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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
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Submit Smoldyn 2.73 #671

Open ssandrews opened 6 months ago

ssandrews commented 6 months ago

id: smoldyn version: "2.73" specificationsUrl: https://raw.githubusercontent.com/ssandrews/Smoldyn/dbe75c127c950e8deb2bce1cc8b719a6c8fa4a03/biosimulators.json specificationsPatch: version: "2.73" image: url: ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.73 digest: "sha256:8161742ed03f092a082bdab00013a69684e49bfddbb83e8fc5c24a8b3b6bb189" validateImage: true commitSimulator: true

biosimulators-daemon commented 6 months ago

Thank you @ssandrews 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 6 months ago

The specifications of your simulator is valid!

biosimulators-daemon commented 6 months ago

Summary of tests

biosimulators-daemon commented 6 months ago

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)
Test that SED documents in nested directories can be executed Exception: ``` No module named 'simulariumio' ``` Log: None
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths Exception: ``` No module named 'simulariumio' ``` Log: None
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'simulariumio' ``` Log: None
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)
Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files. Exception: ``` No module named 'simulariumio' ``` Log: None
docker_image.SingularityImageExecutesSimulationsSuccessfully (0.1 s)
Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives Exception: ``` No module named 'simulariumio' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)
Test that simulator logs the execution of COMBINE/OMEX archives Exception: ``` No module named 'simulariumio' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives Exception: ``` No module named 'simulariumio' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives Exception: ``` No module named 'simulariumio' ``` Log: None
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives Exception: ``` No module named 'simulariumio' ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (105.6 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) Exception: ``` The image 'ghcr.io/ssandrews/smoldyn/biosimulators_smoldyn:2.73' could not execute the archive: Unknown error ``` Log: ``` GENERATING A SIMULARIUM FILE ------------- -------------------------------------------------------------- Running Smoldyn 2.73 CONFIGURATION FILE Path: '/tmp/tmpvykb10qa/' Name: 'model.txt' Reading file: '/tmp/tmpvykb10qa/model.txt' Loaded file successfully setting up molecules setting up virtual boxes setting up reactions setting up graphics SIMULATION PARAMETERS file: /tmp/tmpvykb10qa/model.txt starting clock time: Tue Feb 27 22:07:18 2024 3 dimensions Random number seed: 1709071638 Time from 0 to 20 step 0.001 GRAPHICS PARAMETERS No graphical output WALL PARAMETERS wall 0: dimension x, at -100, periodic wall 1: dimension x, at 100, periodic wall 2: dimension y, at -100, periodic wall 3: dimension y, at 100, periodic wall 4: dimension z, at -10, periodic wall 5: dimension z, at 10, periodic system volume: 800000 system corners: (-100,-100,-10) and (100,100,10) MOLECULE PARAMETERS 3 molecule lists: rlist, flist, unassignedlist 2 species defined: rabbit: solution: difc=100, rms step=0.447214, list=rlist, number=1000 solution: color= 1,0,0, display size= 2 fox: solution: difc=100, rms step=0.447214, list=flist, number=1000 solution: color= 0,0.5,0, display size= 3 Overall spatial resolution: 0.447214 SURFACE PARAMETERS No internal surfaces RUNTIME COMMAND INTERPRETER No output files No output data tables No commands VIRTUAL BOX PARAMETERS 2352 boxes Number of boxes on each side: 28 28 3 Requested molecules per box: 1 Box dimensions: 7.14286 7.14286 6.66667 Box volumes: 340.136 Molecules per box= 0.85034 ORDER 0 REACTION PARAMETERS No reactions of order 0 ORDER 1 REACTION PARAMETERS 2 reactions defined Reactive molecule lists: rlist flist Reactants, sorted by molecule species: rabbit : r1 fox : r3 Reaction details: Reaction r1: rabbit -> rabbit + rabbit requested and actual rate constants: 10, 10 characteristic time: 0.1 conditional reaction probability per time step: 0.00995017 unbinding radius: 0 Reaction r3: fox -> 0 requested and actual rate constants: 10, 10 characteristic time: 0.1 conditional reaction probability per time step: 0.00995017 ORDER 2 REACTION PARAMETERS 1 reactions defined Reactive molecule lists: flist+rlist rlist+flist Reactants, sorted by molecule species: rabbit+fox : r2 Reaction details: Reaction r2: rabbit + fox -> fox + fox requested and actual rate constants: 8000, 8000.09 characteristic time: 0.199998 binding radius: 3.55359 unbinding radius: 0 RULES: none PARAMETER CHECK WARNING: reactive volume of rabbit is 23.4963 % of total volume WARNING: reactive volume of fox is 23.4963 % of total volume WARNING: total reactive volume is a large fraction of total volume No errors 3 total warnings Simulating Libsmoldyn notification from smolRunSim: Simulation complete [] generated polydata metadata.rdf simulation.sedml manifest.xml model.txt expected-results.json reports.h5 -------------------------------------------------------------- Running Smoldyn 2.73 CONFIGURATION FILE Path: '/tmp/tmpvykb10qa/' Name: 'model.txt' Reading file: '/tmp/tmpvykb10qa/model.txt' Loaded file successfully setting up molecules setting up virtual boxes setting up reactions setting up graphics SIMULATION PARAMETERS file: /tmp/tmpvykb10qa/model.txt starting clock time: Tue Feb 27 22:08:30 2024 3 dimensions Random number seed: 1709071710 Time from 0 to 20 step 0.001 GRAPHICS PARAMETERS No graphical output WALL PARAMETERS wall 0: dimension x, at -100, periodic wall 1: dimension x, at 100, periodic wall 2: dimension y, at -100, periodic wall 3: dimension y, at 100, periodic wall 4: dimension z, at -10, periodic wall 5: dimension z, at 10, periodic system volume: 800000 system corners: (-100,-100,-10) and (100,100,10) MOLECULE PARAMETERS 3 molecule lists: rlist, flist, unassignedlist 2 species defined: rabbit: solution: difc=100, rms step=0.447214, list=rlist, number=1000 solution: color= 1,0,0, display size= 2 fox: solution: difc=100, rms step=0.447214, list=flist, number=1000 solution: color= 0,0.5,0, display size= 3 Overall spatial resolution: 0.447214 SURFACE PARAMETERS No internal surfaces RUNTIME COMMAND INTERPRETER No output files No output data tables No commands VIRTUAL BOX PARAMETERS 2352 boxes Number of boxes on each side: 28 28 3 Requested molecules per box: 1 Box dimensions: 7.14286 7.14286 6.66667 Box volumes: 340.136 Molecules per box= 0.85034 ORDER 0 REACTION PARAMETERS No reactions of order 0 ORDER 1 REACTION PARAMETERS 2 reactions defined Reactive molecule lists: rlist flist Reactants, sorted by molecule species: rabbit : r1 fox : r3 Reaction details: Reaction r1: rabbit -> rabbit + rabbit requested and actual rate constants: 10, 10 characteristic time: 0.1 conditional reaction probability per time step: 0.00995017 unbinding radius: 0 Reaction r3: fox -> 0 requested and actual rate constants: 10, 10 characteristic time: 0.1 conditional reaction probability per time step: 0.00995017 ORDER 2 REACTION PARAMETERS 1 reactions defined Reactive molecule lists: flist+rlist rlist+flist Reactants, sorted by molecule species: rabbit+fox : r2 Reaction details: Reaction r2: rabbit + fox -> fox + fox requested and actual rate constants: 8000, 8000.09 characteristic time: 0.199998 binding radius: 3.55359 unbinding radius: 0 RULES: none PARAMETER CHECK WARNING: reactive volume of rabbit is 23.4963 % of total volume WARNING: reactive volume of fox is 23.4963 % of total volume WARNING: total reactive volume is a large fraction of total volume No errors 3 total warnings Writing trajectory to VTK ------------- Successfully wrote VTK file to /tmp/out/simulation.vtk. Reading Smoldyn Data ------------- Problem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpvykb10qa/modelout.txt'. ```
results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file. Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorProducesLinear2DPlots (0.0 s)
Test that a simulator produces linear 2D plots Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorProducesLinear3DPlots (0.0 s)
Test that a simulator produces linear 3D plots Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)
Test that a simulator produces logarithmic 2D plots Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)
Test that a simulator produces logarithmic 3D plots Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorProducesMultiplePlots (0.0 s)
Test that a simulator produces multiple plots Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)
Test that that the curated number of output dimensions matches the actual number of output dimensions Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsAlgorithmParameters (0.0 s)
Test that a simulator supports setting the values of parameters of algorithms Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)
Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)
Test that a simulator supports multiple reports per SED document Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)
Test that a simulator supports multiple tasks per SED document Exception: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)
Test that a simulator supports time courses with non-zero output start times Exception: ``` No module named 'simulariumio' ``` Log: None
biosimulators-daemon commented 6 months ago

Warnings

docker_image.DeclaresSupportedEnvironmentVariables (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_IMPORTED_MODEL_FILES' - 'VALIDATE_OMEX_MANIFESTS' - 'VALIDATE_OMEX_METADATA' - 'VALIDATE_RESULTS' - 'VALIDATE_SEDML' - 'VALIDATE_SEDML_MODELS' - 'VIZ_FORMATS' If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator. Note, support for these environment variables is optional. Simulation tools are not required to support these variables. ``` Log: None
biosimulators-daemon commented 6 months ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000086 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019, KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000027 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-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:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9000`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9000) 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_9000 and simulation algorithms KISAO_0000019 ``` 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 (0.0 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 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: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsComputeModelChanges (0.0 s)
Test that a simulator supports compute model changes Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)
Test that a simulator supports data generators with different shapes Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsModelAttributeChanges (0.0 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)
Test that a simulator supports repeated tasks with multiple subtasks Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their ``order`` attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes. Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)
Test that a simulator supports repeated tasks over vector ranges Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.SAME_METHOD`. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:`AlgorithmSubstitutionPolicy.NONE`. Reason for skip: ``` No module named 'simulariumio' ``` Log: None
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)
Test that a simulator supports multiple time courses with non-zero initial times Reason for skip: ``` No module named 'simulariumio' ``` Log: None
biosimulators-daemon commented 6 months ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/8071896564). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/8071896564).