Closed biosimulators-daemon closed 2 years ago
Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
The validation/submission of your simulator failed.
- The simulator specifications from `https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/14965e3d1f0a408ad7d817d2bbb02400c1aaa1d4/biosimulators.json` are invalid. The specifications of simulation tools must adhere to BioSimulators' schema. BioSimulators' schema is available in both JSON Schema and Open API Specifications formats. Documentation is available at https://api.biosimulators.org/.
-
- - Validation Error (400):
-
- Property or parameter 'references' is invalid.
-
- Value:
- ExternalReferences {
- identifiers: [
- Identifier {
- namespace: 'pypi',
- id: 'cobra',
- url: 'https://pypi.org/project/cobra/'
- },
- Identifier {
- namespace: 'pypi',
- id: 'biosimulators-cobrapy',
- url: 'https://pypi.org/project/biosimulators-cobrapy/'
- },
- Identifier {
- namespace: 'biocontainers',
- id: 'cobra',
- url: 'https://biocontainers.pro/#/tools/cobra'
- },
- Identifier {
- namespace: 'biotools',
- id: 'cobrapy',
- url: 'https://bio.tools/cobrapy'
- }
- ],
- citations: [
- Citation {
- journal: 'BMC Systems Biology',
- volume: 7,
- issue: null,
- pages: '74',
- title: 'COBRApy: COnstraints-Based Reconstruction and Analysis for Python',
- authors: 'Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson & Daniel R. Hyduke',
- year: 2013,
- identifiers: [Array]
- }
- ]
- }
-
- Error(s):
- - Property or parameter 'citations' is invalid.
-
- Value:
- [
- Citation {
- journal: 'BMC Systems Biology',
- volume: 7,
- issue: null,
- pages: '74',
- title: 'COBRApy: COnstraints-Based Reconstruction and Analysis for Python',
- authors: 'Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson & Daniel R. Hyduke',
- year: 2013,
- identifiers: [ [Identifier] ]
- }
- ]
-
- Error(s):
- - Property or parameter '0' is invalid.
-
- Value:
- Citation {
- journal: 'BMC Systems Biology',
- volume: 7,
- issue: null,
- pages: '74',
- title: 'COBRApy: COnstraints-Based Reconstruction and Analysis for Python',
- authors: 'Ali Ebrahim, Joshua A. Lerman, Bernhard Ø. Palsson & Daniel R. Hyduke',
- year: 2013,
- identifiers: [
- Identifier {
- namespace: 'doi',
- id: '10.1186/1752-0509-7-74',
- url: 'https://doi.org/10.1186/1752-0509-7-74'
- }
- ]
- }
-
- Error(s):
- - Property or parameter 'volume' is invalid.
-
- Value:
- 7
-
- Error(s):
- - isString: volume must be a string
-
- Property 'algorithms' is invalid.
-
- Value:
- [
- Algorithm {
- parameters: [ [AlgorithmParameter] ],
- outputDimensions: [],
- id: 'fba',
- name: 'flux balance analysis',
- dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
- kisaoId: KisaoAlgorithmOntologyId {
- namespace: 'KISAO',
- id: 'KISAO_0000437'
- },
- modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
- modelFormats: [ [EdamOntologyIdVersion] ],
- modelChangePatterns: [
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern]
- ],
- simulationFormats: [ [EdamOntologySedmlIdVersion] ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
- citations: [ [Citation] ],
- outputVariablePatterns: [
- [OutputVariablePattern],
- [OutputVariablePattern],
- [OutputVariablePattern],
- [OutputVariablePattern]
- ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- },
- Algorithm {
- parameters: [
- [AlgorithmParameter],
- [AlgorithmParameter],
- [AlgorithmParameter],
- [AlgorithmParameter],
- [AlgorithmParameter]
- ],
- outputDimensions: [],
- id: 'fva',
- name: 'flux variability analysis',
- dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
- kisaoId: KisaoAlgorithmOntologyId {
- namespace: 'KISAO',
- id: 'KISAO_0000526'
- },
- modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
- modelFormats: [ [EdamOntologyIdVersion] ],
- modelChangePatterns: [
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern]
- ],
- simulationFormats: [ [EdamOntologySedmlIdVersion] ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
- citations: [ [Citation] ],
- outputVariablePatterns: [
- [OutputVariablePattern],
- [OutputVariablePattern],
- [OutputVariablePattern],
- [OutputVariablePattern]
- ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- },
- Algorithm {
- parameters: [ [AlgorithmParameter], [AlgorithmParameter] ],
- outputDimensions: [],
- id: 'pfba',
- name: 'parsimonious enzyme usage flux balance analysis',
- dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
- kisaoId: KisaoAlgorithmOntologyId {
- namespace: 'KISAO',
- id: 'KISAO_0000528'
- },
- modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
- modelFormats: [ [EdamOntologyIdVersion] ],
- modelChangePatterns: [
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern]
- ],
- simulationFormats: [ [EdamOntologySedmlIdVersion] ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
- citations: [ [Citation] ],
- outputVariablePatterns: [ [OutputVariablePattern], [OutputVariablePattern] ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- },
- Algorithm {
- parameters: [
- [AlgorithmParameter],
- [AlgorithmParameter],
- [AlgorithmParameter],
- [AlgorithmParameter]
- ],
- outputDimensions: [],
- id: 'geometric fba',
- name: 'geometric flux balance analysis',
- dependencies: [ [DependentPackage], [DependentPackage], [DependentPackage] ],
- kisaoId: KisaoAlgorithmOntologyId {
- namespace: 'KISAO',
- id: 'KISAO_0000527'
- },
- modelingFrameworks: [ [SboModelingFrameworkOntologyId] ],
- modelFormats: [ [EdamOntologyIdVersion] ],
- modelChangePatterns: [
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern],
- [ModelChangePattern]
- ],
- simulationFormats: [ [EdamOntologySedmlIdVersion] ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [ [EdamOntologyCombineArchiveIdVersion] ],
- citations: [ [Citation] ],
- outputVariablePatterns: [
- [OutputVariablePattern],
- [OutputVariablePattern],
- [OutputVariablePattern],
- [OutputVariablePattern]
- ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- }
- ]
-
- Error(s):
- - Property or parameter '0' is invalid.
-
- Value:
- Algorithm {
- parameters: [
- AlgorithmParameter {
- id: null,
- name: 'solver',
- value: 'GLPK',
- recommendedRange: [Array],
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'string',
- availableSoftwareInterfaceTypes: [Array]
- }
- ],
- outputDimensions: [],
- id: 'fba',
- name: 'flux balance analysis',
- dependencies: [
- DependentPackage {
- version: null,
- url: 'https://www.gnu.org/software/glpk/',
- name: 'GLPK',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.ibm.com/analytics/cplex-optimizer',
- name: 'CPLEX',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.gurobi.com/',
- name: 'Gurobi',
- required: false,
- freeNonCommercialLicense: true
- }
- ],
- kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000437' },
- modelingFrameworks: [
- SboModelingFrameworkOntologyId {
- namespace: 'SBO',
- id: 'SBO_0000624'
- }
- ],
- modelFormats: [
- EdamOntologyIdVersion {
- version: null,
- supportedFeatures: [Array],
- namespace: 'EDAM',
- id: 'format_2585'
- }
- ],
- modelChangePatterns: [
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change component attributes',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Add components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Remove components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change components',
- types: [Array]
- }
- ],
- simulationFormats: [
- EdamOntologySedmlIdVersion {
- version: 'L1V3',
- supportedFeatures: [],
- namespace: 'EDAM',
- id: 'format_3685'
- }
- ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [
- EdamOntologyCombineArchiveIdVersion {
- version: null,
- supportedFeatures: [],
- namespace: 'EDAM',
- id: 'format_3686'
- }
- ],
- citations: [
- Citation {
- journal: 'Nature Biotechnology',
- volume: 28,
- issue: 3,
- pages: '245-248',
- title: 'What is flux balance analysis?',
- authors: 'Jeffrey D. Orth, Ines Thiele & Bernhard Ø. Palsson',
- year: 2010,
- identifiers: [Array]
- }
- ],
- outputVariablePatterns: [
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'objective value'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'reaction fluxes'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'reaction reduced costs'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'species shadow prices'
- }
- ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- }
-
- Error(s):
- - Property or parameter 'citations' is invalid.
-
- Value:
- [
- Citation {
- journal: 'Nature Biotechnology',
- volume: 28,
- issue: 3,
- pages: '245-248',
- title: 'What is flux balance analysis?',
- authors: 'Jeffrey D. Orth, Ines Thiele & Bernhard Ø. Palsson',
- year: 2010,
- identifiers: [ [Identifier] ]
- }
- ]
-
- Error(s):
- - Property or parameter '0' is invalid.
-
- Value:
- Citation {
- journal: 'Nature Biotechnology',
- volume: 28,
- issue: 3,
- pages: '245-248',
- title: 'What is flux balance analysis?',
- authors: 'Jeffrey D. Orth, Ines Thiele & Bernhard Ø. Palsson',
- year: 2010,
- identifiers: [
- Identifier {
- namespace: 'doi',
- id: '10.1038/nbt.1614',
- url: 'https://doi.org/10.1038/nbt.1614'
- }
- ]
- }
-
- Error(s):
- - Property or parameter 'volume' is invalid.
-
- Value:
- 28
-
- Error(s):
- - isString: volume must be a string
- Property 'issue' is invalid.
-
- Value:
- 3
-
- Error(s):
- - isString: issue must be a string
- Property '1' is invalid.
-
- Value:
- Algorithm {
- parameters: [
- AlgorithmParameter {
- id: 'loopless',
- name: 'loopless',
- value: 'false',
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'boolean',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: 'fraction_of_optimum',
- name: 'fraction_of_optimum',
- value: '1.0',
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'float',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: 'pfba_factor',
- name: 'pfba_factor',
- value: null,
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'float',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: 'processes',
- name: 'processes',
- value: null,
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'integer',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: null,
- name: 'solver',
- value: 'GLPK',
- recommendedRange: [Array],
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'string',
- availableSoftwareInterfaceTypes: [Array]
- }
- ],
- outputDimensions: [],
- id: 'fva',
- name: 'flux variability analysis',
- dependencies: [
- DependentPackage {
- version: null,
- url: 'https://www.gnu.org/software/glpk/',
- name: 'GLPK',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.ibm.com/analytics/cplex-optimizer',
- name: 'CPLEX',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.gurobi.com/',
- name: 'Gurobi',
- required: false,
- freeNonCommercialLicense: true
- }
- ],
- kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000526' },
- modelingFrameworks: [
- SboModelingFrameworkOntologyId {
- namespace: 'SBO',
- id: 'SBO_0000624'
- }
- ],
- modelFormats: [
- EdamOntologyIdVersion {
- version: null,
- supportedFeatures: [Array],
- namespace: 'EDAM',
- id: 'format_2585'
- }
- ],
- modelChangePatterns: [
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change component attributes',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Add components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Remove components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change components',
- types: [Array]
- }
- ],
- simulationFormats: [
- EdamOntologySedmlIdVersion {
- version: 'L1V3',
- supportedFeatures: [],
- namespace: 'EDAM',
- id: 'format_3685'
- }
- ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [
- EdamOntologyCombineArchiveIdVersion {
- version: null,
- supportedFeatures: [],
- namespace: 'EDAM',
- id: 'format_3686'
- }
- ],
- citations: [
- Citation {
- journal: 'Metabolic Engineering',
- volume: 5,
- issue: 4,
- pages: '264-276',
- title: 'The effects of alternate optimal solutions in constraint-based genome-scale metabolic models',
- authors: 'Radhakrishnan Mahadevan & Christophe. H. Schilling',
- year: 2003,
- identifiers: [Array]
- }
- ],
- outputVariablePatterns: [
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'objective value'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'reaction fluxes'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'reaction reduced costs'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'species shadow prices'
- }
- ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- }
-
- Error(s):
- - Property or parameter 'citations' is invalid.
-
- Value:
- [
- Citation {
- journal: 'Metabolic Engineering',
- volume: 5,
- issue: 4,
- pages: '264-276',
- title: 'The effects of alternate optimal solutions in constraint-based genome-scale metabolic models',
- authors: 'Radhakrishnan Mahadevan & Christophe. H. Schilling',
- year: 2003,
- identifiers: [ [Identifier] ]
- }
- ]
-
- Error(s):
- - Property or parameter '0' is invalid.
-
- Value:
- Citation {
- journal: 'Metabolic Engineering',
- volume: 5,
- issue: 4,
- pages: '264-276',
- title: 'The effects of alternate optimal solutions in constraint-based genome-scale metabolic models',
- authors: 'Radhakrishnan Mahadevan & Christophe. H. Schilling',
- year: 2003,
- identifiers: [
- Identifier {
- namespace: 'doi',
- id: '10.1016/j.ymben.2003.09.002',
- url: 'https://doi.org/10.1016/j.ymben.2003.09.002'
- }
- ]
- }
-
- Error(s):
- - Property or parameter 'volume' is invalid.
-
- Value:
- 5
-
- Error(s):
- - isString: volume must be a string
- Property 'issue' is invalid.
-
- Value:
- 4
-
- Error(s):
- - isString: issue must be a string
- Property '2' is invalid.
-
- Value:
- Algorithm {
- parameters: [
- AlgorithmParameter {
- id: 'fraction_of_optimum',
- name: 'fraction_of_optimum',
- value: '1.0',
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'float',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: null,
- name: 'solver',
- value: 'GLPK',
- recommendedRange: [Array],
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'string',
- availableSoftwareInterfaceTypes: [Array]
- }
- ],
- outputDimensions: [],
- id: 'pfba',
- name: 'parsimonious enzyme usage flux balance analysis',
- dependencies: [
- DependentPackage {
- version: null,
- url: 'https://www.gnu.org/software/glpk/',
- name: 'GLPK',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.ibm.com/analytics/cplex-optimizer',
- name: 'CPLEX',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.gurobi.com/',
- name: 'Gurobi',
- required: false,
- freeNonCommercialLicense: true
- }
- ],
- kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000528' },
- modelingFrameworks: [
- SboModelingFrameworkOntologyId {
- namespace: 'SBO',
- id: 'SBO_0000624'
- }
- ],
- modelFormats: [
- EdamOntologyIdVersion {
- version: null,
- supportedFeatures: [Array],
- namespace: 'EDAM',
- id: 'format_2585'
- }
- ],
- modelChangePatterns: [
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change component attributes',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Add components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Remove components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change components',
- types: [Array]
- }
- ],
- simulationFormats: [
- EdamOntologySedmlIdVersion {
- version: 'L1V3',
- supportedFeatures: [],
- namespace: 'EDAM',
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- }
- ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [
- EdamOntologyCombineArchiveIdVersion {
- version: null,
- supportedFeatures: [],
- namespace: 'EDAM',
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- }
- ],
- citations: [
- Citation {
- journal: 'Molecular Systems Biology',
- volume: 6,
- issue: null,
- pages: '390',
- title: 'Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models',
- authors: 'Nathan E. Lewis, Kim K. Hixson, Tom M. Conrad, Joshua A. Lerman, Pep Charusanti, Ashoka D. Polpitiya, Joshua N. Adkins, Gunnar Schramm, Samuel O. Purvine, Daniel Lopez‐Ferrer, Karl K. Weitz, Roland Eils, Rainer König, Richard D. Smith & Bernhard Ø. Palsson',
- year: 2010,
- identifiers: [Array]
- }
- ],
- outputVariablePatterns: [
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'minimum reaction fluxes'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'maximum reaction fluxes'
- }
- ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- }
-
- Error(s):
- - Property or parameter 'citations' is invalid.
-
- Value:
- [
- Citation {
- journal: 'Molecular Systems Biology',
- volume: 6,
- issue: null,
- pages: '390',
- title: 'Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models',
- authors: 'Nathan E. Lewis, Kim K. Hixson, Tom M. Conrad, Joshua A. Lerman, Pep Charusanti, Ashoka D. Polpitiya, Joshua N. Adkins, Gunnar Schramm, Samuel O. Purvine, Daniel Lopez‐Ferrer, Karl K. Weitz, Roland Eils, Rainer König, Richard D. Smith & Bernhard Ø. Palsson',
- year: 2010,
- identifiers: [ [Identifier] ]
- }
- ]
-
- Error(s):
- - Property or parameter '0' is invalid.
-
- Value:
- Citation {
- journal: 'Molecular Systems Biology',
- volume: 6,
- issue: null,
- pages: '390',
- title: 'Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models',
- authors: 'Nathan E. Lewis, Kim K. Hixson, Tom M. Conrad, Joshua A. Lerman, Pep Charusanti, Ashoka D. Polpitiya, Joshua N. Adkins, Gunnar Schramm, Samuel O. Purvine, Daniel Lopez‐Ferrer, Karl K. Weitz, Roland Eils, Rainer König, Richard D. Smith & Bernhard Ø. Palsson',
- year: 2010,
- identifiers: [
- Identifier {
- namespace: 'doi',
- id: '10.1038/msb.2010.47',
- url: 'https://doi.org/10.1038/msb.2010.47'
- }
- ]
- }
-
- Error(s):
- - Property or parameter 'volume' is invalid.
-
- Value:
- 6
-
- Error(s):
- - isString: volume must be a string
- Property '3' is invalid.
-
- Value:
- Algorithm {
- parameters: [
- AlgorithmParameter {
- id: 'epsilon',
- name: 'epsilon',
- value: '1e-6',
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'float',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: 'max_tries',
- name: 'max_tries',
- value: '200',
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'integer',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: 'processes',
- name: 'processes',
- value: '1',
- recommendedRange: null,
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'integer',
- availableSoftwareInterfaceTypes: [Array]
- },
- AlgorithmParameter {
- id: null,
- name: 'solver',
- value: 'GLPK',
- recommendedRange: [Array],
- kisaoId: [KisaoAlgorithmParameterOntologyId],
- type: 'string',
- availableSoftwareInterfaceTypes: [Array]
- }
- ],
- outputDimensions: [],
- id: 'geometric fba',
- name: 'geometric flux balance analysis',
- dependencies: [
- DependentPackage {
- version: null,
- url: 'https://www.gnu.org/software/glpk/',
- name: 'GLPK',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.ibm.com/analytics/cplex-optimizer',
- name: 'CPLEX',
- required: false,
- freeNonCommercialLicense: true
- },
- DependentPackage {
- version: null,
- url: 'https://www.gurobi.com/',
- name: 'Gurobi',
- required: false,
- freeNonCommercialLicense: true
- }
- ],
- kisaoId: KisaoAlgorithmOntologyId { namespace: 'KISAO', id: 'KISAO_0000527' },
- modelingFrameworks: [
- SboModelingFrameworkOntologyId {
- namespace: 'SBO',
- id: 'SBO_0000624'
- }
- ],
- modelFormats: [
- EdamOntologyIdVersion {
- version: null,
- supportedFeatures: [Array],
- namespace: 'EDAM',
- id: 'format_2585'
- }
- ],
- modelChangePatterns: [
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change component attributes',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Add components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Remove components',
- types: [Array]
- },
- ModelChangePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'Change components',
- types: [Array]
- }
- ],
- simulationFormats: [
- EdamOntologySedmlIdVersion {
- version: 'L1V3',
- supportedFeatures: [],
- namespace: 'EDAM',
- id: 'format_3685'
- }
- ],
- simulationTypes: [ 'SedSteadyStateSimulation' ],
- archiveFormats: [
- EdamOntologyCombineArchiveIdVersion {
- version: null,
- supportedFeatures: [],
- namespace: 'EDAM',
- id: 'format_3686'
- }
- ],
- citations: [
- Citation {
- journal: 'Journal of Theoretical Biology',
- volume: 258,
- issue: null,
- pages: '311-315',
- title: 'Flux balance analysis: A geometric perspective',
- authors: 'Kieran Smallbone & Evangelos Simeonidis',
- year: 2009,
- identifiers: [Array]
- }
- ],
- outputVariablePatterns: [
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'objective value'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'reaction fluxes'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'reaction reduced costs'
- },
- OutputVariablePattern {
- target: [ModelTarget],
- symbol: null,
- name: 'species shadow prices'
- }
- ],
- availableSoftwareInterfaceTypes: [
- 'library',
- 'command-line application',
- 'BioSimulators Docker image'
- ]
- }
-
- Error(s):
- - Property or parameter 'citations' is invalid.
-
- Value:
- [
- Citation {
- journal: 'Journal of Theoretical Biology',
- volume: 258,
- issue: null,
- pages: '311-315',
- title: 'Flux balance analysis: A geometric perspective',
- authors: 'Kieran Smallbone & Evangelos Simeonidis',
- year: 2009,
- identifiers: [ [Identifier] ]
- }
- ]
-
- Error(s):
- - Property or parameter '0' is invalid.
-
- Value:
- Citation {
- journal: 'Journal of Theoretical Biology',
- volume: 258,
- issue: null,
- pages: '311-315',
- title: 'Flux balance analysis: A geometric perspective',
- authors: 'Kieran Smallbone & Evangelos Simeonidis',
- year: 2009,
- identifiers: [
- Identifier {
- namespace: 'doi',
- id: '10.1016/j.jtbi.2009.01.027',
- url: 'https://doi.org/10.1016/j.jtbi.2009.01.027'
- }
- ]
- }
-
- Error(s):
- - Property or parameter 'volume' is invalid.
-
- Value:
- 258
-
- Error(s):
- - isString: volume must be a string
The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.
If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators
(without the backticks).
Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image, and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available for 90 days here. The results of the validation of your tool will also be saved as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.
The specifications of your simulator is valid!
Executed 73 test cases
Passed 33 test cases:
cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
docker_image.SingularityImageExecutesSimulationsSuccessfully
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
Failed 0 test cases
Skipped 40 test cases:
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
cli.CliDescribesSupportedEnvironmentVariablesInline
(4.4 s)docker_image.DeclaresSupportedEnvironmentVariables
(0.6 s)docker_image.HasBioContainersLabels
(0.6 s)published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
(0.0 s)published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
(0.0 s)published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
(0.0 s)published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
(0.0 s)published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
(0.0 s)published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
(0.0 s)published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
(0.0 s)published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
(0.0 s)published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
(0.0 s)published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
(0.0 s)published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
(0.0 s)sedml.SimulatorProducesLinear2DPlots
(0.2 s)sedml.SimulatorProducesLinear3DPlots
(0.2 s)sedml.SimulatorProducesLogarithmic2DPlots
(0.2 s)sedml.SimulatorProducesLogarithmic3DPlots
(0.1 s)sedml.SimulatorProducesMultiplePlots
(0.1 s)sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
(0.2 s)sedml.SimulatorSupportsComputeModelChanges
(0.5 s)sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
(0.2 s)sedml.SimulatorSupportsDataSetsWithDifferentShapes
(0.1 s)sedml.SimulatorSupportsModelAttributeChanges
(1.0 s)The image for your simulator is valid!
Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of cobrapy to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.
id: cobrapy version: 0.22.1 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_COBRApy/eccb9db64e44b41e026708957f12983e4bb1a24a/biosimulators.json specificationsPatch: version: 0.22.1 image: url: ghcr.io/biosimulators/biosimulators_cobrapy/cobrapy:0.22.1 digest: "sha256:fdd4b517cb3cf8b53d56da2ca27ecba6606552651fbc38e4b093b337e48e968b" validateImage: true commitSimulator: true
Changelog