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"initial version"
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@tommorse
tommorse committed May 31, 2019
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127 changes: 127 additions & 0 deletions BuffersNPumps.ses
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{load_file("nrngui.hoc")}
objectvar save_window_, rvp_, g1, g2, g3, g4, g5, g6, g7, g8, g9
objectvar scene_vector_[11]
objectvar ocbox_, ocbox_list_, scene_, scene_list_
{ocbox_list_ = new List() scene_list_ = new List()}
{pwman_place(0,0,0)}
{
save_window_ = new Graph(0)
g1 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,0,2e-3)
scene_vector_[2] = save_window_
{save_window_.view(0, 0, 2000, 2e-3, 477, 10, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.color(4)
save_window_.addvar("[Ca2+]=0.5uM", "dend[0].cai(.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[Ca2+]=1uM", "dend[1].cai(.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[Ca2+]=2uM", "dend[2].cai(.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g2 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,15e-3,26e-3)
scene_vector_[3] = save_window_
{save_window_.view(0, 15e-3, 2000, 11e-3, 877, 10, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("[PV.Ca]", "dend[0].PV_ca_cdp3[0](0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[PV.Ca]", "dend[1].PV_ca_cdp3[0](0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[PV.Ca]", "dend[2].PV_ca_cdp3[0](0.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g3 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,10e-3,20e-3)
scene_vector_[4] = save_window_
{save_window_.view(0, 10e-3, 2000, 10e-3, 1277, 10, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("[CB.f.Ca]", "dend[0].CB_f_ca_cdp3[0](0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[CB.f.Ca]", "dend[1].CB_f_ca_cdp3[0](0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[CB.f.Ca]", "dend[2].CB_f_ca_cdp3[0](0.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g4 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,0,40e-3)
scene_vector_[5] = save_window_
{save_window_.view(0, 0, 2000, 40e-3, 477, 330, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("[CB.Ca.s]", "dend[0].CB_ca_s_cdp3[0](0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[CB.Ca.s]", "dend[1].CB_ca_s_cdp3[0](0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[CB.Ca.s]", "dend[2].CB_ca_s_cdp3[0](0.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g5 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,0,6e-3)
scene_vector_[6] = save_window_
{save_window_.view(0, 0, 2000, 6e-3, 877, 330, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("[CB.Ca.Ca]", "dend[0].CB_ca_ca_cdp3[0](0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[CB.Ca.Ca]", "dend[1].CB_ca_ca_cdp3[0](0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[CB.Ca.Ca]", "dend[2].CB_ca_ca_cdp3[0](0.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g6 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,2e-3,6e-3)
scene_vector_[7] = save_window_
{save_window_.view(0, 2e-3, 2000, 4e-3, 1277, 330, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("[iCB.f.Ca]", "dend[0].iCB_f_ca_cdp3[0](0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[iCB.f.Ca]", "dend[1].iCB_f_ca_cdp3[0](0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[iCB.f.Ca]", "dend[2].iCB_f_ca_cdp3[0](0.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g7 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,0,15e-3)
scene_vector_[8] = save_window_
{save_window_.view(0, 0, 2000, 15e-3, 477, 650, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("[iCB.Ca.s]", "dend[0].iCB_ca_s_cdp3[0](0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[iCB.Ca.s]", "dend[1].iCB_ca_s_cdp3[0](0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[iCB.Ca.s]", "dend[2].iCB_ca_s_cdp3[0](0.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g8 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,0,4e-3)
scene_vector_[9] = save_window_
{save_window_.view(0, 0, 2000, 4e-3, 877, 650, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("[iCB.Ca.Ca]", "dend[0].iCB_ca_ca_cdp3[0](0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("[iCB.Ca.Ca]", "dend[1].iCB_ca_ca_cdp3[0](0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("[iCB.Ca.Ca]", "dend[2].iCB_ca_ca_cdp3[0](0.5)", 4, 1, 0.7, 0.9, 2)
}

{
save_window_ = new Graph(0)
g9 = save_window_ // so that View = plot can be made
save_window_.size(0,2000,0,0.8e-5)
scene_vector_[10] = save_window_
{save_window_.view(0, 0, 2000, 0.8e-5, 1277, 650, 400, 240)}
graphList[0].append(save_window_)
save_window_.save_name("graphList[0].")
save_window_.addvar("ica_pump", "dend[0].ica_pmp_cdp3(0.5)", 3, 1, 0.7, 0.9, 2)
save_window_.addvar("ica_pump", "dend[1].ica_pmp_cdp3(0.5)", 2, 1, 0.7, 0.9, 2)
save_window_.addvar("ica_pump", "dend[2].ica_pmp_cdp3(0.5)", 4, 1, 0.7, 0.9, 2)
}

objectvar scene_vector_[1]
{doNotify()}

54 changes: 54 additions & 0 deletions CALC.mod
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TITLE Cerebellum Golgi Cell Model

COMMENT
Calcium first order kinetics

Author: A. Fontana
Revised: 12.12.98

Adapted by: Haroon Anwar ([email protected])

ENDCOMMENT

NEURON {
SUFFIX CALC
USEION ca READ ica, cao WRITE cai
RANGE d, beta, cai0
}

UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
(um) = (micron)
(molar) = (1/liter)
(mM) = (millimolar)
F = (faraday) (coulomb)
}

PARAMETER {
ica (mA/cm2)
celsius (degC)
d = .2 (um)
cao = 2. (mM)
cai0 = 45e-6 (mM)
beta = 1.3 (/ms)
}

STATE {
cai (mM)
}

INITIAL {
cai = cai0
}

BREAKPOINT {
SOLVE conc METHOD derivimplicit
}

DERIVATIVE conc {
: total outward Ca current
cai' = -ica/(2*F*d)*(1e4) - beta*(cai-cai0)
}


55 changes: 55 additions & 0 deletions CALC_DP.mod
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TITLE Cerebellum Golgi Cell Model

COMMENT
Calcium first order kinetics

Author: A. Fontana
Revised: 12.12.98

Adapted by: Haroon Anwar ([email protected])

ENDCOMMENT

NEURON {
SUFFIX CALC_DP
USEION ca READ ica, cao WRITE cai
USEION ca2 READ ica2 VALENCE 2
RANGE d, beta, cai0
}

UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
(um) = (micron)
(molar) = (1/liter)
(mM) = (millimolar)
F = (faraday) (coulomb)
}

PARAMETER {
ica (mA/cm2)
ica2 (mA/cm2)
celsius (degC)
d = .2 (um)
cao = 2. (mM)
cai0 = 45e-6 (mM)
beta = 1.3 (/ms)
}

STATE {
cai (mM)
}

INITIAL {
cai = cai0
}

BREAKPOINT {
SOLVE conc METHOD derivimplicit
}

DERIVATIVE conc {
cai' = -(ica+ica2)/(2*F*d)*(1e4) - beta*(cai-cai0)
}


54 changes: 54 additions & 0 deletions CALC_ca2_DP.mod
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TITLE Cerebellum Golgi Cell Model

COMMENT
Calcium first order kinetics

Author: A. Fontana
Revised: 12.12.98

Adapted by: Haroon Anwar ([email protected])

ENDCOMMENT

NEURON {
SUFFIX CALC2
USEION ca READ ica
USEION ca2 READ ica2 WRITE ca2i VALENCE 2
RANGE d, beta, ca2i0
}

UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
(um) = (micron)
(molar) = (1/liter)
(mM) = (millimolar)
F = (faraday) (coulomb)
}

PARAMETER {
ica (mA/cm2)
ica2 (mA/cm2)
celsius (degC)
d = .2 (um)
ca2i0 (mM)
beta = 1.3 (/ms)
}

STATE {
ca2i (mM)
}

INITIAL {
ca2i = ca2i0
}

BREAKPOINT {
SOLVE conc METHOD derivimplicit
}

DERIVATIVE conc {
ca2i' = -(ica+ica2)/(2*F*d)*(1e4) - beta*(ca2i-ca2i0)
}


22 changes: 22 additions & 0 deletions CaBufferingModels.hoc
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load_file("nrngui.hoc")

xpanel("Calcium Buffering Models")
xbutton("Detailed Calcium dynamics model","restart(\"runDM\")")
xbutton("Calcium transients using different buffering models","restart(\"runCaTransients\")")
xbutton("Calcium spikes using single pool model","restart(\"runCaSpikesSP\")")
xbutton("Calcium spikes using double pool model","restart(\"runCaSpikesDP\")")
xbutton("Calcium spikes using detailed model","restart(\"runCaSpikesDM\")")
xbutton("Calcium spikes using DCM","restart(\"runCaSpikesDCM\")")
xpanel(5,100)

pwmcnt = PWManager[0].count // the initial gui should not be dismissed

proc restart() {local i
for (i= PWManager[0].count-1; i >= pwmcnt; i -= 1) {
PWManager[0].close(i)
doNotify()
}
sprint(tstr, "%s.hoc", $s1)
load_file(1, tstr)
}

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