Submit Smoldyn 2.73 #671

ssandrews · 2024-02-27T22:00:00Z

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 · 2024-02-27T22:05:03Z

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 · 2024-02-27T22:05:05Z

The specifications of your simulator is valid!

biosimulators-daemon · 2024-02-27T22:09:01Z

Summary of tests

Executed 74 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 22 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 45 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-fbc/Escherichia-coli-core-metabolism
- 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:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsComputeModelChanges
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelAttributeChanges
- sedml.SimulatorSupportsRepeatedTasksWithChanges
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
- sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
- sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
- sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
- sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
- sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
- sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
- sedml.SimulatorSupportsSubstitutingAlgorithms
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

biosimulators-daemon · 2024-02-27T22:09:01Z

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
Algorithm: KISAO_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 -------------

�[31mProblem with input file: Error reading input smoldyn data: [Errno 2] No such file or directory: '/tmp/tmpvykb10qa/modelout.txt'.�[0m

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 · 2024-02-27T22:09:02Z

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 · 2024-02-27T22:09:02Z

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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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
Algorithm: KISAO_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 · 2024-02-27T22:09:03Z

- 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).

ssandrews added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Feb 27, 2024

biosimulators-daemon added the Invalid This doesn't seem right label Feb 27, 2024

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Submit Smoldyn 2.73 #671

Submit Smoldyn 2.73 #671

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biosimulators-daemon commented Feb 27, 2024

Submit Smoldyn 2.73 #671

Submit Smoldyn 2.73 #671

Comments

ssandrews commented Feb 27, 2024

biosimulators-daemon commented Feb 27, 2024

biosimulators-daemon commented Feb 27, 2024

biosimulators-daemon commented Feb 27, 2024

Summary of tests

biosimulators-daemon commented Feb 27, 2024

Failures

biosimulators-daemon commented Feb 27, 2024

Warnings

biosimulators-daemon commented Feb 27, 2024

Skips

biosimulators-daemon commented Feb 27, 2024