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@jonrkarr
jonrkarr committed Dec 29, 2020
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2 changes: 1 addition & 1 deletion biosimulators_test_suite/_version.py
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__version__ = '0.1.5'
__version__ = '0.1.6'
5 changes: 3 additions & 2 deletions examples/README.md
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Expand Up @@ -55,9 +55,10 @@ Below is information about the compatibility of a selection of archives.

| Archive | Modeling framework (SBO id) | Simulation algorithm (KiSAO id) | Model format (EDAM id) | Compatibile simulators |
| ------------------------ | -------------------------------- | -------------------------------- | ---------------------- | ---------------------- |
| [`Caravagna-J-Theor-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [tellurium](https://biosimulators.org/simulators/tellurium), [VCell](https://biosimulators.org/simulators/vcell) |
| [`Caravagna-J-Theor-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [PySCeS](https://biosimulators.org/simulators/pysces), [tellurium](https://biosimulators.org/simulators/tellurium), [VCell](https://biosimulators.org/simulators/vcell) |
| [`Ciliberto-J-Cell-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.omex) | non-spatial discrete ([0000295](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000295)) | SSA ([0000029](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [COPASI](https://biosimulators.org/simulators/copasi), [GillesPy2](https://biosimulators.org/simulators/gillespy2), [tellurium](https://biosimulators.org/simulators/tellurium) |
| [`Parmar-BMC-Syst-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [tellurium](https://biosimulators.org/simulators/tellurium), [VCell](https://biosimulators.org/simulators/vcell) |
| [`Edelstein-Biol-Cybern....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | LSODA ([0000088](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [PySCeS](https://biosimulators.org/simulators/pysces) |
| [`Parmar-BMC-Syst-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [PySCeS](https://biosimulators.org/simulators/pysces), [tellurium](https://biosimulators.org/simulators/tellurium), [VCell](https://biosimulators.org/simulators/vcell) |
| [`Szymanska-J-Theor-Biol....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODES ([0000496](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [AMICI](https://biosimulators.org/simulators/amici)
| [`test-bngl.omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/bngl/test-bngl.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | CVODE ([0000019](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019)) | BNGL ([format_3972](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972)) | [BioNetGen](https://biosimulators.org/simulators/bionetgen) |
| [`Tomida-EMBO-J....omex`](https://github.com/biosimulators/Biosimulators_test_suite/raw/dev/examples/sbml-core/Tomida-EMBO-J-2003-NFAT-translocation.omex) | non-spatial continuous ([0000293](https://www.ebi.ac.uk/ols/ontologies/sbo/terms?iri=http%3A%2F%2Fbiomodels.net%2FSBO%2FSBO_0000293)) | LSODA/LSODAR ([0000560](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560)) | SBML ([format_2585](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585)) | [COPASI](https://biosimulators.org/simulators/copasi) |
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31 changes: 31 additions & 0 deletions examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.json
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{
"name": "Edelstein et al. Biological Cybernetics 1996: Nicotinic excitatory post-synaptic potential",
"filename": "Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex",
"taskRequirements": [{
"modelFormat": "format_2585",
"simulationAlgorithm": "KISAO_0000088"
}],
"expectedReports": [{
"id": "BIOMD0000000002_sim.sedml/BIOMD0000000002_sim",
"dataSets": ["time", "BLL", "IL", "AL"],
"points": [1001],
"values": {
"time": {
"0": 0.0,
"1": 0.0005,
"2": 0.0010,
"999": 0.4995,
"1000": 0.5000
}
}
}],
"expectedPlots": [],
"runtimeFailureAlertType": "exception",
"identifiers": [{
"namespace": "biomodels.db",
"id": "BIOMD0000000002"
}, {
"namespace": "doi",
"id": "10.1007/s004220050302"
}]
}
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