Implemented by Erin Munro, 
+copied largely from:
+The NEURON Book by Nicholas T. Carnevale, Michael L. Hines
+online at Google books
+ENDCOMMENT
+
+
+UNITS { 
+	(mV) = (millivolt) 
+	(nA) = (nanoamp) 
+  (uS) = (microsiemens)
+} 
+
+
+NEURON { 
+    POINT_PROCESS gapjunction
+    POINTER vpre
+	  RANGE weight
+    RANGE i
+	  NONSPECIFIC_CURRENT i
+}
+
+
+PARAMETER { 
+	  weight = 0.0 	   (uS)
+} 
+
+
+ASSIGNED {
+    v (mV)
+    vpre (mV)
+    i (nA)
+}
+
+
+BREAKPOINT { 
+	  i = weight * (v - vpre) 
+} 

wormsim/components/mechanism/modfile/gapjunction_advance.mod

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+TITLE Gap junction current for parallel computation
+
+COMMENT
+Implemented by Erin Munro, 
+copied largely from:
+The NEURON Book by Nicholas T. Carnevale, Michael L. Hines
+online at Google books
+ENDCOMMENT
+
+
+UNITS { 
+	(mV) = (millivolt) 
+	(nA) = (nanoamp) 
+  (uS) = (microsiemens)
+} 
+
+
+NEURON { 
+    POINT_PROCESS gapjunction_advance
+	  RANGE weight, vpre
+    RANGE i
+	  NONSPECIFIC_CURRENT i
+}
+
+
+PARAMETER { 
+	  weight = 0.0 	   (uS)
+} 
+
+
+ASSIGNED {
+    v (mV)
+    vpre (mV)
+    i (nA)
+}
+
+
+BREAKPOINT { 
+	  i = weight * (v - vpre) 
+} 

wormsim/components/mechanism/modfile/inh_syn_advance.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 inh_syn_advance
+    NONSPECIFIC_CURRENT i
+    RANGE weight, conductance, vpre
+    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 = 0 (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/irk.mod

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+TITLE irk 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 irk
+    USEION k READ ek WRITE ik
+    RANGE gbirk, minf, tm, m
+}
+
+
+PARAMETER {
+    gbirk = 1 (nS/um2)
+    vhm = -82 (mV)
+    ka = 13 (mV)
+    atm = 17.1 (ms)
+    btm = -17.8 (mV)
+    ctm = 20.3 (mV)
+    dtm = -43.4 (mV)
+    etm = 11.2 (mV)
+    ftm = 3.8 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    tm (ms)
+}
+
+
+STATE {
+    m
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ik = gbirk * m * (v - ek)
+    ik = gbirk * m * (v + 80) : ek = -80
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / tm
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp((v - vhm) / ka))
+    tm = atm / (exp(-(v - btm) / ctm) + exp((v - dtm) / etm)) + ftm
+} 

wormsim/components/mechanism/modfile/kcnl.mod

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+TITLE kcnl current for C. elegans neuron model
+
+
+COMMENT
+channel type: calcium-related potassium channel
+
+regulated soly by calcium concentration in microdomain surrounding the 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)
+    (molar) = (1/liter)  : moles do not appear in units
+    (uM)    = (micromolar)
+}
+
+
+NEURON {
+    SUFFIX kcnl
+    USEION k READ ek WRITE ik
+    USEION ca READ cai
+    RANGE gbkcnl
+}
+
+
+PARAMETER {
+    : kcnl
+    gbkcnl = 1 (nS/um2)
+    kca = 0.33 (uM/um2)
+    a = 6.3 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    cai (uM/um2)
+    minf
+    tm (ms)
+}
+
+
+STATE {
+    m
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    ik = gbkcnl * m * (v + 80) : ek=-80
+}
+
+
+INITIAL {
+    setparames(v)
+    m = minf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    m' = (minf - m) / tm    
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = cai / (kca + cai)
+    tm = a
+}

wormsim/components/mechanism/modfile/kqt3.mod

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+TITLE kqt3 current for C. elegans neuron model
+
+
+COMMENT
+voltage-gated potassium channel
+ENDCOMMENT
+
+
+UNITS {
+    (nS) = (nanosiemens)
+    (mV) = (millivolt)
+    (pA) = (picoamp)
+    (um) = (micron)
+}
+
+
+NEURON {
+    SUFFIX kqt3
+    USEION k READ ek WRITE ik
+    RANGE gbkqt3, minf, tmf, tms, winf, sinf, tw, ts, mf, ms, w, s
+}
+
+
+PARAMETER {
+    gbkqt3 = 1 (nS/um2)
+    vhm = -12.6726 (mV)
+    ka = 15.8008 (mV)
+    vhw = -1.084 (mV)
+    kiw = 28.78 (mV)
+    aw = 0.49
+    bw = 0.51
+    vhs = -45.3 (mV)
+    kis = 12.3 (mV)
+    as = 0.34
+    bs =  0.66
+    atmf = 395.3 (ms)
+    btmf = 38.1 (mV)
+    ctmf = 33.59 (mV)
+    atms = 5503.0 (ms)
+    btms = -5345.4 (ms)
+    ctms = 0.02827 (1/mV)
+    dtms = -23.9 (mV)
+    etms = -4590.6 (ms)
+    ftms = 0.0357 (1/mV)
+    gtms = 14.15 (mV)
+    atw = 0.544 (ms)
+    btw = 29.2 (ms)
+    ctw = -48.09 (mV)
+    dtw = 48.83 (mV)
+    ats = 500e3 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    tmf (ms)
+    tms (ms)
+    winf
+    sinf
+    tw (ms)
+    ts (ms)
+}
+
+
+STATE {
+    mf
+    ms
+    w
+    s
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    ik = gbkqt3 * (0.3 * mf + 0.7 * ms) * w * s * (v - ek)
+    :ik = gbkqt3 * (0.3 * mf + 0.7 * ms) * (v + 80)
+    :ek = -80
+}
+
+
+INITIAL {
+    setparames(v)
+    mf = 0
+    ms = 0
+    w = winf
+    s = sinf
+}
+
+
+DERIVATIVE states {
+    setparames(v)
+    mf' = (minf - mf) / tmf
+    ms' = (minf - ms) / tms
+    w' = (winf - w) / tw
+    s' = (sinf - s) / ts
+}
+
+
+PROCEDURE setparames(v (mV)) {
+    minf = 1 / (1 + exp(-(v - vhm) / ka))
+    tmf = atmf / (1 + ((v + btmf) / ctmf) ^ 2)
+    tms = atms + btms / (1 + 10 ^ (-ctms * (dtms - v))) + etms / (1 + 10 ^ (-ftms * (gtms + v)))
+    winf = aw + bw / (1 + exp((v - vhw) / kiw))
+    sinf = as + bs / (1 + exp((v - vhs) / kis))
+    tw = (atw + btw / (1 + ((v - ctw) / dtw) ^ 2))
+    ts = ats
+}

wormsim/components/mechanism/modfile/kvs1.mod

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+TITLE kvs1 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 kvs1
+    USEION k READ ek WRITE ik
+    RANGE gbkvs1, minf, hinf, tm, th, m, h
+}
+
+
+PARAMETER {
+    gbkvs1 = 1 (nS/um2)
+    vhm = 57.1 (mV)
+    ka = 25.0 (mV)
+    vhh = 47.3 (mV)
+    ki = 11.1 (mV)
+    atm = 30.0 (ms)
+    btm = 18.1 (mV)
+    ctm = 20.0 (mV)
+    dtm = 1.0 (ms)
+    ath = 88.5 (ms)
+    bth = 50.0 (mV)
+    cth = 15.0 (mV)
+    dth = 53.4 (ms)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ek (mV)
+    ik (pA/um2)
+    minf
+    hinf
+    tm (ms)
+    th (ms)
+}
+
+
+STATE {
+    m
+    h
+}
+
+
+BREAKPOINT {
+    SOLVE states METHOD cnexp
+    :ik = gbkvs1 * m * h * (v - ek)
+    ik = gbkvs1 * 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 / (1 + exp((v - btm) / ctm)) + dtm
+    th = ath / (1 + exp((v - bth) / cth)) + dth
+} 

wormsim/components/mechanism/modfile/nca.mod

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+TITLE nca current for C. elegans neuron model
+
+
+COMMENT
+channel type: sodium passive currents
+
+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 nca
+    USEION na READ ena WRITE ina
+    RANGE gbnca
+}
+
+
+PARAMETER {
+    gbnca = 1 (nS/um2)
+}
+
+
+ASSIGNED {
+    v (mV)
+    ena (mV)
+    ina (pA/um2)
+}
+
+
+BREAKPOINT {
+    ina = gbnca * (v - 30)  :ena=30mV
+}

wormsim/components/mechanism/modfile/neuron_to_neuron_exc_syn.mod

@@ -0,0 +1,92 @@
+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_exc_syn
+    POINTER vpre
+    NONSPECIFIC_CURRENT i
+    RANGE weight, conductance, i
+    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 = 4.9E-4 (uS)
+    delta = 5 (mV)
+    k = 0.5 (kHz)
+    Vth = -20 (mV)
+    erev = 30 (mV) : -10
+}
+
+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
+}