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feat: added algorithm parameters for Gillespie and NLEQ2 in RoadRunner
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‎.github/workflows/ci.yml

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@@ -6,7 +6,7 @@ on:
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jobs:
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test:
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name: Run unit tests on the ontology
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if: "!(github.event_name == 'push' && github.event.pusher.email == '[email protected]')"
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if: "!contains(github.event.head_commit.message, '[Skip CI]')"
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runs-on: ubuntu-latest
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steps:
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# Check out the repository
@@ -212,7 +212,7 @@ jobs:
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set +e
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git stash pop
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git add docs
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git commit -m "Updating compiled documentation"
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git commit -m "Updated compiled documentation [Skip CI]"
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git checkout .
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git clean -f -d
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if [[ $? = 0 ]]; then

‎CHANGELOG.md

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# Changelog
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## 2.26 (OWL 2)
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- Added algorithm parameters for Gillespie and NLEQ2 in RoadRunner
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## 2.26 (OWL 2)
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- Added RKQS method in XPP
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- Added documentation for XPP methods

‎kisao.owl

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<rdfs:label xml:lang="en">Kinetic Simulation Algorithm Ontology (KiSAO)</rdfs:label>
2020
<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://co.mbine.org/standards/kisao</rdfs:seeAlso>
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<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/pubmed/22027554</rdfs:seeAlso>
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<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.26</owl:versionInfo>
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<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.27</owl:versionInfo>
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<skos:definition xml:lang="en">The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.</skos:definition>
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</owl:Ontology>
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@@ -14319,6 +14319,208 @@ This method only involves evaluations of f. This method is suitable for non-stif
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000673 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000673">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000243"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">skip reactions that produce negative species amounts</rdfs:label>
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<skos:definition xml:lang="en">Parameter which instructs a simulation tool to skip reactions that would result in negative amounts of species.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000673"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000674 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000674">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000243"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">presimulate</rdfs:label>
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<skos:definition xml:lang="en">Whether a model should be presimulated prior to analysis.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000674"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000675 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000675">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000243"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">Broyden method</rdfs:label>
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<skos:definition xml:lang="en">Family of Quasi-Newton methods for finding roots in k variables originally described by C. G. Broyden in 1965.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000675"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000676 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000676">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000243"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">degree of linearity</rdfs:label>
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<skos:definition xml:lang="en">The degree of linearity of a system.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000676"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000677 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000677">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000415"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">maximum number of steps for presimulation</rdfs:label>
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<skos:definition xml:lang="en">Maximum number of steps to take in presimulating a model prior to analysis.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000677"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000678 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000678">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000415"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">maximum number of steps for approximation</rdfs:label>
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<skos:definition xml:lang="en">Maximum number of steps to take in approximating an analysis.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000678"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000679 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000679">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000681"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">maximum time for approximation</rdfs:label>
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<skos:definition xml:lang="en">Maximum amount of time to spend approximating an analysis.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000679"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000680 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000680">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000201"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">duration</rdfs:label>
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<skos:definition xml:lang="en">Length of time to simulate.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000680"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000681 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000681">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000244"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<rdfs:label xml:lang="en">maximum time</rdfs:label>
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<skos:definition xml:lang="en">Maximum amount of wall time for an operation.</skos:definition>
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</owl:Class>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000682 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000682">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000243"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">allow approximation</rdfs:label>
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<skos:definition xml:lang="en">Whether to find an approximate solution if an exact solution could not be found.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000682"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000683 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000683">
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<rdfs:subClassOf rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000209"/>
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<dc:created rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2021-08-23</dc:created>
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<dc:creator xml:lang="en">JRK</dc:creator>
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<isImplementedIn rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</isImplementedIn>
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<rdfs:label xml:lang="en">relative tolerance for approximation</rdfs:label>
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<skos:definition xml:lang="en">Relatative tolerance for an alternative approximate solution to an exact solution which could not be found.</skos:definition>
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</owl:Class>
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<owl:Axiom>
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<owl:annotatedSource rdf:resource="http://www.biomodels.net/kisao/KISAO#KISAO_0000683"/>
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<owl:annotatedProperty rdf:resource="http://www.biomodels.net/kisao/KISAO#isImplementedIn"/>
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<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/biosimulators/tellurium</owl:annotatedTarget>
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<rdfs:comment xml:lang="en">tellurium</rdfs:comment>
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</owl:Axiom>
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<!-- http://www.biomodels.net/kisao/KISAO#KISAO_0000800 -->
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<owl:Class rdf:about="http://www.biomodels.net/kisao/KISAO#KISAO_0000800">

‎kisao_full.owl

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<rdfs:comment xml:lang="en">Kinetic Simulation Algorithm Ontology (full version, containing deprecated classes)</rdfs:comment>
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<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://co.mbine.org/standards/kisao</rdfs:seeAlso>
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<rdfs:seeAlso rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://identifiers.org/pubmed/22027554</rdfs:seeAlso>
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<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.26</owl:versionInfo>
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<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#decimal">2.27</owl:versionInfo>
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<skos:definition xml:lang="en">The Kinetic Simulation Algorithm Ontology (KiSAO) classifies algorithms available for the simulation and analysis of models in biology, and their characteristics and the parameters required for their use.</skos:definition>
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</owl:Ontology>
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‎libkisao/python/kisao/_version.py

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__version__ = '2.26'
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__version__ = '2.27'

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