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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.4.0.26 #464

Closed vcdaemon closed 3 years ago

vcdaemon commented 3 years ago

id: vcell version: 7.4.0.26 specificationsUrl: https://raw.githubusercontent.com/virtualcell/vcell/86a4ad9c795f8903a3ddb32f1fa2a7551c973208/biosimulators.json specificationsPatch: version: 7.4.0.26 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.26 digest: "sha256:c4316a5fbb5732dbe8d99c55e9ffa01990c1760e5b0c3395b576e5c18a0247a7" validateImage: true commitSimulator: true

Changelog

biosimulators-daemon commented 3 years ago

Thank you @vcdaemon 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 commented 3 years ago

The validation/submission of your simulator failed.

- The simulator specifications from `https://github.com/virtualcell/vcell/releases/download/7.4.0.26/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 'algorithms' is invalid.
-       
-         Value:
-           [
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'cvode',
-               name: 'C-language Variable-coefficient Ordinary Differential Equation solver',
-               dependencies: [ [DependentPackage] ],
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000019'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter] ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'RungeKutta2',
-               name: 'Runge-Kutta (Second Order, Fixed Time Step)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000381'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter] ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'ForwardEuler',
-               name: 'Forward Euler (First Order, Fixed Time Step)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000030'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter] ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'RungeKutta4',
-               name: 'Runge-Kutta (Fourth Order, Fixed Time Step)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000032'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'RungeKuttaFehlberg',
-               name: 'Runge-Kutta-Fehlberg (Fifth Order, Variable Time Step)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000086'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter] ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'AdamsMoulton',
-               name: 'Adams-Moulton (Fifth Order, Fixed Time Step)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000280'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'IDA',
-               name: 'IDA (Variable Order, Variable Time Step, ODE/DAE)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000283'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter] ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'StochGibson',
-               name: 'Gibson (Next Reaction Stochastic Method)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000027'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'HybridEuler',
-               name: 'Hybrid (Gibson + Euler-Maruyama Method)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000599'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'Hybrid_Gibson_Milstein',
-               name: 'Hybrid (Gibson + Milstein Method)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000598'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [ [SioOntologyId] ],
-               id: 'Hybrid_AdaptiveGibson_Milstein',
-               name: 'Hybrid (Adaptive Gibson + Milstein Method)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000600'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter], [AlgorithmParameter] ],
-               outputDimensions: [
-                 [SioOntologyId],
-                 [SioOntologyId],
-                 [SioOntologyId],
-                 [SioOntologyId]
-               ],
-               id: 'Semi-Implicit_FiniteVolume-ParticleHybrid_RegularGrid_FixedTimeStep',
-               name: 'Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000616'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [
-                 [AlgorithmParameter],
-                 [AlgorithmParameter],
-                 [AlgorithmParameter]
-               ],
-               outputDimensions: [
-                 [SioOntologyId],
-                 [SioOntologyId],
-                 [SioOntologyId],
-                 [SioOntologyId]
-               ],
-               id: 'Fully-Implicit_FiniteVolume_RegularGrid_VariableTimeStep',
-               name: 'Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000615'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             },
-             Algorithm {
-               parameters: [ [AlgorithmParameter] ],
-               outputDimensions: [
-                 [SioOntologyId],
-                 [SioOntologyId],
-                 [SioOntologyId],
-                 [SioOntologyId]
-               ],
-               id: 'Smoldyn',
-               name: 'Smoldyn (Spatial Stochastic Simulator)',
-               dependencies: null,
-               kisaoId: KisaoAlgorithmOntologyId {
-                 namespace: 'KISAO',
-                 id: 'KISAO_0000057'
-               },
-               modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
-               modelFormats: [ [EdamOntologyIdVersion] ],
-               modelChangePatterns: [
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern],
-                 [ModelChangePattern]
-               ],
-               simulationFormats: [ [EdamOntologySedmlIdVersion] ],
-               simulationTypes: [ 'SedUniformTimeCourseSimulation' ],
-               archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
-               citations: [ [Citation] ],
-               outputVariablePatterns: [
-                 [OutputVariablePattern],
-                 [OutputVariablePattern],
-                 [OutputVariablePattern]
-               ],
-               availableSoftwareInterfaceTypes: [
-                 'desktop application',
-                 'command-line application',
-                 'BioSimulators Docker image'
-               ]
-             }
-           ]
-       
-         Error(s):
-           - Property or parameter '0' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: 'rtol',
-                       name: 'Relative tolerance',
-                       value: '1e-9',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'atol',
-                       name: 'Absolute tolerance',
-                       value: '1e-9',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'maxtimestep',
-                       name: 'Maximum time step',
-                       value: '1.0',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [ SioOntologyId { namespace: 'SIO', id: 'SIO_000418' } ],
-                   id: 'cvode',
-                   name: 'C-language Variable-coefficient Ordinary Differential Equation solver',
-                   dependencies: [
-                     DependentPackage {
-                       version: null,
-                       url: 'https://computing.llnl.gov/projects/sundials',
-                       name: 'SUNDIALS',
-                       required: true,
-                       freeNonCommercialLicense: true
-                     }
-                   ],
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000019' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000293'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       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: [ 'SedUniformTimeCourseSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Computers in Physics',
-                       volume: 10,
-                       issue: 2,
-                       pages: '138-143',
-                       title: 'CVODE, a stiff/nonstiff ODE solver in C',
-                       authors: 'Scott D. Cohen, Alan C. Hindmarsh & Paul F. Dubois',
-                       year: 1996,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: null,
-                       symbol: [ModelSymbol],
-                       name: 'time'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species concentrations'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'parameter values'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'desktop application',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Computers in Physics',
-                           volume: 10,
-                           issue: 2,
-                           pages: '138-143',
-                           title: 'CVODE, a stiff/nonstiff ODE solver in C',
-                           authors: 'Scott D. Cohen, Alan C. Hindmarsh & Paul F. Dubois',
-                           year: 1996,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Computers in Physics',
-                               volume: 10,
-                               issue: 2,
-                               pages: '138-143',
-                               title: 'CVODE, a stiff/nonstiff ODE solver in C',
-                               authors: 'Scott D. Cohen, Alan C. Hindmarsh & Paul F. Dubois',
-                               year: 1996,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1063/1.4822377',
-                                   url: 'https://doi.org/10.1063/1.4822377'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   10
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-                               Property 'issue' is invalid.
-                               
-                                 Value:
-                                   2
-                               
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-                       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: [ 'SedUniformTimeCourseSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Discrete and Continuous Dynamical Systems',
-                       volume: 24,
-                       issue: 8,
-                       pages: '3475-3502',
-                       title: 'A randomized Milstein method for stochastic differential equations with non-differentiable drift coefficients',
-                       authors: 'Raphel Kruse & Yue Wu',
-                       year: 2010,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: null,
-                       symbol: [ModelSymbol],
-                       name: 'time'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species concentrations'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'parameter values'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'desktop application',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Discrete and Continuous Dynamical Systems',
-                           volume: 24,
-                           issue: 8,
-                           pages: '3475-3502',
-                           title: 'A randomized Milstein method for stochastic differential equations with non-differentiable drift coefficients',
-                           authors: 'Raphel Kruse & Yue Wu',
-                           year: 2010,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Discrete and Continuous Dynamical Systems',
-                               volume: 24,
-                               issue: 8,
-                               pages: '3475-3502',
-                               title: 'A randomized Milstein method for stochastic differential equations with non-differentiable drift coefficients',
-                               authors: 'Raphel Kruse & Yue Wu',
-                               year: 2010,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.3934/dcdsb.2018253',
-                                   url: 'https://doi.org/10.3934/dcdsb.2018253'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   24
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-                               Property 'issue' is invalid.
-                               
-                                 Value:
-                                   8
-                               
-                                 Error(s):
-                                   - isString: issue must be a string
-             Property '11' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: 'rtol',
-                       name: 'Relative tolerance',
-                       value: '1e-9',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'initial_step_size',
-                       name: 'initial step size',
-                       value: '0.1',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000452' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000453' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000454' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000418' }
-                   ],
-                   id: 'Semi-Implicit_FiniteVolume-ParticleHybrid_RegularGrid_FixedTimeStep',
-                   name: 'Semi-Implicit Finite Volume-Particle Hybrid, Regular Grid (Fixed Time Step)',
-                   dependencies: null,
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000616' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000292'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       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: [ 'SedUniformTimeCourseSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Handbook of Numerical Analysis',
-                       volume: 7,
-                       issue: '',
-                       pages: '731-1020',
-                       title: 'Finite volume methods',
-                       authors: 'Robert Eymard, Gallouet Thierry & Raphaèle Herbin',
-                       year: 2000,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: null,
-                       symbol: [ModelSymbol],
-                       name: 'time'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species concentrations'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'parameter values'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'desktop application',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Handbook of Numerical Analysis',
-                           volume: 7,
-                           issue: '',
-                           pages: '731-1020',
-                           title: 'Finite volume methods',
-                           authors: 'Robert Eymard, Gallouet Thierry & Raphaèle Herbin',
-                           year: 2000,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Handbook of Numerical Analysis',
-                               volume: 7,
-                               issue: '',
-                               pages: '731-1020',
-                               title: 'Finite volume methods',
-                               authors: 'Robert Eymard, Gallouet Thierry & Raphaèle Herbin',
-                               year: 2000,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1016/S1570-8659(00)07005-8',
-                                   url: 'https://doi.org/10.1016/S1570-8659(00)07005-8'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   7
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-             Property '12' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: 'rtol',
-                       name: 'Relative tolerance',
-                       value: '1e-9',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'atol',
-                       name: 'Absolute tolerance',
-                       value: '1e-9',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     },
-                     AlgorithmParameter {
-                       id: 'maxtimestep',
-                       name: 'Maximum time step',
-                       value: '1.0',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000452' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000453' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000454' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000418' }
-                   ],
-                   id: 'Fully-Implicit_FiniteVolume_RegularGrid_VariableTimeStep',
-                   name: 'Fully-Implicit Finite Volume, Regular Grid (Variable Time Step)',
-                   dependencies: null,
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000615' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000292'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       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: [ 'SedUniformTimeCourseSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Handbook of Numerical Analysis',
-                       volume: 7,
-                       issue: '',
-                       pages: '731-1020',
-                       title: 'Finite volume methods',
-                       authors: 'Robert Eymard, Gallouet Thierry & Raphaèle Herbin',
-                       year: 2000,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: null,
-                       symbol: [ModelSymbol],
-                       name: 'time'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species concentrations'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'parameter values'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'desktop application',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Handbook of Numerical Analysis',
-                           volume: 7,
-                           issue: '',
-                           pages: '731-1020',
-                           title: 'Finite volume methods',
-                           authors: 'Robert Eymard, Gallouet Thierry & Raphaèle Herbin',
-                           year: 2000,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Handbook of Numerical Analysis',
-                               volume: 7,
-                               issue: '',
-                               pages: '731-1020',
-                               title: 'Finite volume methods',
-                               authors: 'Robert Eymard, Gallouet Thierry & Raphaèle Herbin',
-                               year: 2000,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1016/S1570-8659(00)07005-8',
-                                   url: 'https://doi.org/10.1016/S1570-8659(00)07005-8'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   7
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-             Property '13' is invalid.
-             
-               Value:
-                 Algorithm {
-                   parameters: [
-                     AlgorithmParameter {
-                       id: 'initial_step_size',
-                       name: 'initial step size',
-                       value: '0.1',
-                       recommendedRange: null,
-                       type: 'float',
-                       kisaoId: [KisaoAlgorithmParameterOntologyId],
-                       availableSoftwareInterfaceTypes: [Array]
-                     }
-                   ],
-                   outputDimensions: [
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000452' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000453' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000454' },
-                     SioOntologyId { namespace: 'SIO', id: 'SIO_000418' }
-                   ],
-                   id: 'Smoldyn',
-                   name: 'Smoldyn (Spatial Stochastic Simulator)',
-                   dependencies: null,
-                   kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000057' },
-                   modelingFrameworks: [
-                     SboModelingFrameworkOntologyId {
-                       namespace: 'SBO',
-                       id: 'SBO_0000678'
-                     }
-                   ],
-                   modelFormats: [
-                     EdamOntologyIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       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: [ 'SedUniformTimeCourseSimulation' ],
-                   archiveFormats: [
-                     EdamOntologyCombineArchiveIdVersion {
-                       version: null,
-                       supportedFeatures: [],
-                       namespace: 'EDAM',
-                       id: 'format_3686'
-                     }
-                   ],
-                   citations: [
-                     Citation {
-                       journal: 'Philosophical Magazine',
-                       volume: 4,
-                       issue: 21,
-                       pages: '161-173',
-                       title: 'A brief account of microscopical observations made in the months of June, July and August 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies',
-                       authors: 'Robert Brown',
-                       year: 1827,
-                       identifiers: [Array]
-                     }
-                   ],
-                   outputVariablePatterns: [
-                     OutputVariablePattern {
-                       target: null,
-                       symbol: [ModelSymbol],
-                       name: 'time'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'species concentrations'
-                     },
-                     OutputVariablePattern {
-                       target: [ModelTarget],
-                       symbol: null,
-                       name: 'parameter values'
-                     }
-                   ],
-                   availableSoftwareInterfaceTypes: [
-                     'desktop application',
-                     'command-line application',
-                     'BioSimulators Docker image'
-                   ]
-                 }
-             
-               Error(s):
-                 - Property or parameter 'citations' is invalid.
-                   
-                     Value:
-                       [
-                         Citation {
-                           journal: 'Philosophical Magazine',
-                           volume: 4,
-                           issue: 21,
-                           pages: '161-173',
-                           title: 'A brief account of microscopical observations made in the months of June, July and August 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies',
-                           authors: 'Robert Brown',
-                           year: 1827,
-                           identifiers: [ [Identifier] ]
-                         }
-                       ]
-                   
-                     Error(s):
-                       - Property or parameter '0' is invalid.
-                         
-                           Value:
-                             Citation {
-                               journal: 'Philosophical Magazine',
-                               volume: 4,
-                               issue: 21,
-                               pages: '161-173',
-                               title: 'A brief account of microscopical observations made in the months of June, July and August 1827, on the particles contained in the pollen of plants; and on the general existence of active molecules in organic and inorganic bodies',
-                               authors: 'Robert Brown',
-                               year: 1827,
-                               identifiers: [
-                                 Identifier {
-                                   namespace: 'doi',
-                                   id: '10.1080/14786442808674769',
-                                   url: 'https://doi.org/10.1080/14786442808674769'
-                                 }
-                               ]
-                             }
-                         
-                           Error(s):
-                             - Property or parameter 'volume' is invalid.
-                               
-                                 Value:
-                                   4
-                               
-                                 Error(s):
-                                   - isString: volume must be a string
-                               Property 'issue' is invalid.
-                               
-                                 Value:
-                                   21
-                               
-                                 Error(s):
-                                   - isString: issue 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 commented 3 years ago

Thank you @vcdaemon 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 commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.6 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
cli.CliDisplaysHelpInline (3.0 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
cli.CliDisplaysVersionInformationInline (2.3 s)
Test that a command-line interface provides version information inline. Warnings: ``` Command-line interface should support the `-v` option for displaying version information inline. The command-line interface displayed the following when executed with `-v`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--version` option for displaying version information inline. The command-line interface displayed the following when executed with `--version`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.4 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: - '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 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 (0.3 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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (20.2 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) Warnings: ``` Unexpected reports were produced: BIOMD0000000912_sim.sedml/Figure_1_bottom_left ``` Log: ``` Nov 10, 2021 2:54:41 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_b3bc49fa-92cd-4638-9ba2-c50023520de24499822169099236682 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=5000, outputEndTime=1000.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, name=I, getId()=data_gen_I] Plot2D [listOfCurves=[Curve [id=plot_1_T_time, logX=false, logY=false, name=T, xDataReference=data_gen_time, yDataReference=data_gen_T], Curve [id=plot_1_E_time, logX=false, logY=false, name=E, xDataReference=data_gen_time, yDataReference=data_gen_E], Curve [id=plot_1_I_time, logX=false, logY=false, name=I, xDataReference=data_gen_time, yDataReference=data_gen_I]], name=Figure 1 bottom, left] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@6ca13e92 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp5545526168435748310.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 199 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. Generating report `report`. Generating report `__plot__Figure_1_bottom_left`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (40.2 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) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 10, 2021 2:55:01 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_4b5b1083-6ef9-4036-a717-df83898db6d69097343865157703843 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- name: simulation_1 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000086], getId()=simulation_1] Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1] DataGenerator [math=org.jmathml.ASTRootNode@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, name=Swe1T, getId()=data_gen_Swe1T] Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a] Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b] Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c] Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@49f8ba87 org.jlibsedml.Report@49f8ba88 org.jlibsedml.Report@49f8ba89 org.jlibsedml.Report@49f8ba8a SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg Succesful model import: SBML file /tmp/temp2013394432156624990.xml final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000) Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg__Ciliberto2003_Morphogenesis' Task 'simulation 1'. Running simulation task_1_simulation 1, 955 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_3a` while CSV generation. Ignoring unsupported output `Figure_3b` while CSV generation. Ignoring unsupported output `Figure_3c` while CSV generation. Ignoring unsupported output `Figure_3d` while CSV generation. Generating report `report`. Generating report `__plot__Figure_3a`. Generating report `__plot__Figure_3b`. Generating report `__plot__Figure_3c`. Generating report `__plot__Figure_3d`. report : /tmp/out/./simulation_1.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (39.3 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) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 10, 2021 2:55:42 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_d7b79863-6fea-41f3-a9a1-18e1dae3ad373776712729088768572 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- name: simulation_1 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation_1] Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1] DataGenerator [math=org.jmathml.ASTRootNode@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, name=Swe1T, getId()=data_gen_Swe1T] Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a] Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b] Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c] Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@49f8ba87 org.jlibsedml.Report@49f8ba88 org.jlibsedml.Report@49f8ba89 org.jlibsedml.Report@49f8ba8a SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp8038208300269723281.xml /tmp/out/simulation_1.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@74834afd Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'. Running simulation task_1_simulation 1, 163 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_3a` while CSV generation. Ignoring unsupported output `Figure_3b` while CSV generation. Ignoring unsupported output `Figure_3c` while CSV generation. Ignoring unsupported output `Figure_3d` while CSV generation. Generating report `report`. Generating report `__plot__Figure_3a`. Generating report `__plot__Figure_3b`. Generating report `__plot__Figure_3c`. Generating report `__plot__Figure_3d`. report : /tmp/out/./simulation_1.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (20.5 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_1c ``` Log: ``` Nov 10, 2021 2:56:21 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_7ae0a1ef-da05-4e30-91cb-b8084138cb153135334379747847458 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=model, name=null, language=urn:sedml:language:sbml, src=BIOMD0000000012_url.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=600, outputEndTime=1000.0, outputStartTime=400.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation] Task [modelReference=model, name=null, simulationReference=simulation, getId()=task] DataGenerator [math=org.jmathml.ASTRootNode@146dfe6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@4716be8b, name=LacI protein, getId()=data_gen_px] DataGenerator [math=org.jmathml.ASTRootNode@1fc32e4f, name=TetR protein, getId()=data_gen_py] DataGenerator [math=org.jmathml.ASTRootNode@2f67b837, name=cI protein, getId()=data_gen_pz] DataGenerator [math=org.jmathml.ASTRootNode@1869fbd2, name=LacI mRNA, getId()=data_gen_x] DataGenerator [math=org.jmathml.ASTRootNode@6af9fcb2, name=TetR mRNA, getId()=data_gen_y] DataGenerator [math=org.jmathml.ASTRootNode@6cce16f4, name=cI mRNA, getId()=data_gen_z] Plot2D [listOfCurves=[Curve [id=Figure_1c_laci_protein, logX=false, logY=false, name=LacI protein, xDataReference=data_gen_time, yDataReference=data_gen_px], Curve [id=Figure_1c_tetr_protein, logX=false, logY=false, name=TetR protein, xDataReference=data_gen_time, yDataReference=data_gen_py], Curve [id=Figure_1c_ci_protein, logX=false, logY=false, name=cI protein, xDataReference=data_gen_time, yDataReference=data_gen_pz]], name=Figure 1c] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@49f8ba4b SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp6355782655732703120.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@64f16277 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Elowitz-Nature-2000-Repressilator__model' Task 'task'. Running simulation task_task, 193 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_1c` while CSV generation. Generating report `report`. Generating report `__plot__Figure_1c`. report : /tmp/out/simulation.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (102.3 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/plot2d_Euler_default simulation.sedml/plot2d_Euler_small_step_size simulation.sedml/plot2d_Fig_1_c simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det simulation.sedml/plot2d_low_delta_R_stoch ``` Log: ``` Nov 10, 2021 2:58:05 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_e42ed191-280d-4736-b301-39395d54fdf95843646061317929311 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6 report(s), 6 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=ODE_deterministic, name=ODE deterministic, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_stochastic, name=ODE stochastic, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] Model [id=ODE_stochastic_0, name=ODE stochastic modified, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Fig_1a] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=low_delta_R_det] UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000030 AlgorithmParameter [kisaoID=KISAO:0000483 value=0.1] ], getId()=Euler_default] UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000030 AlgorithmParameter [kisaoID=KISAO:0000483 value=0.001] ], getId()=Euler_small_step_size] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=Fig_1_c] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=low_delta_R_stoch] Task [modelReference=ODE_deterministic, name=tsk_0_0, simulationReference=Fig_1a, getId()=tsk_0_0] Task [modelReference=ODE_deterministic_0, name=tsk_0_1, simulationReference=low_delta_R_det, getId()=tsk_0_1] Task [modelReference=ODE_deterministic, name=tsk_0_2, simulationReference=Euler_default, getId()=tsk_0_2] Task [modelReference=ODE_deterministic, name=tsk_0_3, simulationReference=Euler_small_step_size, getId()=tsk_0_3] Task [modelReference=ODE_stochastic, name=tsk_1_0, simulationReference=Fig_1_c, getId()=tsk_1_0] Task [modelReference=ODE_stochastic_0, name=tsk_1_1, simulationReference=low_delta_R_stoch, getId()=tsk_1_1] DataGenerator [math=org.jmathml.ASTRootNode@635572a7, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@79d94571, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4dd02341, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3212a8d7, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@7a1a3478, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@495b0487, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@55dfcc6, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@222eb8aa, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@93cf163, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@1852a3ff, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@7203c7ff, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@25bfcafd, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4b6690c0, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@46268f08, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@2a76840c, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@71454b9d, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@eda25e5, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@7cf6a5f9, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@623e088f, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@39fcbef6, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@66565121, name=time_tsk_0_2, getId()=time_tsk_0_2] DataGenerator [math=org.jmathml.ASTRootNode@2fc6f97f, name=dataGen_tsk_0_2_mRNA_R, getId()=dataGen_tsk_0_2_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@3d2ee678, name=dataGen_tsk_0_2_A, getId()=dataGen_tsk_0_2_A] DataGenerator [math=org.jmathml.ASTRootNode@6179e425, name=dataGen_tsk_0_2_R, getId()=dataGen_tsk_0_2_R] DataGenerator [math=org.jmathml.ASTRootNode@35f26e72, name=dataGen_tsk_0_2_PrmA, getId()=dataGen_tsk_0_2_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@2d6764b2, name=dataGen_tsk_0_2_PrmR, getId()=dataGen_tsk_0_2_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@67304a40, name=dataGen_tsk_0_2_C, getId()=dataGen_tsk_0_2_C] DataGenerator [math=org.jmathml.ASTRootNode@49c6c24f, name=dataGen_tsk_0_2_PrmA_bound, getId()=dataGen_tsk_0_2_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@6fe1b4fb, name=dataGen_tsk_0_2_PrmR_bound, getId()=dataGen_tsk_0_2_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@79351f41, name=dataGen_tsk_0_2_mRNA_A_, getId()=dataGen_tsk_0_2_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@1c32386d, name=time_tsk_0_3, getId()=time_tsk_0_3] DataGenerator [math=org.jmathml.ASTRootNode@6399551e, name=dataGen_tsk_0_3_mRNA_R, getId()=dataGen_tsk_0_3_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@13d73fa, name=dataGen_tsk_0_3_A, getId()=dataGen_tsk_0_3_A] DataGenerator [math=org.jmathml.ASTRootNode@5023bb8b, name=dataGen_tsk_0_3_R, getId()=dataGen_tsk_0_3_R] DataGenerator [math=org.jmathml.ASTRootNode@5d5f10b2, name=dataGen_tsk_0_3_PrmA, getId()=dataGen_tsk_0_3_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@74c79fa2, name=dataGen_tsk_0_3_PrmR, getId()=dataGen_tsk_0_3_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1e0f9063, name=dataGen_tsk_0_3_C, getId()=dataGen_tsk_0_3_C] DataGenerator [math=org.jmathml.ASTRootNode@53bd8fca, name=dataGen_tsk_0_3_PrmA_bound, getId()=dataGen_tsk_0_3_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@7642df8f, name=dataGen_tsk_0_3_PrmR_bound, getId()=dataGen_tsk_0_3_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@3e30646a, name=dataGen_tsk_0_3_mRNA_A_, getId()=dataGen_tsk_0_3_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@5cde6747, name=time_tsk_1_0, getId()=time_tsk_1_0] DataGenerator [math=org.jmathml.ASTRootNode@63a270c9, name=dataGen_tsk_1_0_mRNA_R, getId()=dataGen_tsk_1_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@37c7595, name=dataGen_tsk_1_0_A, getId()=dataGen_tsk_1_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3ed242a4, name=dataGen_tsk_1_0_R, getId()=dataGen_tsk_1_0_R] DataGenerator [math=org.jmathml.ASTRootNode@1199fe66, name=dataGen_tsk_1_0_PrmA, getId()=dataGen_tsk_1_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@614df0a4, name=dataGen_tsk_1_0_PrmR, getId()=dataGen_tsk_1_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1fdf1c5, name=dataGen_tsk_1_0_C, getId()=dataGen_tsk_1_0_C] DataGenerator [math=org.jmathml.ASTRootNode@2d96543c, name=dataGen_tsk_1_0_PrmA_bound, getId()=dataGen_tsk_1_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@73a2e526, name=dataGen_tsk_1_0_PrmR_bound, getId()=dataGen_tsk_1_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@7d64e326, name=dataGen_tsk_1_0_mRNA_A_, getId()=dataGen_tsk_1_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@13f95696, name=time_tsk_1_1, getId()=time_tsk_1_1] DataGenerator [math=org.jmathml.ASTRootNode@cd1d761, name=dataGen_tsk_1_1_mRNA_R, getId()=dataGen_tsk_1_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@68be8808, name=dataGen_tsk_1_1_A, getId()=dataGen_tsk_1_1_A] DataGenerator [math=org.jmathml.ASTRootNode@32193bea, name=dataGen_tsk_1_1_R, getId()=dataGen_tsk_1_1_R] DataGenerator [math=org.jmathml.ASTRootNode@6b8d96d9, name=dataGen_tsk_1_1_PrmA, getId()=dataGen_tsk_1_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@69653e16, name=dataGen_tsk_1_1_PrmR, getId()=dataGen_tsk_1_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@758705fa, name=dataGen_tsk_1_1_C, getId()=dataGen_tsk_1_1_C] DataGenerator [math=org.jmathml.ASTRootNode@ebaa6cb, name=dataGen_tsk_1_1_PrmA_bound, getId()=dataGen_tsk_1_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@906d29b, name=dataGen_tsk_1_1_PrmR_bound, getId()=dataGen_tsk_1_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@49d3c823, name=dataGen_tsk_1_1_mRNA_A_, getId()=dataGen_tsk_1_1_mRNA_A_] Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1a_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_R], Curve [id=plot2d_Fig_1a_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=plot2d_Fig_1a_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R], Curve [id=plot2d_Fig_1a_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA], Curve [id=plot2d_Fig_1a_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR], Curve [id=plot2d_Fig_1a_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_C], Curve [id=plot2d_Fig_1a_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA_bound], Curve [id=plot2d_Fig_1a_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR_bound], Curve [id=plot2d_Fig_1a_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_detcurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_R], Curve [id=plot2d_low_delta_R_detcurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_A], Curve [id=plot2d_low_delta_R_detcurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_R], Curve [id=plot2d_low_delta_R_detcurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA], Curve [id=plot2d_low_delta_R_detcurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR], Curve [id=plot2d_low_delta_R_detcurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_C], Curve [id=plot2d_low_delta_R_detcurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA_bound], Curve [id=plot2d_low_delta_R_detcurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR_bound], Curve [id=plot2d_low_delta_R_detcurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_Euler_default_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_R], Curve [id=plot2d_Euler_default_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_A], Curve [id=plot2d_Euler_default_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_R], Curve [id=plot2d_Euler_default_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA], Curve [id=plot2d_Euler_default_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR], Curve [id=plot2d_Euler_default_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_C], Curve [id=plot2d_Euler_default_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA_bound], Curve [id=plot2d_Euler_default_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR_bound], Curve [id=plot2d_Euler_default_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_Euler_small_step_size_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_R], Curve [id=plot2d_Euler_small_step_size_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_A], Curve [id=plot2d_Euler_small_step_size_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_R], Curve [id=plot2d_Euler_small_step_size_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA], Curve [id=plot2d_Euler_small_step_size_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR], Curve [id=plot2d_Euler_small_step_size_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_C], Curve [id=plot2d_Euler_small_step_size_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA_bound], Curve [id=plot2d_Euler_small_step_size_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR_bound], Curve [id=plot2d_Euler_small_step_size_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1_ccurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_mRNA_R], Curve [id=plot2d_Fig_1_ccurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_A], Curve [id=plot2d_Fig_1_ccurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_R], Curve [id=plot2d_Fig_1_ccurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmA], Curve [id=plot2d_Fig_1_ccurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmR], Curve [id=plot2d_Fig_1_ccurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_C], Curve [id=plot2d_Fig_1_ccurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmA_bound], Curve [id=plot2d_Fig_1_ccurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmR_bound], Curve [id=plot2d_Fig_1_ccurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_mRNA_A_]], name=ODE stochasticplots] Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_stochcurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_mRNA_R], Curve [id=plot2d_low_delta_R_stochcurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_A], Curve [id=plot2d_low_delta_R_stochcurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_R], Curve [id=plot2d_low_delta_R_stochcurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmA], Curve [id=plot2d_low_delta_R_stochcurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmR], Curve [id=plot2d_low_delta_R_stochcurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_C], Curve [id=plot2d_low_delta_R_stochcurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmA_bound], Curve [id=plot2d_low_delta_R_stochcurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmR_bound], Curve [id=plot2d_low_delta_R_stochcurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_mRNA_A_]], name=ODE stochasticplots] org.jlibsedml.Report@86b24215 org.jlibsedml.Report@9b741608 org.jlibsedml.Report@2d86479f org.jlibsedml.Report@e0c6e6ba org.jlibsedml.Report@4f95fd0e org.jlibsedml.Report@8fa06b88 org.jlibsedml.Report@64458c95 org.jlibsedml.Report@b2ac9b88 org.jlibsedml.Report@7c222d1f org.jlibsedml.Report@bde54c3a org.jlibsedml.Report@246c028e org.jlibsedml.Report@bacd9108 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp3370772238799929574.xml Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp9085032028744435928.xml Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson Succesful model import: SBML file /tmp/temp3414595535403917409.xml Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson Succesful model import: SBML file /tmp/temp7639777994183524788.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@7dee835 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'. Running simulation tsk_0_0_tsk_0_0, 128 ms ----------------------------------------------------------------------------------------------------- Solver status: 3 Solver message: simulation failed at time=1.3: consider using smaller default or max time step. values are: A = NaN C = Infinity PrmA = Infinity PrmA_bound = -Infinity PrmR = Infinity PrmR_bound = -Infinity R = -Infinity Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_2'. Running simulation for 24 ms simulation failed at time=1.3: consider using smaller default or max time step. values are: A = NaN C = Infinity PrmA = Infinity PrmA_bound = -Infinity PrmR = Infinity PrmR_bound = -Infinity R = -Infinity ----------------------------------------------------------------------------------------------------- final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000) Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'. Running simulation tsk_0_3_tsk_0_3, 906 ms ----------------------------------------------------------------------------------------------------- /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@43471a7e Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'. Running simulation tsk_0_1_tsk_0_1, 54 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@4b56b031 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'. Running simulation tsk_1_0_tsk_1_0, 297 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@740fefc6 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'. Running simulation tsk_1_1_tsk_1_1, 232 ms ----------------------------------------------------------------------------------------------------- Ran 6 simulations for 4 biomodels. Ignoring unsupported output `plot2d_Fig_1a` while CSV generation. Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation. Ignoring unsupported output `plot2d_Euler_default` while CSV generation. Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation. Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation. Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation. Generating report `report_Fig_1a`. Generating report `report_low_delta_R_det`. Generating report `report_Euler_default`. Generating report `report_Euler_small_step_size`. Generating report `report_Fig_1_c`. Generating report `report_low_delta_R_stoch`. Generating report `__plot__plot2d_Fig_1a`. Generating report `__plot__plot2d_low_delta_R_det`. Generating report `__plot__plot2d_Euler_default`. Generating report `__plot__plot2d_Euler_small_step_size`. Generating report `__plot__plot2d_Fig_1_c`. Generating report `__plot__plot2d_low_delta_R_stoch`. report : /tmp/out/simulation.sedml/report_Euler_default.csv report : /tmp/out/simulation.sedml/report_Fig_1_c.csv report : /tmp/out/simulation.sedml/report_low_delta_R_stoch.csv report : /tmp/out/simulation.sedml/report_Fig_1a.csv report : /tmp/out/simulation.sedml/report_Euler_small_step_size.csv report : /tmp/out/simulation.sedml/report_low_delta_R_det.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (41.4 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_2ab simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det ``` Log: ``` Nov 10, 2021 2:56:41 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_60172a14-0aa6-49cc-ada6-1eec6676ba234611007100632557384 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 3 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=ODE_deterministic, name=ODE deterministic, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Fig_1a] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=low_delta_R_det] Task [modelReference=ODE_deterministic, name=tsk_0_0, simulationReference=Fig_1a, getId()=tsk_0_0] Task [modelReference=ODE_deterministic_0, name=tsk_0_1, simulationReference=low_delta_R_det, getId()=tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@7fb95505, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@58be6e8, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@7331196b, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3f9342d4, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@ab7395e, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@50d13246, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@2bd08376, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@e70f13a, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@3d3e5463, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@64a40280, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@4b40f651, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@42b02722, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@d62fe5b, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@49964d75, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@528c868, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@466276d8, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@5ce8d869, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@27eedb64, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@64c63c79, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@31c7528f, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_] Plot2D [listOfCurves=[Curve [id=Figure_2ab_curve_1, logX=false, logY=false, name=A, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=Figure_2ab_curve_2, logX=false, logY=false, name=R, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R]], name=Figure 2ab] Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1a_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_R], Curve [id=plot2d_Fig_1a_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=plot2d_Fig_1a_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R], Curve [id=plot2d_Fig_1a_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA], Curve [id=plot2d_Fig_1a_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR], Curve [id=plot2d_Fig_1a_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_C], Curve [id=plot2d_Fig_1a_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA_bound], Curve [id=plot2d_Fig_1a_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR_bound], Curve [id=plot2d_Fig_1a_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_det_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_R], Curve [id=plot2d_low_delta_R_det_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_A], Curve [id=plot2d_low_delta_R_det_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_R], Curve [id=plot2d_low_delta_R_det_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA], Curve [id=plot2d_low_delta_R_det_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR], Curve [id=plot2d_low_delta_R_det_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_C], Curve [id=plot2d_low_delta_R_det_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA_bound], Curve [id=plot2d_low_delta_R_det_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR_bound], Curve [id=plot2d_low_delta_R_det_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_A_]], name=ODE deterministicplots] org.jlibsedml.Report@86b24215 org.jlibsedml.Report@9b741608 org.jlibsedml.Report@f51e8f58 org.jlibsedml.Report@64458c95 org.jlibsedml.Report@b2ac9b88 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='tsk_0_0') is compatible, solver match found in ontology: 'K ...
biosimulators-daemon commented 3 years ago

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (16.5 s)
Test that simulator logs the execution of COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 2:53:34 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1b581087-7345-4844-86d8-b574d14539867451369794874948144 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp5604129171048419656.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 98 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (17.1 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 2:53:51 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2bf70cac-f571-4a45-8b01-45831c87a6904217924015166174136 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp3612333873683314991.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 113 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (16.1 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 2:54:08 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a6adea74-0f82-4bb1-9a11-4b782ae7c1f74902278113419427864 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp7408539309149212330.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 114 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (16.6 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 2:54:24 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5fa0dd24-f59a-4e55-a921-47f4c919ef7e4253224303596235318 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp355130944202257904.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 131 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
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/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/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-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-fbc/Escherichia-coli-core-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_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` 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.SimulatorCanResolveModelSourcesDefinedByUriFragments (8.9 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 10, 2021 2:46:27 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a7a0e425-1b51-425c-91d5-33215d6e85786795049218739559278 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. All sedml documents in this archive failed to execute ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (8.8 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 10, 2021 2:46:36 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_fd8b8bd0-f327-4beb-adde-0308564de1931801262655406182355 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@26ceffa8, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. All sedml documents in this archive failed to execute ```
sedml.SimulatorProducesLinear3DPlots (0.7 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.SimulatorProducesLogarithmic3DPlots (0.5 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.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.5 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.SimulatorSupportsAddReplaceRemoveModelElementChanges (16.1 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 10, 2021 2:48:38 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_0e1972f6-1fdc-427d-a486-e1b6984ffd0b2596422602698141612 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp2535085112905939796.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 111 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (17.6 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 10, 2021 2:49:10 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_492dc29f-69a2-477c-b2e4-cc6455f2baab5984690067377283595 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7ca33c24, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@fade1fc, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@67c2e933, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@41dd05a, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp5612370348307141959.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@6f952d6c Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 103 ms --------- ...
biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

A member of the BioSimulators team will review your submission and publish your image before final committment to the registry.

biosimulators-daemon commented 3 years ago

Thank you @vcdaemon 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 commented 3 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 3 years ago

Summary of tests

biosimulators-daemon commented 3 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.3 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
cli.CliDisplaysHelpInline (3.1 s)
Test that a command-line interface provides inline help. Warnings: ``` Command-line interface should support the `-h` option for displaying help inline. The command-line interface displayed the following when executed with `-h`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--help` option for displaying help inline. The command-line interface displayed the following when executed with `--help`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
cli.CliDisplaysVersionInformationInline (2.4 s)
Test that a command-line interface provides version information inline. Warnings: ``` Command-line interface should support the `-v` option for displaying version information inline. The command-line interface displayed the following when executed with `-v`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` ``` Command-line interface should support the `--version` option for displaying version information inline. The command-line interface displayed the following when executed with `--version`: usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml] ``` Log: None
docker_image.DeclaresSupportedEnvironmentVariables (0.7 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: - '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 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 (0.5 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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (19.5 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) Warnings: ``` Unexpected reports were produced: BIOMD0000000912_sim.sedml/Figure_1_bottom_left ``` Log: ``` Nov 10, 2021 3:24:38 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a8d5fd3f-8445-4dc9-9b6f-d04d800b78804520529181953841457 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=5000, outputEndTime=1000.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, name=I, getId()=data_gen_I] Plot2D [listOfCurves=[Curve [id=plot_1_T_time, logX=false, logY=false, name=T, xDataReference=data_gen_time, yDataReference=data_gen_T], Curve [id=plot_1_E_time, logX=false, logY=false, name=E, xDataReference=data_gen_time, yDataReference=data_gen_E], Curve [id=plot_1_I_time, logX=false, logY=false, name=I, xDataReference=data_gen_time, yDataReference=data_gen_I]], name=Figure 1 bottom, left] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@6ca13e92 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp7805926890154575825.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 194 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_1_bottom_left` while CSV generation. Generating report `report`. Generating report `__plot__Figure_1_bottom_left`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (38.7 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) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 10, 2021 3:24:58 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a5878b08-2676-4ed1-9caf-decb8d05d8cc5603414655574896134 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- name: simulation_1 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000086], getId()=simulation_1] Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1] DataGenerator [math=org.jmathml.ASTRootNode@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, name=Swe1T, getId()=data_gen_Swe1T] Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a] Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b] Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c] Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@49f8ba87 org.jlibsedml.Report@49f8ba88 org.jlibsedml.Report@49f8ba89 org.jlibsedml.Report@49f8ba8a SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg Succesful model import: SBML file /tmp/temp3186810170590142184.xml final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000) Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg__Ciliberto2003_Morphogenesis' Task 'simulation 1'. Running simulation task_1_simulation 1, 1218 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_3a` while CSV generation. Ignoring unsupported output `Figure_3b` while CSV generation. Ignoring unsupported output `Figure_3c` while CSV generation. Ignoring unsupported output `Figure_3d` while CSV generation. Generating report `report`. Generating report `__plot__Figure_3a`. Generating report `__plot__Figure_3b`. Generating report `__plot__Figure_3c`. Generating report `__plot__Figure_3d`. report : /tmp/out/./simulation_1.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (37.5 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) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 10, 2021 3:25:37 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_49de8edd-4b27-45f9-8943-036347fa8e231990257805370068668 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 4 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation_1.sedml ----------------------------------------------------------------------------------------------------- name: simulation_1 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation_1] Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1] DataGenerator [math=org.jmathml.ASTRootNode@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, name=Swe1T, getId()=data_gen_Swe1T] Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a] Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b] Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c] Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@49f8ba87 org.jlibsedml.Report@49f8ba88 org.jlibsedml.Report@49f8ba89 org.jlibsedml.Report@49f8ba8a SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp7023286459361013199.xml /tmp/out/simulation_1.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@74834afd Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'. Running simulation task_1_simulation 1, 197 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_3a` while CSV generation. Ignoring unsupported output `Figure_3b` while CSV generation. Ignoring unsupported output `Figure_3c` while CSV generation. Ignoring unsupported output `Figure_3d` while CSV generation. Generating report `report`. Generating report `__plot__Figure_3a`. Generating report `__plot__Figure_3b`. Generating report `__plot__Figure_3c`. Generating report `__plot__Figure_3d`. report : /tmp/out/./simulation_1.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (19.4 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_1c ``` Log: ``` Nov 10, 2021 3:26:14 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_a3552651-a8aa-44d3-9715-1f567056c2e92147391180955532799 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 1 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=model, name=null, language=urn:sedml:language:sbml, src=BIOMD0000000012_url.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=600, outputEndTime=1000.0, outputStartTime=400.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation] Task [modelReference=model, name=null, simulationReference=simulation, getId()=task] DataGenerator [math=org.jmathml.ASTRootNode@146dfe6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@4716be8b, name=LacI protein, getId()=data_gen_px] DataGenerator [math=org.jmathml.ASTRootNode@1fc32e4f, name=TetR protein, getId()=data_gen_py] DataGenerator [math=org.jmathml.ASTRootNode@2f67b837, name=cI protein, getId()=data_gen_pz] DataGenerator [math=org.jmathml.ASTRootNode@1869fbd2, name=LacI mRNA, getId()=data_gen_x] DataGenerator [math=org.jmathml.ASTRootNode@6af9fcb2, name=TetR mRNA, getId()=data_gen_y] DataGenerator [math=org.jmathml.ASTRootNode@6cce16f4, name=cI mRNA, getId()=data_gen_z] Plot2D [listOfCurves=[Curve [id=Figure_1c_laci_protein, logX=false, logY=false, name=LacI protein, xDataReference=data_gen_time, yDataReference=data_gen_px], Curve [id=Figure_1c_tetr_protein, logX=false, logY=false, name=TetR protein, xDataReference=data_gen_time, yDataReference=data_gen_py], Curve [id=Figure_1c_ci_protein, logX=false, logY=false, name=cI protein, xDataReference=data_gen_time, yDataReference=data_gen_pz]], name=Figure 1c] org.jlibsedml.Report@c84c5553 org.jlibsedml.Report@49f8ba4b SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp6298572171608093697.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@64f16277 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Elowitz-Nature-2000-Repressilator__model' Task 'task'. Running simulation task_task, 187 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_1c` while CSV generation. Generating report `report`. Generating report `__plot__Figure_1c`. report : /tmp/out/simulation.sedml/report.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (97.7 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/plot2d_Euler_default simulation.sedml/plot2d_Euler_small_step_size simulation.sedml/plot2d_Fig_1_c simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det simulation.sedml/plot2d_low_delta_R_stoch ``` Log: ``` Nov 10, 2021 3:27:53 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5cd85015-35de-4a7d-8093-08d7f3ec0b333281440380429700465 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6 report(s), 6 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=ODE_deterministic, name=ODE deterministic, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_stochastic, name=ODE stochastic, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] Model [id=ODE_stochastic_0, name=ODE stochastic modified, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Fig_1a] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=low_delta_R_det] UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000030 AlgorithmParameter [kisaoID=KISAO:0000483 value=0.1] ], getId()=Euler_default] UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000030 AlgorithmParameter [kisaoID=KISAO:0000483 value=0.001] ], getId()=Euler_small_step_size] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=Fig_1_c] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=low_delta_R_stoch] Task [modelReference=ODE_deterministic, name=tsk_0_0, simulationReference=Fig_1a, getId()=tsk_0_0] Task [modelReference=ODE_deterministic_0, name=tsk_0_1, simulationReference=low_delta_R_det, getId()=tsk_0_1] Task [modelReference=ODE_deterministic, name=tsk_0_2, simulationReference=Euler_default, getId()=tsk_0_2] Task [modelReference=ODE_deterministic, name=tsk_0_3, simulationReference=Euler_small_step_size, getId()=tsk_0_3] Task [modelReference=ODE_stochastic, name=tsk_1_0, simulationReference=Fig_1_c, getId()=tsk_1_0] Task [modelReference=ODE_stochastic_0, name=tsk_1_1, simulationReference=low_delta_R_stoch, getId()=tsk_1_1] DataGenerator [math=org.jmathml.ASTRootNode@635572a7, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@79d94571, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4dd02341, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3212a8d7, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@7a1a3478, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@495b0487, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@55dfcc6, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@222eb8aa, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@93cf163, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@1852a3ff, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@7203c7ff, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@25bfcafd, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4b6690c0, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@46268f08, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@2a76840c, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@71454b9d, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@eda25e5, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@7cf6a5f9, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@623e088f, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@39fcbef6, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@66565121, name=time_tsk_0_2, getId()=time_tsk_0_2] DataGenerator [math=org.jmathml.ASTRootNode@2fc6f97f, name=dataGen_tsk_0_2_mRNA_R, getId()=dataGen_tsk_0_2_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@3d2ee678, name=dataGen_tsk_0_2_A, getId()=dataGen_tsk_0_2_A] DataGenerator [math=org.jmathml.ASTRootNode@6179e425, name=dataGen_tsk_0_2_R, getId()=dataGen_tsk_0_2_R] DataGenerator [math=org.jmathml.ASTRootNode@35f26e72, name=dataGen_tsk_0_2_PrmA, getId()=dataGen_tsk_0_2_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@2d6764b2, name=dataGen_tsk_0_2_PrmR, getId()=dataGen_tsk_0_2_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@67304a40, name=dataGen_tsk_0_2_C, getId()=dataGen_tsk_0_2_C] DataGenerator [math=org.jmathml.ASTRootNode@49c6c24f, name=dataGen_tsk_0_2_PrmA_bound, getId()=dataGen_tsk_0_2_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@6fe1b4fb, name=dataGen_tsk_0_2_PrmR_bound, getId()=dataGen_tsk_0_2_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@79351f41, name=dataGen_tsk_0_2_mRNA_A_, getId()=dataGen_tsk_0_2_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@1c32386d, name=time_tsk_0_3, getId()=time_tsk_0_3] DataGenerator [math=org.jmathml.ASTRootNode@6399551e, name=dataGen_tsk_0_3_mRNA_R, getId()=dataGen_tsk_0_3_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@13d73fa, name=dataGen_tsk_0_3_A, getId()=dataGen_tsk_0_3_A] DataGenerator [math=org.jmathml.ASTRootNode@5023bb8b, name=dataGen_tsk_0_3_R, getId()=dataGen_tsk_0_3_R] DataGenerator [math=org.jmathml.ASTRootNode@5d5f10b2, name=dataGen_tsk_0_3_PrmA, getId()=dataGen_tsk_0_3_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@74c79fa2, name=dataGen_tsk_0_3_PrmR, getId()=dataGen_tsk_0_3_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1e0f9063, name=dataGen_tsk_0_3_C, getId()=dataGen_tsk_0_3_C] DataGenerator [math=org.jmathml.ASTRootNode@53bd8fca, name=dataGen_tsk_0_3_PrmA_bound, getId()=dataGen_tsk_0_3_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@7642df8f, name=dataGen_tsk_0_3_PrmR_bound, getId()=dataGen_tsk_0_3_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@3e30646a, name=dataGen_tsk_0_3_mRNA_A_, getId()=dataGen_tsk_0_3_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@5cde6747, name=time_tsk_1_0, getId()=time_tsk_1_0] DataGenerator [math=org.jmathml.ASTRootNode@63a270c9, name=dataGen_tsk_1_0_mRNA_R, getId()=dataGen_tsk_1_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@37c7595, name=dataGen_tsk_1_0_A, getId()=dataGen_tsk_1_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3ed242a4, name=dataGen_tsk_1_0_R, getId()=dataGen_tsk_1_0_R] DataGenerator [math=org.jmathml.ASTRootNode@1199fe66, name=dataGen_tsk_1_0_PrmA, getId()=dataGen_tsk_1_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@614df0a4, name=dataGen_tsk_1_0_PrmR, getId()=dataGen_tsk_1_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1fdf1c5, name=dataGen_tsk_1_0_C, getId()=dataGen_tsk_1_0_C] DataGenerator [math=org.jmathml.ASTRootNode@2d96543c, name=dataGen_tsk_1_0_PrmA_bound, getId()=dataGen_tsk_1_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@73a2e526, name=dataGen_tsk_1_0_PrmR_bound, getId()=dataGen_tsk_1_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@7d64e326, name=dataGen_tsk_1_0_mRNA_A_, getId()=dataGen_tsk_1_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@13f95696, name=time_tsk_1_1, getId()=time_tsk_1_1] DataGenerator [math=org.jmathml.ASTRootNode@cd1d761, name=dataGen_tsk_1_1_mRNA_R, getId()=dataGen_tsk_1_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@68be8808, name=dataGen_tsk_1_1_A, getId()=dataGen_tsk_1_1_A] DataGenerator [math=org.jmathml.ASTRootNode@32193bea, name=dataGen_tsk_1_1_R, getId()=dataGen_tsk_1_1_R] DataGenerator [math=org.jmathml.ASTRootNode@6b8d96d9, name=dataGen_tsk_1_1_PrmA, getId()=dataGen_tsk_1_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@69653e16, name=dataGen_tsk_1_1_PrmR, getId()=dataGen_tsk_1_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@758705fa, name=dataGen_tsk_1_1_C, getId()=dataGen_tsk_1_1_C] DataGenerator [math=org.jmathml.ASTRootNode@ebaa6cb, name=dataGen_tsk_1_1_PrmA_bound, getId()=dataGen_tsk_1_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@906d29b, name=dataGen_tsk_1_1_PrmR_bound, getId()=dataGen_tsk_1_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@49d3c823, name=dataGen_tsk_1_1_mRNA_A_, getId()=dataGen_tsk_1_1_mRNA_A_] Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1a_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_R], Curve [id=plot2d_Fig_1a_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=plot2d_Fig_1a_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R], Curve [id=plot2d_Fig_1a_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA], Curve [id=plot2d_Fig_1a_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR], Curve [id=plot2d_Fig_1a_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_C], Curve [id=plot2d_Fig_1a_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA_bound], Curve [id=plot2d_Fig_1a_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR_bound], Curve [id=plot2d_Fig_1a_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_detcurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_R], Curve [id=plot2d_low_delta_R_detcurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_A], Curve [id=plot2d_low_delta_R_detcurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_R], Curve [id=plot2d_low_delta_R_detcurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA], Curve [id=plot2d_low_delta_R_detcurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR], Curve [id=plot2d_low_delta_R_detcurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_C], Curve [id=plot2d_low_delta_R_detcurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA_bound], Curve [id=plot2d_low_delta_R_detcurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR_bound], Curve [id=plot2d_low_delta_R_detcurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_Euler_default_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_R], Curve [id=plot2d_Euler_default_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_A], Curve [id=plot2d_Euler_default_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_R], Curve [id=plot2d_Euler_default_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA], Curve [id=plot2d_Euler_default_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR], Curve [id=plot2d_Euler_default_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_C], Curve [id=plot2d_Euler_default_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA_bound], Curve [id=plot2d_Euler_default_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR_bound], Curve [id=plot2d_Euler_default_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_Euler_small_step_size_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_R], Curve [id=plot2d_Euler_small_step_size_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_A], Curve [id=plot2d_Euler_small_step_size_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_R], Curve [id=plot2d_Euler_small_step_size_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA], Curve [id=plot2d_Euler_small_step_size_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR], Curve [id=plot2d_Euler_small_step_size_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_C], Curve [id=plot2d_Euler_small_step_size_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA_bound], Curve [id=plot2d_Euler_small_step_size_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR_bound], Curve [id=plot2d_Euler_small_step_size_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1_ccurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_mRNA_R], Curve [id=plot2d_Fig_1_ccurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_A], Curve [id=plot2d_Fig_1_ccurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_R], Curve [id=plot2d_Fig_1_ccurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmA], Curve [id=plot2d_Fig_1_ccurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmR], Curve [id=plot2d_Fig_1_ccurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_C], Curve [id=plot2d_Fig_1_ccurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmA_bound], Curve [id=plot2d_Fig_1_ccurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmR_bound], Curve [id=plot2d_Fig_1_ccurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_mRNA_A_]], name=ODE stochasticplots] Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_stochcurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_mRNA_R], Curve [id=plot2d_low_delta_R_stochcurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_A], Curve [id=plot2d_low_delta_R_stochcurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_R], Curve [id=plot2d_low_delta_R_stochcurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmA], Curve [id=plot2d_low_delta_R_stochcurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmR], Curve [id=plot2d_low_delta_R_stochcurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_C], Curve [id=plot2d_low_delta_R_stochcurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmA_bound], Curve [id=plot2d_low_delta_R_stochcurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmR_bound], Curve [id=plot2d_low_delta_R_stochcurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_mRNA_A_]], name=ODE stochasticplots] org.jlibsedml.Report@86b24215 org.jlibsedml.Report@9b741608 org.jlibsedml.Report@2d86479f org.jlibsedml.Report@e0c6e6ba org.jlibsedml.Report@4f95fd0e org.jlibsedml.Report@8fa06b88 org.jlibsedml.Report@64458c95 org.jlibsedml.Report@b2ac9b88 org.jlibsedml.Report@7c222d1f org.jlibsedml.Report@bde54c3a org.jlibsedml.Report@246c028e org.jlibsedml.Report@bacd9108 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp5424112289741431242.xml Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp4861040680622708169.xml Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson Succesful model import: SBML file /tmp/temp6055094684485245015.xml Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson Succesful model import: SBML file /tmp/temp3977651232714277721.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@7dee835 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'. Running simulation tsk_0_0_tsk_0_0, 200 ms ----------------------------------------------------------------------------------------------------- Solver status: 3 Solver message: simulation failed at time=1.3: consider using smaller default or max time step. values are: A = NaN C = Infinity PrmA = Infinity PrmA_bound = -Infinity PrmR = Infinity PrmR_bound = -Infinity R = -Infinity Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_2'. Running simulation for 29 ms simulation failed at time=1.3: consider using smaller default or max time step. values are: A = NaN C = Infinity PrmA = Infinity PrmA_bound = -Infinity PrmR = Infinity PrmR_bound = -Infinity R = -Infinity ----------------------------------------------------------------------------------------------------- final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000) Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'. Running simulation tsk_0_3_tsk_0_3, 970 ms ----------------------------------------------------------------------------------------------------- /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@43471a7e Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'. Running simulation tsk_0_1_tsk_0_1, 60 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@4b56b031 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'. Running simulation tsk_1_0_tsk_1_0, 318 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@733e6df7 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'. Running simulation tsk_1_1_tsk_1_1, 234 ms ----------------------------------------------------------------------------------------------------- Ran 6 simulations for 4 biomodels. Ignoring unsupported output `plot2d_Fig_1a` while CSV generation. Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation. Ignoring unsupported output `plot2d_Euler_default` while CSV generation. Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation. Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation. Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation. Generating report `report_Fig_1a`. Generating report `report_low_delta_R_det`. Generating report `report_Euler_default`. Generating report `report_Euler_small_step_size`. Generating report `report_Fig_1_c`. Generating report `report_low_delta_R_stoch`. Generating report `__plot__plot2d_Fig_1a`. Generating report `__plot__plot2d_low_delta_R_det`. Generating report `__plot__plot2d_Euler_default`. Generating report `__plot__plot2d_Euler_small_step_size`. Generating report `__plot__plot2d_Fig_1_c`. Generating report `__plot__plot2d_low_delta_R_stoch`. report : /tmp/out/simulation.sedml/report_Euler_default.csv report : /tmp/out/simulation.sedml/report_Fig_1_c.csv report : /tmp/out/simulation.sedml/report_low_delta_R_stoch.csv report : /tmp/out/simulation.sedml/report_Fig_1a.csv report : /tmp/out/simulation.sedml/report_Euler_small_step_size.csv report : /tmp/out/simulation.sedml/report_low_delta_R_det.csv HDF conversion successful Archiving resultant PDF files to `plots.zip`. Archiving resultant CSV files to `reports.zip`. ```
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (39.8 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_2ab simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det ``` Log: ``` Nov 10, 2021 3:26:34 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_db3f935f-223b-49e6-9268-e5385c1fb6065049041076345626120 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2 report(s), 3 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=ODE_deterministic, name=ODE deterministic, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Fig_1a] UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9] AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=low_delta_R_det] Task [modelReference=ODE_deterministic, name=tsk_0_0, simulationReference=Fig_1a, getId()=tsk_0_0] Task [modelReference=ODE_deterministic_0, name=tsk_0_1, simulationReference=low_delta_R_det, getId()=tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@7fb95505, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@58be6e8, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@7331196b, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3f9342d4, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@ab7395e, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@50d13246, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@2bd08376, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@e70f13a, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@3d3e5463, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@64a40280, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@4b40f651, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@42b02722, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@d62fe5b, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@49964d75, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@528c868, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@466276d8, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@5ce8d869, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@27eedb64, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@64c63c79, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@31c7528f, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_] Plot2D [listOfCurves=[Curve [id=Figure_2ab_curve_1, logX=false, logY=false, name=A, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=Figure_2ab_curve_2, logX=false, logY=false, name=R, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R]], name=Figure 2ab] Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1a_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_R], Curve [id=plot2d_Fig_1a_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=plot2d_Fig_1a_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R], Curve [id=plot2d_Fig_1a_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA], Curve [id=plot2d_Fig_1a_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR], Curve [id=plot2d_Fig_1a_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_C], Curve [id=plot2d_Fig_1a_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA_bound], Curve [id=plot2d_Fig_1a_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR_bound], Curve [id=plot2d_Fig_1a_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_A_]], name=ODE deterministicplots] Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_det_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_R], Curve [id=plot2d_low_delta_R_det_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_A], Curve [id=plot2d_low_delta_R_det_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_R], Curve [id=plot2d_low_delta_R_det_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA], Curve [id=plot2d_low_delta_R_det_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR], Curve [id=plot2d_low_delta_R_det_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_C], Curve [id=plot2d_low_delta_R_det_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA_bound], Curve [id=plot2d_low_delta_R_det_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR_bound], Curve [id=plot2d_low_delta_R_det_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_A_]], name=ODE deterministicplots] org.jlibsedml.Report@86b24215 org.jlibsedml.Report@9b741608 org.jlibsedml.Report@f51e8f58 org.jlibsedml.Report@64458c95 org.jlibsedml.Report@b2ac9b88 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='tsk_0_0') is compatible, solver match found in ontology: 'K ...
biosimulators-daemon commented 3 years ago

Skips

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (16.1 s)
Test that simulator logs the execution of COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 3:23:34 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_c3ba2211-784c-43f1-b9ab-4da155f1101b4995739788650721060 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp6267809426152900199.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 106 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (16.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 3:23:50 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8bd4a64f-1528-4ea5-a837-4b2f1b9b48fd5156014273588333387 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp6374448534758476975.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 110 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (16.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 3:24:07 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_68923b42-fc62-448f-94ee-ab246cdc35738851962994605407497 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp9048230111140843883.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 101 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (15.8 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Reason for skip: ``` The simulation log is invalid. Documentation about the log format is available at https://biosimulators.org/conventions and https://api.biosimulators.org. Property or parameter 'sedDocuments' is invalid. Value: [ SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ [SedTaskLog] ], outputs: [ [SedReportLog] ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedDocumentLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing sedml document... done. Successful translation of SED-ML file. Starting simulate all tasks... done. Generating outputs... done. ', duration: null, tasks: [ SedTaskLog { exception: [Exception], skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ], outputs: [ SedReportLog { exception: null, skipReason: null, output: null, duration: null, dataSets: [Array], _type: 'SedReportLog', id: 'report', status: 'SUCCEEDED' } ], location: 'BIOMD0000000912_sim.sedml', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty Property 'tasks' is invalid. Value: [ SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } ] Error(s): - Property or parameter '0' is invalid. Value: SedTaskLog { exception: Exception { message: null, type: null }, skipReason: null, output: 'Initializing simulation... done. Starting simulation... done. ', duration: 1, algorithm: 'KISAO_0000019', simulatorDetails: null, id: 'BIOMD0000000912_task', status: 'SUCCEEDED' } Error(s): - Property or parameter 'exception' is invalid. Value: Exception { message: null, type: null } Error(s): - Property or parameter 'type' is invalid. Value: null Error(s): - isString: type must be a string - isNotEmpty: type should not be empty Property 'message' is invalid. Value: null Error(s): - isString: message must be a string - isNotEmpty: message should not be empty ``` Log: ``` Nov 10, 2021 3:24:23 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_dde821b8-928b-4103-a14b-8dd51db629307738715742576838457 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp1765220463317698046.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@676f0a60 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 103 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
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/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/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-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-fbc/Escherichia-coli-core-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_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` 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.SimulatorCanResolveModelSourcesDefinedByUriFragments (8.8 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 10, 2021 3:16:50 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_cde83dbe-d28f-443b-9eda-1ab23f1b72417966808114593367707 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. All sedml documents in this archive failed to execute ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (8.7 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``) and inherit the changes of the model. Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 10, 2021 3:16:59 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_30fac661-e33b-4152-ad59-6ed5b305e7358438732996847138530 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. All sedml documents in this archive failed to execute ```
sedml.SimulatorProducesLinear3DPlots (0.6 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.SimulatorProducesLogarithmic3DPlots (0.4 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.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.5 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.SimulatorSupportsAddReplaceRemoveModelElementChanges (15.6 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 10, 2021 3:18:50 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_4cce09fd-46f7-478d-869b-13f01ce40edd6714683727447442689 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp4394725034453231195.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 119 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (17.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 10, 2021 3:19:22 PM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_44975768-4fce-4e47-a549-425035720671596563945132089562 Python 3.8.10 utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1 report(s), 0 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : BIOMD0000000912_sim.sedml ----------------------------------------------------------------------------------------------------- name: BIOMD0000000912_sim SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Starting simulate all tasks... Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml] UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim] Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task] DataGenerator [math=org.jmathml.ASTRootNode@7ca33c24, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@fade1fc, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@67c2e933, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@41dd05a, name=I, getId()=data_gen_I] org.jlibsedml.Report@c84c5553 SED-ML version level not supported, import may fail SED-ML version level not supported, import may fail Unsupported version, import may fail Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE SBML Import: no assignment rules. SBML Import: no assignment rules. LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import: - WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in. Succesful model import: SBML file /tmp/temp8204923554900715518.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@6f952d6c Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 96 ms --------- ...
biosimulators-daemon commented 3 years ago

The image for your simulator is valid!

biosimulators-daemon commented 3 years ago

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

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