diff --git a/NEURON/CaClamp.mod b/NEURON/CaClamp.mod
new file mode 100644
index 0000000..16bba61
--- /dev/null
+++ b/NEURON/CaClamp.mod
@@ -0,0 +1,114 @@
+TITLE Mod file for component: Component(id=CaClamp type=caClamp)
+
+COMMENT
+
+ This NEURON file has been generated by org.neuroml.export (see https://github.com/NeuroML/org.neuroml.export)
+ org.neuroml.export v1.4.3
+ org.neuroml.model v1.4.3
+ jLEMS v0.9.8.1
+
+ENDCOMMENT
+
+NEURON {
+ SUFFIX CaClamp
+ USEION ca READ cai, cao, ica WRITE cai VALENCE 2
+ RANGE cai
+ RANGE cao
+ GLOBAL initialConcentration
+ GLOBAL initialExtConcentration
+ RANGE conc0 : parameter
+ RANGE conc1 : parameter
+ RANGE delay : parameter
+ RANGE duration : parameter
+
+}
+
+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 {
+ surfaceArea (um2)
+ iCa (nA)
+ initialConcentration (mM)
+ initialExtConcentration (mM)
+
+ conc0 = 5.0E-5 (mM)
+ conc1 = 0.005 (mM)
+ delay = 200 (ms)
+ duration = 200 (ms)
+}
+
+ASSIGNED {
+ cai (mM)
+ cao (mM)
+ ica (mA/cm2)
+ diam (um)
+ area (um2)
+
+}
+
+STATE {
+ concentration (mM)
+ extConcentration (mM)
+
+}
+
+INITIAL {
+ initialConcentration = cai
+ initialExtConcentration = cao
+ rates()
+ rates() ? To ensure correct initialisation.
+
+ concentration = initialConcentration
+
+ extConcentration = initialExtConcentration
+
+}
+
+BREAKPOINT {
+
+ rates()
+ if (t <= delay) {
+ concentration = conc0 ? standard OnCondition
+ }
+
+ if (t >= delay && t <= duration + delay) {
+ concentration = conc1 ? standard OnCondition
+ }
+
+ if (t >= duration + delay) {
+ concentration = conc0 ? standard OnCondition
+ }
+
+
+ cai = concentration
+
+
+}
+
+PROCEDURE rates() {
+
+ surfaceArea = area : surfaceArea has units (um2), area (built in to NEURON) is in um^2...
+
+ iCa = -1 * (0.01) * ica * surfaceArea : iCa has units (nA) ; ica (built in to NEURON) has units (mA/cm2)...
+
+
+
+
+}
+
diff --git a/NEURON/.test.mep b/NEURON/test/.test.mep
similarity index 100%
rename from NEURON/.test.mep
rename to NEURON/test/.test.mep
diff --git a/NEURON/.test.neuron.omt b/NEURON/test/.test.neuron.omt
similarity index 87%
rename from NEURON/.test.neuron.omt
rename to NEURON/test/.test.neuron.omt
index d01f726..270db8e 100644
--- a/NEURON/.test.neuron.omt
+++ b/NEURON/test/.test.neuron.omt
@@ -1,6 +1,6 @@
# Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation
-target: Test_golgi.hoc
+target: ../Test_golgi.hoc
engine: NEURON
mep: .test.mep
@@ -9,7 +9,7 @@ experiments:
observables:
spike times:
file:
- path: Soma.dat
+ path: ../Soma.dat
columns: [0,1]
scaling: [1, 1]
spike detection:
diff --git a/NEURON/test/Test_SK2.hoc b/NEURON/test/Test_SK2.hoc
index 439f2b1..b717de7 100644
--- a/NEURON/test/Test_SK2.hoc
+++ b/NEURON/test/Test_SK2.hoc
@@ -7,30 +7,29 @@ usegui = 1
create Soma
access Soma
-celsius = 6.3
+celsius = 23
-Soma {pt3dclear() pt3dadd(0.0, 0, 0.0, 13.4715) pt3dadd(0.0, 23.1694, 0.0, 13.4715)}
+Soma {pt3dclear() pt3dadd(0.0, 0, 0.0, 27) pt3dadd(0.0, 27, 0.0, 27)}
define_shape()
forall Ra = 100
insert Golgi_lkg
-
-insert Golgi_Ca_HVA
+glbar_Golgi_lkg=2.1e-05
insert Golgi_SK2
-insert Golgi_CALC
+insert CaClamp
proc initialiseValues0() {
- forall v = -63
+ forall v = -65
}
objref fih0
{fih0 = new FInitializeHandler(0, "initialiseValues0()")}
-
+/*
objref stim1
objref stim2
@@ -45,11 +44,11 @@ Soma {
stim2.del = 800.0
stim2.dur = 200.0
stim2.amp = 0.04
-}
+}*/
-tstop = 1500.0
+tstop = 600.0
dt = 0.01
@@ -91,7 +90,7 @@ if (usegui==1) {
{GraphWin_1.view(0, -0.1, tstop, 1.2, 80, 330, 330, 250)}
{
GraphWin_1.addexpr("o1", "Soma.o1_Golgi_SK2", 1, 1, 0.8, 0.9, 2)
- GraphWin_1.addexpr("o1", "Soma.o2_Golgi_SK2", 2, 1, 0.8, 0.9, 2)
+ GraphWin_1.addexpr("o2", "Soma.o2_Golgi_SK2", 2, 1, 0.8, 0.9, 2)
GraphWin_1.addexpr("c1", "Soma.c1_Golgi_SK2", 3, 1, 0.8, 0.9, 2)
GraphWin_1.addexpr("c2", "Soma.c2_Golgi_SK2", 4, 1, 0.8, 0.9, 2)
GraphWin_1.addexpr("c3", "Soma.c3_Golgi_SK2", 5, 1, 0.8, 0.9, 2)
@@ -149,7 +148,7 @@ if (usegui==1) {
xbutton("Stop","stoprun=1")
t = 0
xvalue("t","t", 2 )
- tstop = 700.0
+ tstop = 600.0
xvalue("Tstop","tstop", 1,"tstop_changed()", 0, 1 )
dt = 0.01
xvalue("dt","dt", 1,"setdt()", 0, 1 )
diff --git a/NeuroML2/CaClamp.nml b/NeuroML2/CaClamp.nml
index a39c1e3..5e88313 100644
--- a/NeuroML2/CaClamp.nml
+++ b/NeuroML2/CaClamp.nml
@@ -4,7 +4,7 @@
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd"
id="CaClamp">
-
+
@@ -17,7 +17,7 @@
-
+
diff --git a/NeuroML2/LEMS_KAHP_Test.xml b/NeuroML2/LEMS_KAHP_Test.xml
index e3d73b2..d2fc868 100644
--- a/NeuroML2/LEMS_KAHP_Test.xml
+++ b/NeuroML2/LEMS_KAHP_Test.xml
@@ -13,7 +13,7 @@
-
+
@@ -31,13 +31,13 @@
-
-
+
+
-
-
-
-
+
+
+
+
@@ -52,13 +52,14 @@
+
+
+
-
-
diff --git a/NeuroML2/TestKAHP.cell.nml b/NeuroML2/TestKAHP.cell.nml
index 943a40c..71fcbae 100644
--- a/NeuroML2/TestKAHP.cell.nml
+++ b/NeuroML2/TestKAHP.cell.nml
@@ -3,8 +3,6 @@
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.githubusercontent.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta4.xsd"
id="TestKAHP">
-
-
@@ -15,8 +13,8 @@
-
-
+
+