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Regenerated mods with latets neuroml libraries
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@pgleeson
pgleeson committed Sep 21, 2023
1 parent 94f4f29 commit 7095501
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49 changes: 21 additions & 28 deletions examples/NeuroMLImport/RS.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,17 +3,17 @@ TITLE Mod file for component: Component(id=RS type=izhikevich2007Cell)
COMMENT

This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.9.0
org.neuroml.model v1.9.0
jLEMS v0.10.7
org.neuroml.export v1.9.1
org.neuroml.model v1.9.1
jLEMS v0.10.8

ENDCOMMENT

NEURON {
POINT_PROCESS RS


NONSPECIFIC_CURRENT i : To ensure v of section follows v_I
NONSPECIFIC_CURRENT i : To ensure v of section follows v_I
RANGE v0 : parameter
RANGE k : parameter
RANGE vr : parameter
Expand All @@ -24,13 +24,9 @@ NEURON {
RANGE c : parameter
RANGE d : parameter
RANGE C : parameter

RANGE iSyn : exposure

RANGE iMemb : exposure

RANGE copy_v : copy of v on section

}

UNITS {
Expand All @@ -42,47 +38,45 @@ UNITS {
(mV) = (millivolt)
(mS) = (millisiemens)
(uS) = (microsiemens)
(nF) = (nanofarad)
(molar) = (1/liter)
(kHz) = (kilohertz)
(mM) = (millimolar)
(um) = (micrometer)
(umol) = (micromole)
(pC) = (picocoulomb)
(S) = (siemens)

}

PARAMETER {

v0 = -60 (mV)
k = 7.0E-4 (uS / mV)
vr = -60 (mV)
vt = -40 (mV)
vpeak = 35 (mV)
a = 0.030000001 (kHz)
b = -0.002 (uS)
c = -50 (mV)
d = 0.1 (nA)
C = 1.0E-4 (microfarads)
v0 = -60 (mV) : was: -0.06 (voltage)
k = 7.0E-4 (uS / mV) : was: 7.0E-7 (conductance_per_voltage)
vr = -60 (mV) : was: -0.06 (voltage)
vt = -40 (mV) : was: -0.04 (voltage)
vpeak = 35 (mV) : was: 0.035 (voltage)
a = 0.030000001 (kHz) : was: 30.0 (per_time)
b = -0.002 (uS) : was: -2.0E-9 (conductance)
c = -50 (mV) : was: -0.05 (voltage)
d = 0.1 (nA) : was: 1.0E-10 (current)
C = 0.1 (nF) : was: 1.0E-10 (capacitance)
}

ASSIGNED {
v (mV)
i (mA/cm2)

copy_v (mV)

v_I (nA)

iSyn (nA) : derived variable
i (nA) : the point process current

iMemb (nA) : derived variable
v_I (mV/ms) : for rate of change of voltage
iSyn (nA) : derived variable
iMemb (nA) : derived variable
rate_v (mV/ms)
rate_u (nA/ms)

}

STATE {
u (nA)
u (nA) : dimension: current

}

Expand All @@ -101,7 +95,6 @@ BREAKPOINT {
SOLVE states METHOD cnexp


copy_v = v
i = v_I * C
}

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53 changes: 24 additions & 29 deletions examples/NeuroMLImport/poissonFiringSyn.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=poissonFiringSyn type=poissonFiringSy
COMMENT

This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.9.0
org.neuroml.model v1.9.0
jLEMS v0.10.7
org.neuroml.export v1.9.1
org.neuroml.model v1.9.1
jLEMS v0.10.8

ENDCOMMENT

Expand All @@ -16,17 +16,14 @@ NEURON {
RANGE averageRate : parameter
RANGE averageIsi : parameter
RANGE SMALL_TIME : parameter

RANGE i : exposure
RANGE syn0_tauRise : parameter
RANGE syn0_tauDecay : parameter
RANGE syn0_peakTime : parameter
RANGE syn0_waveformFactor : parameter
RANGE syn0_gbase : parameter
RANGE syn0_erev : parameter

RANGE syn0_g : exposure

RANGE syn0_i : exposure
RANGE iSyn : derived variable
: Based on netstim.mod
Expand All @@ -43,40 +40,38 @@ UNITS {
(mV) = (millivolt)
(mS) = (millisiemens)
(uS) = (microsiemens)
(nF) = (nanofarad)
(molar) = (1/liter)
(kHz) = (kilohertz)
(mM) = (millimolar)
(um) = (micrometer)
(umol) = (micromole)
(pC) = (picocoulomb)
(S) = (siemens)

}

PARAMETER {

weight = 1
averageRate = 0.05 (kHz)
averageIsi = 20 (ms)
SMALL_TIME = 1.0E-9 (ms)
syn0_tauRise = 0.5 (ms)
syn0_tauDecay = 10 (ms)
syn0_peakTime = 1.5767012 (ms)
syn0_waveformFactor = 1.2324
syn0_gbase = 0.002 (uS)
syn0_erev = 0 (mV)
averageRate = 0.05 (kHz) : was: 50.0 (per_time)
averageIsi = 20 (ms) : was: 0.02 (time)
SMALL_TIME = 1.0E-9 (ms) : was: 1.0000000000000002E-12 (time)
syn0_tauRise = 0.5 (ms) : was: 5.0E-4 (time)
syn0_tauDecay = 10 (ms) : was: 0.01 (time)
syn0_peakTime = 1.5767012 (ms) : was: 0.0015767011966073639 (time)
syn0_waveformFactor = 1.2324 : was: 1.232399909181873 (none)
syn0_gbase = 0.002 (uS) : was: 2.0E-9 (conductance)
syn0_erev = 0 (mV) : was: 0.0 (voltage)
}

ASSIGNED {
v (mV)
isi (ms) : Not a state variable as far as Neuron's concerned...

syn0_g (uS) : derived variable

syn0_i (nA) : derived variable

iSyn (nA) : derived variable

i (nA) : derived variable
isi (ms) : Not a state variable as far as Neuron's concerned...
syn0_g (uS) : derived variable
syn0_i (nA) : derived variable
iSyn (nA) : derived variable
i (nA) : derived variable
rate_tsince (ms/ms)
rate_tnextUsed (ms/ms)
rate_tnextIdeal (ms/ms)
Expand All @@ -86,11 +81,11 @@ ASSIGNED {
}

STATE {
tsince (ms)
tnextIdeal (ms)
tnextUsed (ms)
syn0_A
syn0_B
tsince (ms) : dimension: time
tnextIdeal (ms) : dimension: time
tnextUsed (ms) : dimension: time
syn0_A : dimension: none
syn0_B : dimension: none

}

Expand Down
32 changes: 15 additions & 17 deletions examples/NeuroMLImport/syn0.mod
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Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ TITLE Mod file for component: Component(id=syn0 type=expTwoSynapse)
COMMENT

This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
org.neuroml.export v1.9.0
org.neuroml.model v1.9.0
jLEMS v0.10.7
org.neuroml.export v1.9.1
org.neuroml.model v1.9.1
jLEMS v0.10.8

ENDCOMMENT

Expand All @@ -17,9 +17,7 @@ NEURON {
RANGE waveformFactor : parameter
RANGE gbase : parameter
RANGE erev : parameter

RANGE g : exposure

RANGE i : exposure


Expand All @@ -36,42 +34,42 @@ UNITS {
(mV) = (millivolt)
(mS) = (millisiemens)
(uS) = (microsiemens)
(nF) = (nanofarad)
(molar) = (1/liter)
(kHz) = (kilohertz)
(mM) = (millimolar)
(um) = (micrometer)
(umol) = (micromole)
(pC) = (picocoulomb)
(S) = (siemens)

}

PARAMETER {

tauRise = 0.5 (ms)
tauDecay = 10 (ms)
peakTime = 1.5767012 (ms)
waveformFactor = 1.2324
gbase = 0.002 (uS)
erev = 0 (mV)
tauRise = 0.5 (ms) : was: 5.0E-4 (time)
tauDecay = 10 (ms) : was: 0.01 (time)
peakTime = 1.5767012 (ms) : was: 0.0015767011966073639 (time)
waveformFactor = 1.2324 : was: 1.232399909181873 (none)
gbase = 0.002 (uS) : was: 2.0E-9 (conductance)
erev = 0 (mV) : was: 0.0 (voltage)
}

ASSIGNED {
? Standard Assigned variables with baseSynapse
v (mV)
celsius (degC)
temperature (K)

g (uS) : derived variable

i (nA) : derived variable
g (uS) : derived variable
i (nA) : derived variable
rate_A (/ms)
rate_B (/ms)

}

STATE {
A
B
A : dimension: none
B : dimension: none

}

Expand Down

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