From d297a641624c2351b0afdb3f7f5befeffe279ed7 Mon Sep 17 00:00:00 2001
From: Jonathan Karr <jonrkarr@gmail.com>
Date: Mon, 28 Dec 2020 20:03:09 -0500
Subject: [PATCH] adding LSODA example

---
 biosimulators_test_suite/_version.py          |   2 +-
 examples/README.md                            |   5 +--
 ...Biol-Cybern-1996-Nicotinic-excitation.json |  31 ++++++++++++++++++
 ...Biol-Cybern-1996-Nicotinic-excitation.omex | Bin 0 -> 6042 bytes
 4 files changed, 35 insertions(+), 3 deletions(-)
 create mode 100644 examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.json
 create mode 100644 examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex

diff --git a/biosimulators_test_suite/_version.py b/biosimulators_test_suite/_version.py
index 66a87bb..2fb2513 100644
--- a/biosimulators_test_suite/_version.py
+++ b/biosimulators_test_suite/_version.py
@@ -1 +1 @@
-__version__ = '0.1.5'
+__version__ = '0.1.6'
diff --git a/examples/README.md b/examples/README.md
index fff96dc..d4c0169 100644
--- a/examples/README.md
+++ b/examples/README.md
@@ -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)                  |
diff --git a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.json b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.json
new file mode 100644
index 0000000..6a6f10f
--- /dev/null
+++ b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.json
@@ -0,0 +1,31 @@
+{
+  "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"
+  }]
+}
\ No newline at end of file
diff --git a/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex b/examples/sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation.omex
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