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| # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation | ||
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| target: LEMS_NML2_Ex5_DetCell_cvode.xml | ||
| engine: jNeuroML_EDEN | ||
| mep: .test.ex5.mep | ||
| experiments: | ||
| v: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: ex5_v_cvode.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: 0 | ||
| tolerance: 0.00350330618543931 | ||
| m: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: ex5_vars_cvode.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: 0.9 | ||
| tolerance: 0.0035249957767891716 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation | ||
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| target: LEMS_NML2_Ex5_DetCell_cvode.xml | ||
| engine: jNeuroML | ||
| mep: .test.ex5.mep | ||
| experiments: | ||
| v: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: ex5_v_cvode.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: 0 | ||
| tolerance: 0.005542225676726113 | ||
| m: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: ex5_vars_cvode.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: 0.9 | ||
| tolerance: 0.005574638211610937 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| # Script for running automated tests on OSB using Travis-CI, see https://github.com/OpenSourceBrain/osb-model-validation | ||
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| target: LEMS_NML2_Ex5_DetCell_cvode.xml | ||
| engine: jNeuroML_NEURON | ||
| mep: .test.ex5.mep | ||
| experiments: | ||
| v: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: ex5_v_cvode.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1000] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: 0 | ||
| tolerance: 0.010825060439277775 | ||
| m: | ||
| observables: | ||
| spike times: | ||
| file: | ||
| path: ex5_vars_cvode.dat | ||
| columns: [0,1] | ||
| scaling: [1000, 1] | ||
| spike detection: | ||
| method: threshold | ||
| threshold: 0.9 | ||
| tolerance: 0.010867948469414872 |
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| @@ -0,0 +1,66 @@ | ||
| <Lems> | ||
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| <!-- Example with Simple cell specifying segment details--> | ||
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| <!-- This is a file which can be read and executed by the LEMS Interpreter. | ||
| It imports the LEMS definitions of the core NeuroML 2 Components, | ||
| imports in "pure" NeuroML 2 and contains some LEMS elements for running | ||
| a simulation --> | ||
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| <Target component="sim1" reportFile="report.ex5.__SIMULATOR__.__TIMESTAMP__.txt"/> | ||
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| <Include file="Cells.xml"/> | ||
| <Include file="Networks.xml"/> | ||
| <Include file="Simulation.xml"/> | ||
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| <!-- Including file with a <neuroml> root, a "real" NeuroML 2 file --> | ||
| <Include file="NML2_SingleCompHHCell.nml"/> | ||
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| <Simulation id="sim1" length="1000ms" step="0.01ms" target="net1"> | ||
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| <Meta for="neuron" method="cvode" abs_tolerance="0.0001" rel_tolerance="0.001" /> | ||
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| <Display id="d1" title="Ex5: HH cell with simple morphology: voltage" timeScale="1ms" xmin="-100" xmax="1100" ymin="-90" ymax="50"> | ||
| <Line id="v" quantity="hhpop[0]/v" scale="1mV" color="#cccccc" timeScale="1ms"/> | ||
| <Line id="spiking" quantity="hhpop[0]/spiking" scale="0.1V" color="#004040" timeScale="1ms"/> | ||
| <!--<Line id="l3" quantity="hhpop[0]/debugVal" scale="1V" color="#999999" timeScale="1ms"/>--> | ||
| </Display> | ||
| <Display id="d2" title="Ex5: HH cell with simple morphology: rate variables" timeScale="1ms" xmin="-100" xmax="1100" ymin="-0.1" ymax="1.1"> | ||
| <Line id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q" scale="1" color="#000000" timeScale="1ms"/> | ||
| <Line id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q" scale="1" color="#ff0000" timeScale="1ms"/> | ||
| <Line id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q" scale="1" color="#0000ff" timeScale="1ms"/> | ||
| </Display> | ||
| <Display id="d3" title="Ex5: HH cell with simple morphology: current densities" timeScale="1ms" xmin="-100" xmax="1100" ymin="-0.1" ymax="1.1"> | ||
| <Line id="ina" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity" scale="1" color="#000000" timeScale="1ms"/> | ||
| <Line id="ik" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity" scale="1" color="#ff0000" timeScale="1ms"/> | ||
| </Display> | ||
| <Display id="d4" title="Ex5: HH cell with simple morphology: conductance densities" timeScale="1ms" xmin="-100" xmax="1100" ymin="-50" ymax="350"> | ||
| <Line id="gna" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/gDensity" scale="1" color="#000000" timeScale="1ms"/> | ||
| <Line id="gk" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/gDensity" scale="1" color="#ff0000" timeScale="1ms"/> | ||
| </Display> | ||
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| <OutputFile id="of0" fileName="ex5_v_cvode.dat"> | ||
| <OutputColumn id="v" quantity="hhpop[0]/v"/> | ||
| </OutputFile> | ||
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| <OutputFile id="of1" fileName="ex5_vars_cvode.dat"> | ||
| <OutputColumn id="m" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/m/q"/> | ||
| <OutputColumn id="h" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/naChan/h/q"/> | ||
| <OutputColumn id="n" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/kChan/n/q"/> | ||
| </OutputFile> | ||
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| <!-- Not supported by EDEN... | ||
| <OutputFile id="of2" fileName="results/ex5_curr_dens.dat"> | ||
| <OutputColumn id="ina" quantity="hhpop[0]/bioPhys1/membraneProperties/naChans/iDensity"/> | ||
| <OutputColumn id="ik" quantity="hhpop[0]/bioPhys1/membraneProperties/kChans/iDensity"/> | ||
| </OutputFile>--> | ||
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| </Simulation> | ||
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| </Lems> |