-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
14 changed files
with
1,171 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
|
|
||
| .ipynb_checkpoints | ||
| BallAndStick.hoc | ||
| LEMS_SimTestNet_nrn.py | ||
| *.dat | ||
| arm64 | ||
| report*.txt | ||
| *.gv* | ||
| TestNet.net.png | ||
| *_code.gen.c | ||
| *_code.gen.so | ||
| *_eden.py | ||
| *.mod | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,12 @@ | ||
| system: Test BallAndStick | ||
|
|
||
| experiments: | ||
| soma: | ||
| expected: | ||
| spike times: [118.5, 533.8000000000001] | ||
| mid: | ||
| expected: | ||
| spike times: [125.15, 527.475] | ||
| dend_tip: | ||
| expected: | ||
| spike times: [133.1, 506.07500000000005] |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation | ||
|
|
||
| target: LEMS_SimTestNet.xml | ||
| engine: jNeuroML_EDEN | ||
| mep: .test.bas.mep | ||
| experiments: | ||
| soma: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: SimTestNet.pop0.v.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: -55 | ||
| tolerance: 0.00021097046413506908 | ||
| mid: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: SimTestNet.pop0.v.dat | ||
| columns: [0,5] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: -55 | ||
| tolerance: 4.739561116636288e-05 | ||
| dend_tip: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: SimTestNet.pop0.v.dat | ||
| columns: [0,10] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: -55 | ||
| tolerance: 4.939979252082648e-05 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,40 @@ | ||
| # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation | ||
|
|
||
| target: LEMS_SimTestNet.xml | ||
| engine: jNeuroML_NEURON | ||
| mep: .test.bas.mep | ||
| experiments: | ||
| soma: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: SimTestNet.pop0.v.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: -55 | ||
| tolerance: 0.000 | ||
| mid: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: SimTestNet.pop0.v.dat | ||
| columns: [0,5] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: -55 | ||
| tolerance: 0.000 | ||
| dend_tip: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: SimTestNet.pop0.v.dat | ||
| columns: [0,10] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: -55 | ||
| tolerance: 0.000 | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation | ||
|
|
||
| # This test will validate all of the NeuroML 2 files in the current directory using: jnml -validate *.nml | ||
| target: "*.nml" | ||
| engine: jNeuroML_validate |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,93 @@ | ||
| <neuroml xmlns="http://www.neuroml.org/schema/neuroml2" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2.3.1.xsd" id="BallAndStick"> | ||
| <include href="pas.channel.nml"/> | ||
| <cell id="BallAndStick"> | ||
| <morphology id="morphology"> | ||
| <segment id="0" name="soma"> | ||
| <proximal x="0.0" y="0.0" z="0.0" diameter="20.0"/> | ||
| <distal x="20.0" y="0.0" z="0.0" diameter="20.0"/> | ||
| </segment> | ||
| <segment id="1" name="dend0"> | ||
| <parent segment="0"/> | ||
| <proximal x="20.0" y="0.0" z="0.0" diameter="8.0"/> | ||
| <distal x="60.0" y="0.0" z="0.0" diameter="8.0"/> | ||
| </segment> | ||
| <segment id="2" name="dend1"> | ||
| <parent segment="1"/> | ||
| <proximal x="60.0" y="0.0" z="0.0" diameter="5.5"/> | ||
| <distal x="100.0" y="0.0" z="0.0" diameter="5.5"/> | ||
| </segment> | ||
| <segment id="3" name="dend2"> | ||
| <parent segment="2"/> | ||
| <proximal x="100.0" y="0.0" z="0.0" diameter="4.666666666666667"/> | ||
| <distal x="140.0" y="0.0" z="0.0" diameter="4.666666666666667"/> | ||
| </segment> | ||
| <segment id="4" name="dend3"> | ||
| <parent segment="3"/> | ||
| <proximal x="140.0" y="0.0" z="0.0" diameter="4.25"/> | ||
| <distal x="180.0" y="0.0" z="0.0" diameter="4.25"/> | ||
| </segment> | ||
| <segment id="5" name="dend4"> | ||
| <parent segment="4"/> | ||
| <proximal x="180.0" y="0.0" z="0.0" diameter="4.0"/> | ||
| <distal x="220.0" y="0.0" z="0.0" diameter="4.0"/> | ||
| </segment> | ||
| <segment id="6" name="dend5"> | ||
| <parent segment="5"/> | ||
| <proximal x="220.0" y="0.0" z="0.0" diameter="3.8333333333333335"/> | ||
| <distal x="260.0" y="0.0" z="0.0" diameter="3.8333333333333335"/> | ||
| </segment> | ||
| <segment id="7" name="dend6"> | ||
| <parent segment="6"/> | ||
| <proximal x="260.0" y="0.0" z="0.0" diameter="3.7142857142857144"/> | ||
| <distal x="300.0" y="0.0" z="0.0" diameter="3.7142857142857144"/> | ||
| </segment> | ||
| <segment id="8" name="dend7"> | ||
| <parent segment="7"/> | ||
| <proximal x="300.0" y="0.0" z="0.0" diameter="3.625"/> | ||
| <distal x="340.0" y="0.0" z="0.0" diameter="3.625"/> | ||
| </segment> | ||
| <segment id="9" name="dend8"> | ||
| <parent segment="8"/> | ||
| <proximal x="340.0" y="0.0" z="0.0" diameter="3.5555555555555554"/> | ||
| <distal x="380.0" y="0.0" z="0.0" diameter="3.5555555555555554"/> | ||
| </segment> | ||
| <segmentGroup id="all"> | ||
| <member segment="0"/> | ||
| <member segment="1"/> | ||
| <member segment="2"/> | ||
| <member segment="3"/> | ||
| <member segment="4"/> | ||
| <member segment="5"/> | ||
| <member segment="6"/> | ||
| <member segment="7"/> | ||
| <member segment="8"/> | ||
| <member segment="9"/> | ||
| </segmentGroup> | ||
| <segmentGroup id="soma_group" neuroLexId="GO:0043025"> | ||
| <member segment="0"/> | ||
| </segmentGroup> | ||
| <segmentGroup id="dendrite_group" neuroLexId="GO:0030425"> | ||
| <member segment="1"/> | ||
| <member segment="2"/> | ||
| <member segment="3"/> | ||
| <member segment="4"/> | ||
| <member segment="5"/> | ||
| <member segment="6"/> | ||
| <member segment="7"/> | ||
| <member segment="8"/> | ||
| <member segment="9"/> | ||
| </segmentGroup> | ||
| </morphology> | ||
| <biophysicalProperties id="biophys"> | ||
| <membraneProperties> | ||
| <channelDensity id="pas_chan" ionChannel="pas" condDensity="0.021 mS_per_cm2" erev="-70.0 mV" ion="non_specific"/> | ||
| <spikeThresh value="0mV"/> | ||
| <specificCapacitance value="1.0 uF_per_cm2"/> | ||
| <initMembPotential value="-65mV"/> | ||
| </membraneProperties> | ||
| <intracellularProperties> | ||
| <resistivity value="2000 ohm_cm"/> | ||
| </intracellularProperties> | ||
| </biophysicalProperties> | ||
| </cell> | ||
| </neuroml> |
Oops, something went wrong.