Submit COBRApy 0.22.1

[biosimulators-daemon]

---

id: cobrapy version: 0.22.1 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/eccb9db64e44b41e026708957f12983e4bb1a24a/biosimulators.json specificationsPatch: version: 0.22.1 image: url: ghcr.io/biosimulators/biosimulators_cobrapy/cobrapy:0.22.1 digest: "sha256:fdd4b517cb3cf8b53d56da2ca27ecba6606552651fbc38e4b093b337e48e968b" validateImage: true commitSimulator: true

---

Changelog

• fixed types of volumes and issues in specifications

[biosimulators-daemon]

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

[biosimulators-daemon]

The validation/submission of your simulator failed.

- The simulator specifications from `https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/14965e3d1f0a408ad7d817d2bbb02400c1aaa1d4/biosimulators.json` are invalid. The specifications of simulation tools must adhere to BioSimulators' schema. BioSimulators' schema is available in both JSON Schema and Open API Specifications formats. Documentation is available at https://api.biosimulators.org/.
- 
-   - Validation Error (400):
-     
-       Property or parameter 'references' is invalid.
-       
-         Value:
-           ExternalReferences {
-             identifiers: [
-               Identifier {
-                 namespace: 'pypi',
-                 id: 'cobra',
-                 url: 'https://pypi.org/project/cobra/'
-               },
-               Identifier {
-                 namespace: 'pypi',
-                 id: 'biosimulators-cobrapy',
-                 url: 'https://pypi.org/project/biosimulators-cobrapy/'
-               },
-               Identifier {
-                 namespace: 'biocontainers',
-                 id: 'cobra',
-                 url: 'https://biocontainers.pro/#/tools/cobra'
-               },
-               Identifier {
-                 namespace: 'biotools',
-                 id: 'cobrapy',
-                 url: 'https://bio.tools/cobrapy'
-               }
-             ],
-             citations: [
-               Citation {
-                 journal: 'BMC Systems Biology',
-                 volume: 7,
-                 issue: null,
-                 pages: '74',
-                 title: 'COBRApy: COnstraints-Based Reconstruction and Analysis for Python',
-                 authors: 'Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson & Daniel R. Hyduke',
-                 year: 2013,
-                 identifiers: [Array]
-               }
-             ]
-           }
-       
-         Error(s):
-           - Property or parameter 'citations' is invalid.
-             
-               Value:
-                 [
-                   Citation {
-                     journal: 'BMC Systems Biology',
-                     volume: 7,
-                     issue: null,
-                     pages: '74',
-                     title: 'COBRApy: COnstraints-Based Reconstruction and Analysis for Python',
-                     authors: 'Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson & Daniel R. Hyduke',
-                     year: 2013,
-                     identifiers: [ [Identifier] ]
-                   }
-                 ]
-             
-               Error(s):
-                 - Property or parameter '0' is invalid.
-                   
-                     Value:
-                       Citation {
-                         journal: 'BMC Systems Biology',
-                         volume: 7,
-                         issue: null,
-                         pages: '74',
-                         title: 'COBRApy: COnstraints-Based Reconstruction and Analysis for Python',
-                         authors: 'Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson & Daniel R. Hyduke',
-                         year: 2013,
-                         identifiers: [
-                           Identifier {
-                             namespace: 'doi',
-                             id: '10.1186/1752-0509-7-74',
-                             url: 'https://doi.org/10.1186/1752-0509-7-74'
-                           }
-                         ]
-                       }
-                   
-                     Error(s):
-                       - Property or parameter 'volume' is invalid.
-                         
-                           Value:
-                             7
-                         
-                           Error(s):
-                             - isString: volume must be a string
-       
-       Property 'algorithms' is invalid.
-       
-         Value:
-           [
-             Algorithm {
-               parameters: [ [AlgorithmParameter] ],
-               outputDimensions: [],
-               id: 'fba',
-               name: 'flux balance analysis',
-               dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000437'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedSteadyStateSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'library',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [],
-               id: 'fva',
-               name: 'flux variability analysis',
-               dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000526'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedSteadyStateSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'library',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter], [AlgorithmParameter] ],
-               outputDimensions: [],
-               id: 'pfba',
-               name: 'parsimonious enzyme usage flux balance analysis',
-               dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000528'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedSteadyStateSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [ [OutputVariablePattern], [OutputVariablePattern] ],
-               availableSoftwareInterfaceTypes: [
-                 'library',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [],
-               id: 'geometric fba',
-               name: 'geometric flux balance analysis',
-               dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000527'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedSteadyStateSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'library',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             }
-           ]
-       
-         Error(s):
-           - Property or parameter '0' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: null,
-                       name: 'solver',
-                       value: 'GLPK',
-                       recommendedRange: [Array],
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'string',
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [],
-                   id: 'fba',
-                   name: 'flux balance analysis',
-                   dependencies: [
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gnu.org/software/glpk/',
-                       name: 'GLPK',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.ibm.com/analytics/cplex-optimizer',
-                       name: 'CPLEX',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gurobi.com/',
-                       name: 'Gurobi',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     }
-                   ],
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000437' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000624'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [Array],
-                       namespace: 'EDAM',
-                       id: 'format_2585'
-                     }
-                   ],
-                   modelChangePatterns: [
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change component attributes',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Add components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Remove components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change components',
-                       types: [Array]
-                     }
-                   ],
-                   simulationFormats: [
-                     EdamOntologySedmlIdVersion {
-                       version: 'L1V3',
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3685'
-                     }
-                   ],
-                   simulationTypes: [ 'SedSteadyStateSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Nature Biotechnology',
-                       volume: 28,
-                       issue: 3,
-                       pages: '245-248',
-                       title: 'What is flux balance analysis?',
-                       authors: 'Jeffrey D. Orth, Ines Thiele & Bernhard Ø. Palsson',
-                       year: 2010,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'objective value'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'reaction fluxes'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'reaction reduced costs'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species shadow prices'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'library',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Nature Biotechnology',
-                           volume: 28,
-                           issue: 3,
-                           pages: '245-248',
-                           title: 'What is flux balance analysis?',
-                           authors: 'Jeffrey D. Orth, Ines Thiele & Bernhard Ø. Palsson',
-                           year: 2010,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Nature Biotechnology',
-                               volume: 28,
-                               issue: 3,
-                               pages: '245-248',
-                               title: 'What is flux balance analysis?',
-                               authors: 'Jeffrey D. Orth, Ines Thiele & Bernhard Ø. Palsson',
-                               year: 2010,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1038/nbt.1614',
-                                   url: 'https://doi.org/10.1038/nbt.1614'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   28
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-                               Property 'issue' is invalid.
-                               
-                                 Value:
-                                   3
-                               
-                                 Error(s):
-                                   - isString: issue must be a string
-             Property '1' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: 'loopless',
-                       name: 'loopless',
-                       value: 'false',
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'boolean',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'fraction_of_optimum',
-                       name: 'fraction_of_optimum',
-                       value: '1.0',
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'float',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'pfba_factor',
-                       name: 'pfba_factor',
-                       value: null,
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'float',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'processes',
-                       name: 'processes',
-                       value: null,
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'integer',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: null,
-                       name: 'solver',
-                       value: 'GLPK',
-                       recommendedRange: [Array],
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'string',
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [],
-                   id: 'fva',
-                   name: 'flux variability analysis',
-                   dependencies: [
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gnu.org/software/glpk/',
-                       name: 'GLPK',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.ibm.com/analytics/cplex-optimizer',
-                       name: 'CPLEX',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gurobi.com/',
-                       name: 'Gurobi',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     }
-                   ],
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000526' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000624'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [Array],
-                       namespace: 'EDAM',
-                       id: 'format_2585'
-                     }
-                   ],
-                   modelChangePatterns: [
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change component attributes',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Add components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Remove components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change components',
-                       types: [Array]
-                     }
-                   ],
-                   simulationFormats: [
-                     EdamOntologySedmlIdVersion {
-                       version: 'L1V3',
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3685'
-                     }
-                   ],
-                   simulationTypes: [ 'SedSteadyStateSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Metabolic Engineering',
-                       volume: 5,
-                       issue: 4,
-                       pages: '264-276',
-                       title: 'The effects of alternate optimal solutions in constraint-based genome-scale metabolic models',
-                       authors: 'Radhakrishnan Mahadevan & Christophe. H. Schilling',
-                       year: 2003,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'objective value'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'reaction fluxes'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'reaction reduced costs'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species shadow prices'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'library',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Metabolic Engineering',
-                           volume: 5,
-                           issue: 4,
-                           pages: '264-276',
-                           title: 'The effects of alternate optimal solutions in constraint-based genome-scale metabolic models',
-                           authors: 'Radhakrishnan Mahadevan & Christophe. H. Schilling',
-                           year: 2003,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Metabolic Engineering',
-                               volume: 5,
-                               issue: 4,
-                               pages: '264-276',
-                               title: 'The effects of alternate optimal solutions in constraint-based genome-scale metabolic models',
-                               authors: 'Radhakrishnan Mahadevan & Christophe. H. Schilling',
-                               year: 2003,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1016/j.ymben.2003.09.002',
-                                   url: 'https://doi.org/10.1016/j.ymben.2003.09.002'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   5
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-                               Property 'issue' is invalid.
-                               
-                                 Value:
-                                   4
-                               
-                                 Error(s):
-                                   - isString: issue must be a string
-             Property '2' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: 'fraction_of_optimum',
-                       name: 'fraction_of_optimum',
-                       value: '1.0',
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'float',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: null,
-                       name: 'solver',
-                       value: 'GLPK',
-                       recommendedRange: [Array],
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'string',
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [],
-                   id: 'pfba',
-                   name: 'parsimonious enzyme usage flux balance analysis',
-                   dependencies: [
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gnu.org/software/glpk/',
-                       name: 'GLPK',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.ibm.com/analytics/cplex-optimizer',
-                       name: 'CPLEX',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gurobi.com/',
-                       name: 'Gurobi',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     }
-                   ],
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000528' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000624'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [Array],
-                       namespace: 'EDAM',
-                       id: 'format_2585'
-                     }
-                   ],
-                   modelChangePatterns: [
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change component attributes',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Add components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Remove components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change components',
-                       types: [Array]
-                     }
-                   ],
-                   simulationFormats: [
-                     EdamOntologySedmlIdVersion {
-                       version: 'L1V3',
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3685'
-                     }
-                   ],
-                   simulationTypes: [ 'SedSteadyStateSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Molecular Systems Biology',
-                       volume: 6,
-                       issue: null,
-                       pages: '390',
-                       title: 'Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models',
-                       authors: 'Nathan E. Lewis, Kim K. Hixson, Tom M. Conrad, Joshua A. Lerman, Pep Charusanti, Ashoka D. Polpitiya, Joshua N. Adkins, Gunnar Schramm, Samuel O. Purvine, Daniel Lopez‐Ferrer, Karl K. Weitz, Roland Eils, Rainer König, Richard D. Smith & Bernhard Ø. Palsson',
-                       year: 2010,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'minimum reaction fluxes'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'maximum reaction fluxes'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'library',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Molecular Systems Biology',
-                           volume: 6,
-                           issue: null,
-                           pages: '390',
-                           title: 'Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models',
-                           authors: 'Nathan E. Lewis, Kim K. Hixson, Tom M. Conrad, Joshua A. Lerman, Pep Charusanti, Ashoka D. Polpitiya, Joshua N. Adkins, Gunnar Schramm, Samuel O. Purvine, Daniel Lopez‐Ferrer, Karl K. Weitz, Roland Eils, Rainer König, Richard D. Smith & Bernhard Ø. Palsson',
-                           year: 2010,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Molecular Systems Biology',
-                               volume: 6,
-                               issue: null,
-                               pages: '390',
-                               title: 'Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models',
-                               authors: 'Nathan E. Lewis, Kim K. Hixson, Tom M. Conrad, Joshua A. Lerman, Pep Charusanti, Ashoka D. Polpitiya, Joshua N. Adkins, Gunnar Schramm, Samuel O. Purvine, Daniel Lopez‐Ferrer, Karl K. Weitz, Roland Eils, Rainer König, Richard D. Smith & Bernhard Ø. Palsson',
-                               year: 2010,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1038/msb.2010.47',
-                                   url: 'https://doi.org/10.1038/msb.2010.47'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   6
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-             Property '3' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: 'epsilon',
-                       name: 'epsilon',
-                       value: '1e-6',
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'float',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'max_tries',
-                       name: 'max_tries',
-                       value: '200',
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'integer',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'processes',
-                       name: 'processes',
-                       value: '1',
-                       recommendedRange: null,
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'integer',
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: null,
-                       name: 'solver',
-                       value: 'GLPK',
-                       recommendedRange: [Array],
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       type: 'string',
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [],
-                   id: 'geometric fba',
-                   name: 'geometric flux balance analysis',
-                   dependencies: [
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gnu.org/software/glpk/',
-                       name: 'GLPK',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.ibm.com/analytics/cplex-optimizer',
-                       name: 'CPLEX',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     },
-                     DependentPackage {
-                       version: null,
-                       url: 'https://www.gurobi.com/',
-                       name: 'Gurobi',
-                       required: false,
-                       freeNonCommercialLicense: true
-                     }
-                   ],
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000527' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000624'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [Array],
-                       namespace: 'EDAM',
-                       id: 'format_2585'
-                     }
-                   ],
-                   modelChangePatterns: [
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change component attributes',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Add components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Remove components',
-                       types: [Array]
-                     },
-                     ModelChangePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'Change components',
-                       types: [Array]
-                     }
-                   ],
-                   simulationFormats: [
-                     EdamOntologySedmlIdVersion {
-                       version: 'L1V3',
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3685'
-                     }
-                   ],
-                   simulationTypes: [ 'SedSteadyStateSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Journal of Theoretical Biology',
-                       volume: 258,
-                       issue: null,
-                       pages: '311-315',
-                       title: 'Flux balance analysis: A geometric perspective',
-                       authors: 'Kieran Smallbone & Evangelos Simeonidis',
-                       year: 2009,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'objective value'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'reaction fluxes'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'reaction reduced costs'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species shadow prices'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'library',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Journal of Theoretical Biology',
-                           volume: 258,
-                           issue: null,
-                           pages: '311-315',
-                           title: 'Flux balance analysis: A geometric perspective',
-                           authors: 'Kieran Smallbone & Evangelos Simeonidis',
-                           year: 2009,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Journal of Theoretical Biology',
-                               volume: 258,
-                               issue: null,
-                               pages: '311-315',
-                               title: 'Flux balance analysis: A geometric perspective',
-                               authors: 'Kieran Smallbone & Evangelos Simeonidis',
-                               year: 2009,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1016/j.jtbi.2009.01.027',
-                                   url: 'https://doi.org/10.1016/j.jtbi.2009.01.027'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   258
-                               
-                                 Error(s):
-                                   - isString: volume must be a string

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

[biosimulators-daemon]

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!

The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.

We will discuss any concerns with your submission in this issue.

A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 73 test cases

• Passed 33 test cases:

  • cli.CliDescribesSupportedEnvironmentVariablesInline
  • cli.CliDisplaysHelpInline
  • cli.CliDisplaysVersionInformationInline
  • combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
  • combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
  • combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
  • combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
  • docker_image.DeclaresSupportedEnvironmentVariables
  • docker_image.DefaultUserIsRoot
  • docker_image.HasBioContainersLabels
  • docker_image.HasOciLabels
  • docker_image.SingularityImageExecutesSimulationsSuccessfully
  • log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
  • log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
  • published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
  • results_report.SimulatorGeneratesReportsOfSimulationResults
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
  • sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
  • sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
  • sedml.SimulatorSupportsAlgorithmParameters
  • sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
  • sedml.SimulatorSupportsMultipleReportsPerSedDocument
  • sedml.SimulatorSupportsMultipleTasksPerSedDocument
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
  • sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
  • sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
  • sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
  • sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
  • sedml.SimulatorSupportsRepeatedTasksWithVectorRanges

• Failed 0 test cases

• Skipped 40 test cases:

  • published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
  • published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
  • published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
  • published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
  • published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
  • published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
  • published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
  • published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
  • published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
  • published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
  • sedml.SimulatorProducesLinear2DPlots
  • sedml.SimulatorProducesLinear3DPlots
  • sedml.SimulatorProducesLogarithmic2DPlots
  • sedml.SimulatorProducesLogarithmic3DPlots
  • sedml.SimulatorProducesMultiplePlots
  • sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
  • sedml.SimulatorSupportsComputeModelChanges
  • sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
  • sedml.SimulatorSupportsDataSetsWithDifferentShapes
  • sedml.SimulatorSupportsModelAttributeChanges
  • sedml.SimulatorSupportsRepeatedTasksWithChanges
  • sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
  • sedml.SimulatorSupportsSubstitutingAlgorithms
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
  • sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

[biosimulators-daemon]

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (4.4 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VERBOSE' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be described in the inline help for its command-line interface. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.6 s)

Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None

docker_image.HasBioContainersLabels (0.6 s)

Test that a Docker image has BioContainers labels with metadata about the image Warnings: ``` Docker images are encouraged to have the following BioContainers labels: extra.identifiers.biotools ``` Log: None

[biosimulators-daemon]

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000086 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027, KISAO_0000030 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000027 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None

sedml.SimulatorProducesLinear2DPlots (0.2 s)

Test that a simulator produces linear 2D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorProducesLinear3DPlots (0.2 s)

Test that a simulator produces linear 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorProducesLogarithmic2DPlots (0.2 s)

Test that a simulator produces logarithmic 2D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)

Test that a simulator produces logarithmic 3D plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorProducesMultiplePlots (0.1 s)

Test that a simulator produces multiple plots Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.2 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorSupportsComputeModelChanges (0.5 s)

Test that a simulator supports compute model changes Reason for skip: ``` The SED document is invalid. - Model `model` is invalid. - The changes of the model are invalid. - Change 363 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[72]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_363` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[72]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 364 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[71]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_364` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[71]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 365 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[70]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_365` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[70]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 366 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[69]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_366` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[69]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 367 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[68]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_367` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[68]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 368 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[67]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_368` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[67]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 369 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[66]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_369` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[66]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 370 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[65]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_370` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[65]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 371 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[64]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_371` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[64]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 372 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[63]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_372` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[63]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 373 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[62]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_373` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[62]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 374 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[61]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_374` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[61]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 375 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[60]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_375` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[60]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 376 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[59]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_376` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[59]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 377 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[58]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_377` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[58]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 378 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[57]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_378` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[57]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 379 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[56]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_379` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[56]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 380 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[55]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_380` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[55]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 381 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[54]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_381` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[54]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 382 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[53]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_382` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[53]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 383 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[52]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_383` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[52]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 384 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[51]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_384` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[51]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 385 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[50]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_385` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[50]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 386 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[49]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_386` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[49]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 387 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[48]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_387` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[48]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 388 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[47]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_388` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[47]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 389 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[46]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_389` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[46]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 390 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[45]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_390` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[45]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 391 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[44]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_391` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[44]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 392 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[43]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_392` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[43]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 393 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[42]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_393` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[42]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 394 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[41]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_394` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[41]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 395 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[40]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_395` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[40]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 396 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[39]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_396` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[39]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 397 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[38]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_397` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[38]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 398 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[37]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_398` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[37]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 399 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[36]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_399` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[36]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 400 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[35]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_400` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[35]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 401 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[34]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_401` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[34]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 402 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[33]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_402` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[33]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 403 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[32]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_403` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[32]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 404 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[31]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_404` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[31]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 405 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[30]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_405` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[30]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 406 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[29]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_406` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[29]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 407 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[28]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_407` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[28]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 408 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[27]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_408` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[27]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 409 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[26]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_409` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[26]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 410 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[25]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_410` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[25]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 411 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[24]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_411` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[24]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 412 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[23]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_412` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[23]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 413 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[22]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_413` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[22]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 414 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[21]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_414` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[21]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 415 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[20]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_415` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[20]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 416 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[19]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_416` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[19]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 417 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[18]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_417` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[18]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 418 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[17]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_418` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[17]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 419 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[16]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_419` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[16]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 420 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[15]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_420` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[15]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 421 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[14]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_421` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[14]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 422 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[13]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_422` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[13]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 423 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[12]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_423` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[12]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 424 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[11]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_424` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[11]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 425 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[10]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_425` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[10]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 426 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[9]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_426` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[9]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 427 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[8]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_427` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[8]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 428 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[7]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_428` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[7]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 429 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[6]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_429` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[6]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 430 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[5]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_430` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[5]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 431 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[4]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_431` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[4]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 432 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_432` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[3]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 433 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_433` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[2]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 434 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. - Variable `__var_434` is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfSpecies[1]/sbml:species[1]/@fbc:charge` are not defined. Only the following namespaces are defined for the target: `sbml`. ``` Log: None

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.2 s)

Test that a simulator supports data generators with different shapes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.1 s)

Test that a simulator supports data generators with different shapes Reason for skip: ``` No curated COMBINE/OMEX archives are available to generate archives for testing ``` Log: None

sedml.SimulatorSupportsModelAttributeChanges (1.0 s)

Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The SED document is invalid. - Model `model` is invalid. - The changes of the model are invalid. - Change 4 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/@fbc:required` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 5 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/@fbc:strict` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 12 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[95]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 13 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[95]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 28 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[94]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 29 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[94]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 51 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[93]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 52 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[93]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 74 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[92]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 75 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[92]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 103 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[91]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 104 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[91]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 126 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[90]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 127 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[90]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 155 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[89]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 156 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[89]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 180 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[88]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 181 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[88]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 201 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[87]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 202 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[87]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 223 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[86]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 224 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[86]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 240 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[85]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 241 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[85]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 257 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[84]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 258 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[84]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 278 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[83]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 279 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[83]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 304 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[82]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 305 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[82]/@fbc:lowerFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 327 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[81]/@fbc:upperFluxBound` are not defined. Only the following namespaces are defined for the target: `sbml`. - Change 328 is invalid. - One or more namespaces required for target `/sbml:sbml[1]/sbml:model[1]/sbml:listOfReactions[1]/sbml:reaction[81]/@fbc:lowerFluxBound` are not defined. Only the following namespa ...

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of cobrapy to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.