Skip to content

Commit ccfa4e5

Browse files
pgleesonpgleeson
committed
Test export
1 parent 5c2f268 commit ccfa4e5

File tree

7 files changed

+2170
-0
lines changed

7 files changed

+2170
-0
lines changed

‎.gitignore‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -35,3 +35,5 @@ ChannelTest/*.log
3535
/NMC/NeuroML2/*_main.json
3636
/NMC/NeuroML2/ManyCells.net.nml.png
3737
/NMC/NeuroML2/ManyCells.net.png
38+
/NMC/Connectome/BBP.net.png
39+
/NMC/Connectome/cons_locs_pathways_mc0_Column.tar

‎NMC/Connectome/Example5_bbpNet.net.nml‎

Lines changed: 2032 additions & 0 deletions
Large diffs are not rendered by default.

‎NMC/Connectome/test_files/ampa.synapse.nml‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
4+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5+
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta5.xsd"
6+
id="ampa">
7+
8+
<expTwoSynapse id="ampa" gbase="2nS" erev="0mV"
9+
tauRise="1ms" tauDecay="2ms" >
10+
</expTwoSynapse>
11+
12+
</neuroml>

‎NMC/Connectome/test_files/gaba.synapse.nml‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
4+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5+
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta5.xsd"
6+
id="gaba">
7+
8+
<expTwoSynapse id="gaba" gbase="2nS" erev="-80mV"
9+
tauRise="1ms" tauDecay="10ms" >
10+
</expTwoSynapse>
11+
12+
</neuroml>

‎NMC/Connectome/test_files/hhcell.cell.nml‎

Lines changed: 82 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,82 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
4+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5+
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
6+
id="hhcell">
7+
8+
<!-- Single compartment cell with HH channels -->
9+
10+
<!-- This is a "pure" NeuroML 2 file. It can be included in a LEMS file for use in a simulaton
11+
by the LEMS interpreter, see LEMS_NML2_Ex5_DetCell.xml -->
12+
13+
<ionChannelHH id="passiveChan" conductance="10pS">
14+
<notes>Leak conductance</notes>
15+
</ionChannelHH>
16+
17+
18+
<ionChannelHH id="naChan" conductance="10pS" species="na">
19+
<notes>Na channel</notes>
20+
21+
<gateHHrates id="m" instances="3">
22+
<forwardRate type="HHExpLinearRate" rate="1per_ms" midpoint="-40mV" scale="10mV"/>
23+
<reverseRate type="HHExpRate" rate="4per_ms" midpoint="-65mV" scale="-18mV"/>
24+
</gateHHrates>
25+
26+
<gateHHrates id="h" instances="1">
27+
<forwardRate type="HHExpRate" rate="0.07per_ms" midpoint="-65mV" scale="-20mV"/>
28+
<reverseRate type="HHSigmoidRate" rate="1per_ms" midpoint="-35mV" scale="10mV"/>
29+
</gateHHrates>
30+
31+
</ionChannelHH>
32+
33+
34+
<ionChannelHH id="kChan" conductance="10pS" species="k">
35+
36+
<gateHHrates id="n" instances="4">
37+
<forwardRate type="HHExpLinearRate" rate="0.1per_ms" midpoint="-55mV" scale="10mV"/>
38+
<reverseRate type="HHExpRate" rate="0.125per_ms" midpoint="-65mV" scale="-80mV"/>
39+
</gateHHrates>
40+
41+
</ionChannelHH>
42+
43+
44+
45+
<cell id="hhcell">
46+
47+
<morphology id="morph1">
48+
<segment id="0" name="soma">
49+
<proximal x="0" y="0" z="0" diameter="17.841242"/> <!--Gives a convenient surface area of 1000.0 um^2-->
50+
<distal x="0" y="0" z="0" diameter="17.841242"/>
51+
</segment>
52+
53+
<segmentGroup id="soma_group">
54+
<member segment="0"/>
55+
</segmentGroup>
56+
57+
</morphology>
58+
59+
<biophysicalProperties id="bioPhys1">
60+
61+
<membraneProperties>
62+
63+
<channelDensity id="leak" ionChannel="passiveChan" condDensity="3.0 S_per_m2" erev="-54.3mV" ion="non_specific"/>
64+
<channelDensity id="naChans" ionChannel="naChan" condDensity="120.0 mS_per_cm2" erev="50.0 mV" ion="na"/>
65+
<channelDensity id="kChans" ionChannel="kChan" condDensity="360 S_per_m2" erev="-77mV" ion="k"/>
66+
67+
<spikeThresh value="-20mV"/>
68+
<specificCapacitance value="1.0 uF_per_cm2"/>
69+
<initMembPotential value="-65mV"/>
70+
71+
</membraneProperties>
72+
73+
<intracellularProperties>
74+
<resistivity value="0.03 kohm_cm"/> <!-- Note: not used in single compartment simulations -->
75+
</intracellularProperties>
76+
77+
</biophysicalProperties>
78+
79+
</cell>
80+
81+
</neuroml>
82+

‎NMC/Connectome/test_files/iaf.cell.nml‎

Lines changed: 17 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,17 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
4+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5+
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta4.xsd"
6+
id="isf">
7+
8+
9+
<iafCell id="iaf" leakReversal="-50mV" thresh="-55mV"
10+
reset="-70mV" C="0.2nF" leakConductance="0.01uS"/>
11+
12+
13+
<izhikevichCell id="izBurst" v0 = "-70mV" thresh = "30mV" a="0.02"
14+
b = "0.2" c = "-50.0" d = "2"/>
15+
16+
17+
</neuroml>

‎NMC/Connectome/test_files/inputs.nml‎

Lines changed: 13 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,13 @@
1+
<?xml version="1.0" encoding="UTF-8"?>
2+
3+
<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
4+
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
5+
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 ../Schemas/NeuroML2/NeuroML_v2beta5.xsd"
6+
id="NML2_Inputs">
7+
8+
<pulseGenerator id="iclamp0" delay="20ms" duration="800ms" amplitude="0.1 nA" />
9+
10+
<spikeGeneratorPoisson id="spikeGenPoisson" averageRate="50 Hz"/>
11+
12+
</neuroml>
13+

0 commit comments

Comments
 (0)