Submit VCell 7.4.0.48 #586

vcdaemon · 2022-08-29T15:51:03Z

id: vcell
version: 7.4.0.48
specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.48/biosimulators.json
specificationsPatch:
version: 7.4.0.48
image:
url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.48
digest: "sha256:03f0e622174dfaf313a40e45be7c839aecfca252b4ddefc66dff49838b2ec23e"
validateImage: true
commitSimulator: true

biosimulators-daemon · 2022-08-29T15:58:41Z

Thank you @vcdaemon for your submission to the BioSimulators simulator validation/submission system!

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

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

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

biosimulators-daemon · 2022-08-29T15:58:42Z

The specifications of your simulator is valid!

biosimulators-daemon · 2022-08-29T16:14:40Z

Summary of tests

Executed 74 test cases
Passed 17 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
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
Failed 16 test cases:
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- 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/Elowitz-Nature-2000-Repressilator
- 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:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 41 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/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
- 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-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:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- 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 · 2022-08-29T16:14:41Z

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (15.5 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (16.6 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

Report BIOMD0000000912_sim.sedml/report could not be read

Log:

Aug 29, 2022 4:10:29 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_d12a347a-5385-4175-8088-3ae68f2e809c7717855464870375729

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=5000, outputEndTime=1000.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I]

Plot2D [listOfCurves=[Curve [id=plot_1_T_time, logX=false, logY=false, name=T, xDataReference=data_gen_time, yDataReference=data_gen_T], Curve [id=plot_1_E_time, logX=false, logY=false, name=E, xDataReference=data_gen_time, yDataReference=data_gen_E], Curve [id=plot_1_I_time, logX=false, logY=false, name=I, xDataReference=data_gen_time, yDataReference=data_gen_I]], name=Figure 1 bottom, left]

org.jlibsedml.Report@c84c5553

org.jlibsedml.Report@6ca13e92

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp736587586959291773.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@497570fb

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 208 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Ignoring unsupported output `Figure_1_bottom_left` while CSV generation.

Generating report `report`.

Generating report `__plot__Figure_1_bottom_left`.

Ignoring unsupported output `Figure_1_bottom_left` while generating idNamePlotsMap.

{'report': 'null', '__plot__Figure_1_bottom_left': 'Figure 1 bottom, left', 'Figure_1_bottom_left': 'Figure 1 bottom, left'}

__plot__Figure_1_bottom_left

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (30.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Exception:

Report simulation_1.sedml/report could not be read

Log:

Aug 29, 2022 4:10:46 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_79ccbbdb-bbc4-4e47-b345-7f7f3523ffc14789218200754033930

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : simulation_1.sedml

-----------------------------------------------------------------------------------------------------

name:  simulation_1

sedml_name:  simulation_1

content.location:  ./simulation_1.sedml

content_filename:  /tmp/out/temp/./simulation_1.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000086], getId()=simulation_1]

Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1]

DataGenerator [math=org.jmathml.ASTRootNode@1d3ac898, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@1b73be9f, name=Trim, getId()=data_gen_Trim]

DataGenerator [math=org.jmathml.ASTRootNode@628c4ac0, name=Clb, getId()=data_gen_Clb]

DataGenerator [math=org.jmathml.ASTRootNode@7b84fcf8, name=Sic, getId()=data_gen_Sic]

DataGenerator [math=org.jmathml.ASTRootNode@30b19518, name=PTrim, getId()=data_gen_PTrim]

DataGenerator [math=org.jmathml.ASTRootNode@363042d7, name=PClb, getId()=data_gen_PClb]

DataGenerator [math=org.jmathml.ASTRootNode@366ac49b, name=SBF, getId()=data_gen_SBF]

DataGenerator [math=org.jmathml.ASTRootNode@6ad59d92, name=IE, getId()=data_gen_IE]

DataGenerator [math=org.jmathml.ASTRootNode@56f0cc85, name=Cdc20a, getId()=data_gen_Cdc20a]

DataGenerator [math=org.jmathml.ASTRootNode@62e20a76, name=Cdc20, getId()=data_gen_Cdc20]

DataGenerator [math=org.jmathml.ASTRootNode@2cc44ad, name=Cdh1, getId()=data_gen_Cdh1]

DataGenerator [math=org.jmathml.ASTRootNode@44b3606b, name=Swe1, getId()=data_gen_Swe1]

DataGenerator [math=org.jmathml.ASTRootNode@1477089c, name=Swe1M, getId()=data_gen_Swe1M]

DataGenerator [math=org.jmathml.ASTRootNode@663411de, name=PSwe1, getId()=data_gen_PSwe1]

DataGenerator [math=org.jmathml.ASTRootNode@63dd899, name=PSwe1M, getId()=data_gen_PSwe1M]

DataGenerator [math=org.jmathml.ASTRootNode@59d2400d, name=Mih1a, getId()=data_gen_Mih1a]

DataGenerator [math=org.jmathml.ASTRootNode@75cd8043, name=Mcm, getId()=data_gen_Mcm]

DataGenerator [math=org.jmathml.ASTRootNode@33b1c5c5, name=BE, getId()=data_gen_BE]

DataGenerator [math=org.jmathml.ASTRootNode@5b202a3a, name=Cln, getId()=data_gen_Cln]

DataGenerator [math=org.jmathml.ASTRootNode@10b9db7b, name=mass, getId()=data_gen_mass]

DataGenerator [math=org.jmathml.ASTRootNode@9ef8eb7, name=Swe1T, getId()=data_gen_Swe1T]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d]

org.jlibsedml.Report@c84c5553

org.jlibsedml.Report@49f8ba87

org.jlibsedml.Report@49f8ba88

org.jlibsedml.Report@49f8ba89

org.jlibsedml.Report@49f8ba8a

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000086' matched to RungeKuttaFehlberg

Succesful model import: SBML file /tmp/temp1983982284585066574.xml

final tolerance=0.1 final threshold=0.060000000000000005, 552 remaining (keepAtMost=1000)

Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg__Ciliberto2003_Morphogenesis' Task 'simulation 1'.

Running simulation task_1_simulation 1, 883 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Generating report `__plot__Figure_3a`.

Generating report `__plot__Figure_3b`.

Generating report `__plot__Figure_3c`.

Generating report `__plot__Figure_3d`.

Ignoring unsupported output `Figure_3a` while generating idNamePlotsMap.

Ignoring unsupported output `Figure_3b` while generating idNamePlotsMap.

Ignoring unsupported output `Figure_3c` while generating idNamePlotsMap.

Ignoring unsupported output `Figure_3d` while generating idNamePlotsMap.

{'report': 'null', '__plot__Figure_3a': 'Figure 3a', 'Figure_3a': 'Figure 3a', '__plot__Figure_3b': 'Figure 3b', 'Figure_3b': 'Figure 3b', '__plot__Figure_3c': 'Figure 3c', 'Figure_3c': 'Figure 3c', '__plot__Figure_3d': 'Figure 3d', 'Figure_3d': 'Figure 3d'}

__plot__Figure_3a

__plot__Figure_3c

__plot__Figure_3b

__plot__Figure_3d

report   :  /tmp/out/./simulation_1.sedml/report.csv

report

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (29.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

Report simulation_1.sedml/report could not be read

Log:

Aug 29, 2022 4:11:17 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_18a2fa0f-3754-42fa-9d8e-6236384955503718328879720717054

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  4 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : simulation_1.sedml

-----------------------------------------------------------------------------------------------------

name:  simulation_1

sedml_name:  simulation_1

content.location:  ./simulation_1.sedml

content_filename:  /tmp/out/temp/./simulation_1.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=Ciliberto2003_Morphogenesis, name=Ciliberto2003_Morphogenesis_Checkpoint, language=urn:sedml:language:sbml, src=BIOMD0000000297_url.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=200, outputEndTime=140.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation_1]

Task [modelReference=Ciliberto2003_Morphogenesis, name=simulation 1, simulationReference=simulation_1, getId()=task_1]

DataGenerator [math=org.jmathml.ASTRootNode@1d3ac898, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@1b73be9f, name=Trim, getId()=data_gen_Trim]

DataGenerator [math=org.jmathml.ASTRootNode@628c4ac0, name=Clb, getId()=data_gen_Clb]

DataGenerator [math=org.jmathml.ASTRootNode@7b84fcf8, name=Sic, getId()=data_gen_Sic]

DataGenerator [math=org.jmathml.ASTRootNode@30b19518, name=PTrim, getId()=data_gen_PTrim]

DataGenerator [math=org.jmathml.ASTRootNode@363042d7, name=PClb, getId()=data_gen_PClb]

DataGenerator [math=org.jmathml.ASTRootNode@366ac49b, name=SBF, getId()=data_gen_SBF]

DataGenerator [math=org.jmathml.ASTRootNode@6ad59d92, name=IE, getId()=data_gen_IE]

DataGenerator [math=org.jmathml.ASTRootNode@56f0cc85, name=Cdc20a, getId()=data_gen_Cdc20a]

DataGenerator [math=org.jmathml.ASTRootNode@62e20a76, name=Cdc20, getId()=data_gen_Cdc20]

DataGenerator [math=org.jmathml.ASTRootNode@2cc44ad, name=Cdh1, getId()=data_gen_Cdh1]

DataGenerator [math=org.jmathml.ASTRootNode@44b3606b, name=Swe1, getId()=data_gen_Swe1]

DataGenerator [math=org.jmathml.ASTRootNode@1477089c, name=Swe1M, getId()=data_gen_Swe1M]

DataGenerator [math=org.jmathml.ASTRootNode@663411de, name=PSwe1, getId()=data_gen_PSwe1]

DataGenerator [math=org.jmathml.ASTRootNode@63dd899, name=PSwe1M, getId()=data_gen_PSwe1M]

DataGenerator [math=org.jmathml.ASTRootNode@59d2400d, name=Mih1a, getId()=data_gen_Mih1a]

DataGenerator [math=org.jmathml.ASTRootNode@75cd8043, name=Mcm, getId()=data_gen_Mcm]

DataGenerator [math=org.jmathml.ASTRootNode@33b1c5c5, name=BE, getId()=data_gen_BE]

DataGenerator [math=org.jmathml.ASTRootNode@5b202a3a, name=Cln, getId()=data_gen_Cln]

DataGenerator [math=org.jmathml.ASTRootNode@10b9db7b, name=mass, getId()=data_gen_mass]

DataGenerator [math=org.jmathml.ASTRootNode@9ef8eb7, name=Swe1T, getId()=data_gen_Swe1T]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3a_Sic, logX=false, logY=false, name=Sic1, xDataReference=data_gen_time, yDataReference=data_gen_Sic], Curve [id=curve_Figure_3a_SBF, logX=false, logY=false, name=SBF, xDataReference=data_gen_time, yDataReference=data_gen_SBF], Curve [id=curve_Figure_3a_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3a_Cln, logX=false, logY=false, name=Cln, xDataReference=data_gen_time, yDataReference=data_gen_Cln]], name=Figure 3a]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3b_Cdc20a, logX=false, logY=false, name=Activated Cdc20, xDataReference=data_gen_time, yDataReference=data_gen_Cdc20a], Curve [id=curve_Figure_3b_Cdh1, logX=false, logY=false, name=Cdh1, xDataReference=data_gen_time, yDataReference=data_gen_Cdh1], Curve [id=curve_Figure_3b_Clb, logX=false, logY=false, name=Clb2, xDataReference=data_gen_time, yDataReference=data_gen_Clb], Curve [id=curve_Figure_3b_IE, logX=false, logY=false, name=Intermediary enzyme, xDataReference=data_gen_time, yDataReference=data_gen_IE]], name=Figure 3b]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3c_Swe1, logX=false, logY=false, name=Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1], Curve [id=curve_Figure_3c_Swe1M, logX=false, logY=false, name=Modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1M], Curve [id=curve_Figure_3c_Swe1T, logX=false, logY=false, name=Total Swe1, xDataReference=data_gen_time, yDataReference=data_gen_Swe1T], Curve [id=curve_Figure_3c_PSwe1M, logX=false, logY=false, name=Phosphorylated, modified Swe1, xDataReference=data_gen_time, yDataReference=data_gen_PSwe1M]], name=Figure 3c]

Plot2D [listOfCurves=[Curve [id=curve_Figure_3d_mass, logX=false, logY=false, name=Mass, xDataReference=data_gen_time, yDataReference=data_gen_mass]], name=Figure 3d]

org.jlibsedml.Report@c84c5553

org.jlibsedml.Report@49f8ba87

org.jlibsedml.Report@49f8ba88

org.jlibsedml.Report@49f8ba89

org.jlibsedml.Report@49f8ba8a

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp6690886111731734032.xml

/tmp/out/simulation_1.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7ba93755

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'.

Running simulation task_1_simulation 1, 192 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Generating report `__plot__Figure_3a`.

Generating report `__plot__Figure_3b`.

Generating report `__plot__Figure_3c`.

Generating report `__plot__Figure_3d`.

Ignoring unsupported output `Figure_3a` while generating idNamePlotsMap.

Ignoring unsupported output `Figure_3b` while generating idNamePlotsMap.

Ignoring unsupported output `Figure_3c` while generating idNamePlotsMap.

Ignoring unsupported output `Figure_3d` while generating idNamePlotsMap.

{'report': 'null', '__plot__Figure_3a': 'Figure 3a', 'Figure_3a': 'Figure 3a', '__plot__Figure_3b': 'Figure 3b', 'Figure_3b': 'Figure 3b', '__plot__Figure_3c': 'Figure 3c', 'Figure_3c': 'Figure 3c', '__plot__Figure_3d': 'Figure 3d', 'Figure_3d': 'Figure 3d'}

__plot__Figure_3a

__plot__Figure_3c

__plot__Figure_3b

__plot__Figure_3d

report   :  /tmp/out/./simulation_1.sedml/report.csv

report

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (17.3 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

Report simulation.sedml/report could not be read

Log:

Aug 29, 2022 4:11:47 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_bc421585-7453-4ab2-bba4-52bd1f6ff4f66224523997492072025

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  1 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : simulation.sedml

-----------------------------------------------------------------------------------------------------

name:  simulation

sedml_name:  simulation

content.location:  simulation.sedml

content_filename:  /tmp/out/temp/simulation.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=model, name=null, language=urn:sedml:language:sbml, src=BIOMD0000000012_url.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=600, outputEndTime=1000.0, outputStartTime=400.0, Algorithm [kisaoID=KISAO:0000019], getId()=simulation]

Task [modelReference=model, name=null, simulationReference=simulation, getId()=task]

DataGenerator [math=org.jmathml.ASTRootNode@22295ec4, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@5adb0db3, name=LacI protein, getId()=data_gen_px]

DataGenerator [math=org.jmathml.ASTRootNode@3f270e0a, name=TetR protein, getId()=data_gen_py]

DataGenerator [math=org.jmathml.ASTRootNode@1a760689, name=cI protein, getId()=data_gen_pz]

DataGenerator [math=org.jmathml.ASTRootNode@7241a47d, name=LacI mRNA, getId()=data_gen_x]

DataGenerator [math=org.jmathml.ASTRootNode@70f59913, name=TetR mRNA, getId()=data_gen_y]

DataGenerator [math=org.jmathml.ASTRootNode@77258e59, name=cI mRNA, getId()=data_gen_z]

Plot2D [listOfCurves=[Curve [id=Figure_1c_laci_protein, logX=false, logY=false, name=LacI protein, xDataReference=data_gen_time, yDataReference=data_gen_px], Curve [id=Figure_1c_tetr_protein, logX=false, logY=false, name=TetR protein, xDataReference=data_gen_time, yDataReference=data_gen_py], Curve [id=Figure_1c_ci_protein, logX=false, logY=false, name=cI protein, xDataReference=data_gen_time, yDataReference=data_gen_pz]], name=Figure 1c]

org.jlibsedml.Report@c84c5553

org.jlibsedml.Report@49f8ba4b

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp2920348679128994726.xml

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@1b9776f5

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Elowitz-Nature-2000-Repressilator__model' Task 'task'.

Running simulation task_task, 134 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Ignoring unsupported output `Figure_1c` while CSV generation.

Generating report `report`.

Generating report `__plot__Figure_1c`.

Ignoring unsupported output `Figure_1c` while generating idNamePlotsMap.

{'report': 'Report', '__plot__Figure_1c': 'Figure 1c', 'Figure_1c': 'Figure 1c'}

__plot__Figure_1c

report   :  /tmp/out/simulation.sedml/report.csv

report

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (69.1 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027

Exception:

Report simulation.sedml/report_Fig_1a could not be read

Report simulation.sedml/report_low_delta_R_det could not be read

Report simulation.sedml/report_Euler_small_step_size could not be read

Report simulation.sedml/report_Fig_1_c could not be read

Report simulation.sedml/report_low_delta_R_stoch could not be read

Log:

Aug 29, 2022 4:13:12 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_5a673c94-2eba-4eec-ba84-3aa4a09324152627667177828056193

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 4 model(s), 5 simulation(s), 5 task(s), 5  report(s),  5 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : simulation.sedml

-----------------------------------------------------------------------------------------------------

name:  simulation

sedml_name:  simulation

content.location:  simulation.sedml

content_filename:  /tmp/out/temp/simulation.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=ODE_deterministic, name=ODE deterministic, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml]

There are 0 changes.

Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml]

There are 1 changes.

Model [id=ODE_stochastic, name=ODE stochastic, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml]

There are 0 changes.

Model [id=ODE_stochastic_0, name=ODE stochastic modified, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Fig_1a]

UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=low_delta_R_det]

UniformTimeCourse [initialTime=0.0, numberOfPoints=1000, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000030 AlgorithmParameter [kisaoID=KISAO:0000483 value=0.001] ], getId()=Euler_small_step_size]

UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=Fig_1_c]

UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000027], getId()=low_delta_R_stoch]

Task [modelReference=ODE_deterministic, name=tsk_0_0, simulationReference=Fig_1a, getId()=tsk_0_0]

Task [modelReference=ODE_deterministic_0, name=tsk_0_1, simulationReference=low_delta_R_det, getId()=tsk_0_1]

Task [modelReference=ODE_deterministic, name=tsk_0_3, simulationReference=Euler_small_step_size, getId()=tsk_0_3]

Task [modelReference=ODE_stochastic, name=tsk_1_0, simulationReference=Fig_1_c, getId()=tsk_1_0]

Task [modelReference=ODE_stochastic_0, name=tsk_1_1, simulationReference=low_delta_R_stoch, getId()=tsk_1_1]

DataGenerator [math=org.jmathml.ASTRootNode@4c550889, name=time_tsk_0_0, getId()=time_tsk_0_0]

DataGenerator [math=org.jmathml.ASTRootNode@1d2bd371, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R]

DataGenerator [math=org.jmathml.ASTRootNode@44040454, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A]

DataGenerator [math=org.jmathml.ASTRootNode@65fe9e33, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R]

DataGenerator [math=org.jmathml.ASTRootNode@18bc345, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA]

DataGenerator [math=org.jmathml.ASTRootNode@42f8285e, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR]

DataGenerator [math=org.jmathml.ASTRootNode@26bab2f1, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C]

DataGenerator [math=org.jmathml.ASTRootNode@3724af13, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound]

DataGenerator [math=org.jmathml.ASTRootNode@68ead359, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound]

DataGenerator [math=org.jmathml.ASTRootNode@6b53bcc2, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_]

DataGenerator [math=org.jmathml.ASTRootNode@180da663, name=time_tsk_0_1, getId()=time_tsk_0_1]

DataGenerator [math=org.jmathml.ASTRootNode@a43ce46, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R]

DataGenerator [math=org.jmathml.ASTRootNode@340da44c, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A]

DataGenerator [math=org.jmathml.ASTRootNode@424ebba3, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R]

DataGenerator [math=org.jmathml.ASTRootNode@37052337, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA]

DataGenerator [math=org.jmathml.ASTRootNode@2320fa6f, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR]

DataGenerator [math=org.jmathml.ASTRootNode@7a560583, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C]

DataGenerator [math=org.jmathml.ASTRootNode@4d722ac9, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound]

DataGenerator [math=org.jmathml.ASTRootNode@53f0a4cb, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound]

DataGenerator [math=org.jmathml.ASTRootNode@77a7cf58, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_]

DataGenerator [math=org.jmathml.ASTRootNode@3d97a632, name=time_tsk_0_3, getId()=time_tsk_0_3]

DataGenerator [math=org.jmathml.ASTRootNode@616fe72b, name=dataGen_tsk_0_3_mRNA_R, getId()=dataGen_tsk_0_3_mRNA_R]

DataGenerator [math=org.jmathml.ASTRootNode@37efd131, name=dataGen_tsk_0_3_A, getId()=dataGen_tsk_0_3_A]

DataGenerator [math=org.jmathml.ASTRootNode@7e7b159b, name=dataGen_tsk_0_3_R, getId()=dataGen_tsk_0_3_R]

DataGenerator [math=org.jmathml.ASTRootNode@7e5d9a50, name=dataGen_tsk_0_3_PrmA, getId()=dataGen_tsk_0_3_PrmA]

DataGenerator [math=org.jmathml.ASTRootNode@60957c0f, name=dataGen_tsk_0_3_PrmR, getId()=dataGen_tsk_0_3_PrmR]

DataGenerator [math=org.jmathml.ASTRootNode@293a5f75, name=dataGen_tsk_0_3_C, getId()=dataGen_tsk_0_3_C]

DataGenerator [math=org.jmathml.ASTRootNode@fcb4004, name=dataGen_tsk_0_3_PrmA_bound, getId()=dataGen_tsk_0_3_PrmA_bound]

DataGenerator [math=org.jmathml.ASTRootNode@1dd6d4b7, name=dataGen_tsk_0_3_PrmR_bound, getId()=dataGen_tsk_0_3_PrmR_bound]

DataGenerator [math=org.jmathml.ASTRootNode@56e8b606, name=dataGen_tsk_0_3_mRNA_A_, getId()=dataGen_tsk_0_3_mRNA_A_]

DataGenerator [math=org.jmathml.ASTRootNode@2dd29a59, name=time_tsk_1_0, getId()=time_tsk_1_0]

DataGenerator [math=org.jmathml.ASTRootNode@784c3487, name=dataGen_tsk_1_0_mRNA_R, getId()=dataGen_tsk_1_0_mRNA_R]

DataGenerator [math=org.jmathml.ASTRootNode@53142455, name=dataGen_tsk_1_0_A, getId()=dataGen_tsk_1_0_A]

DataGenerator [math=org.jmathml.ASTRootNode@40dff0b7, name=dataGen_tsk_1_0_R, getId()=dataGen_tsk_1_0_R]

DataGenerator [math=org.jmathml.ASTRootNode@7966baa7, name=dataGen_tsk_1_0_PrmA, getId()=dataGen_tsk_1_0_PrmA]

DataGenerator [math=org.jmathml.ASTRootNode@60975100, name=dataGen_tsk_1_0_PrmR, getId()=dataGen_tsk_1_0_PrmR]

DataGenerator [math=org.jmathml.ASTRootNode@1253e7cb, name=dataGen_tsk_1_0_C, getId()=dataGen_tsk_1_0_C]

DataGenerator [math=org.jmathml.ASTRootNode@2d36e77e, name=dataGen_tsk_1_0_PrmA_bound, getId()=dataGen_tsk_1_0_PrmA_bound]

DataGenerator [math=org.jmathml.ASTRootNode@61c9c3fd, name=dataGen_tsk_1_0_PrmR_bound, getId()=dataGen_tsk_1_0_PrmR_bound]

DataGenerator [math=org.jmathml.ASTRootNode@3b0c9195, name=dataGen_tsk_1_0_mRNA_A_, getId()=dataGen_tsk_1_0_mRNA_A_]

DataGenerator [math=org.jmathml.ASTRootNode@366c4480, name=time_tsk_1_1, getId()=time_tsk_1_1]

DataGenerator [math=org.jmathml.ASTRootNode@2c7b5824, name=dataGen_tsk_1_1_mRNA_R, getId()=dataGen_tsk_1_1_mRNA_R]

DataGenerator [math=org.jmathml.ASTRootNode@302a07d, name=dataGen_tsk_1_1_A, getId()=dataGen_tsk_1_1_A]

DataGenerator [math=org.jmathml.ASTRootNode@5cdd09b1, name=dataGen_tsk_1_1_R, getId()=dataGen_tsk_1_1_R]

DataGenerator [math=org.jmathml.ASTRootNode@8c11eee, name=dataGen_tsk_1_1_PrmA, getId()=dataGen_tsk_1_1_PrmA]

DataGenerator [math=org.jmathml.ASTRootNode@7e8dcdaa, name=dataGen_tsk_1_1_PrmR, getId()=dataGen_tsk_1_1_PrmR]

DataGenerator [math=org.jmathml.ASTRootNode@681a8b4e, name=dataGen_tsk_1_1_C, getId()=dataGen_tsk_1_1_C]

DataGenerator [math=org.jmathml.ASTRootNode@5cbe877d, name=dataGen_tsk_1_1_PrmA_bound, getId()=dataGen_tsk_1_1_PrmA_bound]

DataGenerator [math=org.jmathml.ASTRootNode@5c08c46a, name=dataGen_tsk_1_1_PrmR_bound, getId()=dataGen_tsk_1_1_PrmR_bound]

DataGenerator [math=org.jmathml.ASTRootNode@4cf8b2dc, name=dataGen_tsk_1_1_mRNA_A_, getId()=dataGen_tsk_1_1_mRNA_A_]

Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1a_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_R], Curve [id=plot2d_Fig_1a_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=plot2d_Fig_1a_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R], Curve [id=plot2d_Fig_1a_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA], Curve [id=plot2d_Fig_1a_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR], Curve [id=plot2d_Fig_1a_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_C], Curve [id=plot2d_Fig_1a_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA_bound], Curve [id=plot2d_Fig_1a_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR_bound], Curve [id=plot2d_Fig_1a_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_A_]], name=ODE deterministicplots]

Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_detcurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_R], Curve [id=plot2d_low_delta_R_detcurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_A], Curve [id=plot2d_low_delta_R_detcurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_R], Curve [id=plot2d_low_delta_R_detcurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA], Curve [id=plot2d_low_delta_R_detcurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR], Curve [id=plot2d_low_delta_R_detcurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_C], Curve [id=plot2d_low_delta_R_detcurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA_bound], Curve [id=plot2d_low_delta_R_detcurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR_bound], Curve [id=plot2d_low_delta_R_detcurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_A_]], name=ODE deterministicplots]

Plot2D [listOfCurves=[Curve [id=plot2d_Euler_small_step_size_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_R], Curve [id=plot2d_Euler_small_step_size_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_A], Curve [id=plot2d_Euler_small_step_size_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_R], Curve [id=plot2d_Euler_small_step_size_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA], Curve [id=plot2d_Euler_small_step_size_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR], Curve [id=plot2d_Euler_small_step_size_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_C], Curve [id=plot2d_Euler_small_step_size_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmA_bound], Curve [id=plot2d_Euler_small_step_size_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_PrmR_bound], Curve [id=plot2d_Euler_small_step_size_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_3, yDataReference=dataGen_tsk_0_3_mRNA_A_]], name=ODE deterministicplots]

Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1_ccurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_mRNA_R], Curve [id=plot2d_Fig_1_ccurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_A], Curve [id=plot2d_Fig_1_ccurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_R], Curve [id=plot2d_Fig_1_ccurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmA], Curve [id=plot2d_Fig_1_ccurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmR], Curve [id=plot2d_Fig_1_ccurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_C], Curve [id=plot2d_Fig_1_ccurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmA_bound], Curve [id=plot2d_Fig_1_ccurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_PrmR_bound], Curve [id=plot2d_Fig_1_ccurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_1_0, yDataReference=dataGen_tsk_1_0_mRNA_A_]], name=ODE stochasticplots]

Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_stochcurve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_mRNA_R], Curve [id=plot2d_low_delta_R_stochcurve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_A], Curve [id=plot2d_low_delta_R_stochcurve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_R], Curve [id=plot2d_low_delta_R_stochcurve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmA], Curve [id=plot2d_low_delta_R_stochcurve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmR], Curve [id=plot2d_low_delta_R_stochcurve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_C], Curve [id=plot2d_low_delta_R_stochcurve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmA_bound], Curve [id=plot2d_low_delta_R_stochcurve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_PrmR_bound], Curve [id=plot2d_low_delta_R_stochcurve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_1_1, yDataReference=dataGen_tsk_1_1_mRNA_A_]], name=ODE stochasticplots]

org.jlibsedml.Report@86b24215

org.jlibsedml.Report@9b741608

org.jlibsedml.Report@e0c6e6ba

org.jlibsedml.Report@4f95fd0e

org.jlibsedml.Report@8fa06b88

org.jlibsedml.Report@64458c95

org.jlibsedml.Report@b2ac9b88

org.jlibsedml.Report@bde54c3a

org.jlibsedml.Report@246c028e

org.jlibsedml.Report@bacd9108

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp4860523317363331952.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp8889990253958326900.xml

Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp823410149088250706.xml

Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp2631738380399857899.xml

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@160e99e0

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'.

Running simulation tsk_0_0_tsk_0_0, 114 ms

-----------------------------------------------------------------------------------------------------

Solver status: 3

Solver message: simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity



Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'. 

Running simulation for 29 ms

simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

 

-----------------------------------------------------------------------------------------------------

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@2c1f8dbd

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'.

Running simulation tsk_0_1_tsk_0_1, 48 ms

-----------------------------------------------------------------------------------------------------

cbit.vcell.solver.stoch.GibsonSolver@481b2f10

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'.

Running simulation tsk_1_0_tsk_1_0, 283 ms

-----------------------------------------------------------------------------------------------------

cbit.vcell.solver.stoch.GibsonSolver@5f726750

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'.

Running simulation tsk_1_1_tsk_1_1, 188 ms

-----------------------------------------------------------------------------------------------------

Ran 5 simulations for 4 biomodels.

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_small_step_size`.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Generating report `__plot__plot2d_Fig_1a`.

Generating report `__plot__plot2d_low_delta_R_det`.

Generating report `__plot__plot2d_Euler_small_step_size`.

Generating report `__plot__plot2d_Fig_1_c`.

Generating report `__plot__plot2d_low_delta_R_stoch`.

Ignoring unsupported output `plot2d_Fig_1a` while generating idNamePlotsMap.

Ignoring unsupported output `plot2d_low_delta_R_det` while generating idNamePlotsMap.

Ignoring unsupported output `plot2d_Euler_small_step_size` while generating idNamePlotsMap.

Ignoring unsupported output `plot2d_Fig_1_c` while generating idNamePlotsMap.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while generating idNamePlotsMap.

{'report_Fig_1a': 'null', 'report_low_delta_R_det': 'null', 'report_Euler_small_step_size': 'null', 'report_Fig_1_c': 'null', 'report_low_delta_R_stoch': 'null', '__plot__plot2d_Fig_1a': 'ODE deterministicplots', 'plot2d_Fig_1a': 'ODE deterministicplots', '__plot__plot2d_low_delta_R_det': 'ODE deterministicplots', 'plot2d_low_delta_R_det': 'ODE deterministicplots', '__plot__plot2d_Euler_small_step_size': 'ODE deterministicplots', 'plot2d_Euler_small_step_size': 'ODE deterministicplots', '__plot__plot2d_Fig_1_c': 'ODE stochasticplots', 'plot2d_Fig_1_c': 'ODE stochasticplots', '__plot__plot2d_low_delta_R_stoch': 'ODE stochasticplots', 'plot2d_low_delta_R_stoch': 'ODE stochasticplots'}

__plot__plot2d_Fig_1_c

report   :  /tmp/out/simulation.sedml/report_low_delta_R_stoch.csv

report_low_delta_R_stoch

__plot__plot2d_Fig_1a

report   :  /tmp/out/simulation.sedml/report_Fig_1a.csv

report_Fig_1a

report   :  /tmp/out/simulation.sedml/report_Fig_1_c.csv

report_Fig_1_c

report   :  /tmp/out/simulation.sedml/report_low_delta_R_det.csv

report_low_delta_R_det

report   :  /tmp/out/simulation.sedml/report_Euler_small_step_size.csv

report_Euler_small_step_size

__plot__plot2d_low_delta_R_stoch

__plot__plot2d_Euler_small_step_size

__plot__plot2d_low_delta_R_det

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (34.5 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

Report simulation.sedml/report_Fig_1a could not be read

Report simulation.sedml/report_low_delta_R_det could not be read

Log:

Aug 29, 2022 4:12:04 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_7c80013e-cf4d-453b-a9ad-94f22482ed7e2865470472409588343

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2  report(s),  3 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : simulation.sedml

-----------------------------------------------------------------------------------------------------

name:  simulation

sedml_name:  simulation

content.location:  simulation.sedml

content_filename:  /tmp/out/temp/simulation.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=ODE_deterministic, name=ODE deterministic, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml]

There are 0 changes.

Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=Fig_1a]

UniformTimeCourse [initialTime=0.0, numberOfPoints=400, outputEndTime=200.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019 AlgorithmParameter [kisaoID=KISAO:0000211 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000209 value=1.0E-9]  AlgorithmParameter [kisaoID=KISAO:0000467 value=1.0] ], getId()=low_delta_R_det]

Task [modelReference=ODE_deterministic, name=tsk_0_0, simulationReference=Fig_1a, getId()=tsk_0_0]

Task [modelReference=ODE_deterministic_0, name=tsk_0_1, simulationReference=low_delta_R_det, getId()=tsk_0_1]

DataGenerator [math=org.jmathml.ASTRootNode@eda25e5, name=time_tsk_0_0, getId()=time_tsk_0_0]

DataGenerator [math=org.jmathml.ASTRootNode@7cf6a5f9, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R]

DataGenerator [math=org.jmathml.ASTRootNode@623e088f, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A]

DataGenerator [math=org.jmathml.ASTRootNode@39fcbef6, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R]

DataGenerator [math=org.jmathml.ASTRootNode@66565121, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA]

DataGenerator [math=org.jmathml.ASTRootNode@2fc6f97f, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR]

DataGenerator [math=org.jmathml.ASTRootNode@3d2ee678, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C]

DataGenerator [math=org.jmathml.ASTRootNode@6179e425, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound]

DataGenerator [math=org.jmathml.ASTRootNode@35f26e72, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound]

DataGenerator [math=org.jmathml.ASTRootNode@2d6764b2, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_]

DataGenerator [math=org.jmathml.ASTRootNode@67304a40, name=time_tsk_0_1, getId()=time_tsk_0_1]

DataGenerator [math=org.jmathml.ASTRootNode@49c6c24f, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R]

DataGenerator [math=org.jmathml.ASTRootNode@6fe1b4fb, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A]

DataGenerator [math=org.jmathml.ASTRootNode@79351f41, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R]

DataGenerator [math=org.jmathml.ASTRootNode@1c32386d, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA]

DataGenerator [math=org.jmathml.ASTRootNode@6399551e, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR]

DataGenerator [math=org.jmathml.ASTRootNode@13d73fa, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C]

DataGenerator [math=org.jmathml.ASTRootNode@5023bb8b, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound]

DataGenerator [math=org.jmathml.ASTRootNode@5d5f10b2, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound]

DataGenerator [math=org.jmathml.ASTRootNode@74c79fa2, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_]

Plot2D [listOfCurves=[Curve [id=Figure_2ab_curve_1, logX=false, logY=false, name=A, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=Figure_2ab_curve_2, logX=false, logY=false, name=R, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R]], name=Figure 2ab]

Plot2D [listOfCurves=[Curve [id=plot2d_Fig_1a_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_R], Curve [id=plot2d_Fig_1a_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_A], Curve [id=plot2d_Fig_1a_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_R], Curve [id=plot2d_Fig_1a_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA], Curve [id=plot2d_Fig_1a_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR], Curve [id=plot2d_Fig_1a_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_C], Curve [id=plot2d_Fig_1a_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmA_bound], Curve [id=plot2d_Fig_1a_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_PrmR_bound], Curve [id=plot2d_Fig_1a_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_0, yDataReference=dataGen_tsk_0_0_mRNA_A_]], name=ODE deterministicplots]

Plot2D [listOfCurves=[Curve [id=plot2d_low_delta_R_det_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_R], Curve [id=plot2d_low_delta_R_det_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_A], Curve [id=plot2d_low_delta_R_det_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_R], Curve [id=plot2d_low_delta_R_det_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA], Curve [id=plot2d_low_delta_R_det_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR], Curve [id=plot2d_low_delta_R_det_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_C], Curve [id=plot2d_low_delta_R_det_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmA_bound], Curve [id=plot2d_low_delta_R_det_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_PrmR_bound], Curve [id=plot2d_low_delta_R_det_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_1, yDataReference=dataGen_tsk_0_1_mRNA_A_]], name=ODE deterministicplots]

org.jlibsedml.Report@86b24215

org.jlibsedml.Report@9b741608

org.jlibsedml.Report@f51e8f58

org.jlibsedml.Report@64458c95

org.jlibsedml.Report@b2ac9b88

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp7219904298501203626.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp4460455340156228860.xml

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@17b016ac

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_0'.

Running simulation tsk_0_0_tsk_0_0, 137 ms

-----------------------------------------------------------------------------------------------------

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@62cba181

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic_0' Task 'tsk_0_1'.

Running simulation tsk_0_1_tsk_0_1, 47 ms

-----------------------------------------------------------------------------------------------------

Ran 2 simulations for 2 biomodels.

Ignoring unsupported output `Figure_2ab` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `__plot__Figure_2ab`.

Generating report `__plot__plot2d_Fig_1a`.

Generating report `__plot__plot2d_low_delta_R_det`.

Ignoring unsupported output `Figure_2ab` while generating idNamePlotsMap.

Ignoring unsupported output `plot2d_Fig_1a` while generating idNamePlotsMap.

Ignoring unsupported output `plot2d_low_delta_R_det` while generating idNamePlotsMap.

{'report_Fig_1a': 'null', 'report_low_delta_R_det': 'null', '__plot__Figure_2ab': 'Figure 2ab', 'Figure_2ab': 'Figure 2ab', '__plot__plot2d_Fig_1a': 'ODE deterministicplots', 'plot2d_Fig_1a': 'ODE deterministicplots', '__plot__plot2d_low_delta_R_det': 'ODE deterministicplots', 'plot2d_low_delta_R_det': 'ODE deterministicplots'}

__plot__Figure_2ab

__plot__plot2d_Fig_1a

report   :  /tmp/out/simulation.sedml/report_Fig_1a.csv

report_Fig_1a

report   :  /tmp/out/simulation.sedml/report_low_delta_R_det.csv

report_low_delta_R_det

__plot__plot2d_low_delta_R_det

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (33.5 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Exception:

Report simulation.sedml/report_Fig_1_c could not be read

Report simulation.sedml/report_low_delta_R_stoch could not be read

Log:

Aug 29, 2022 4:12:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_925d1351 ...

biosimulators-daemon · 2022-08-29T16:14:42Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.6 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

cli.CliDisplaysHelpInline (1.7 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log: None

cli.CliDisplaysVersionInformationInline (1.3 s)

Test that a command-line interface provides version information inline.

Warnings:

Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

  usage: VCell [-h] [-q] -i ARCHIVE [-o OUT_DIR] [-v] [-vcml]

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.4 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

biosimulators-daemon · 2022-08-29T16:14:42Z

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/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/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-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:smoldyn/Lotka-Volterra (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:

Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log: None

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

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (12.4 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

Aug 29, 2022 4:03:52 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_44da0b51-be4c-4eb4-b799-312946e001f22461528418128566479

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__]

There are 0 changes.

Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 0 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@176b3f44, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@6ee6f53, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp851615073971963720.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@46baf579

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 86 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (12.5 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:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

Aug 29, 2022 4:04:04 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_5c37135d-56f9-4bc0-8b62-a5c0dfbc87e9979535544595977132

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=#__source__]

There are 0 changes.

Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp3231822485510347676.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@497570fb

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 86 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorProducesLinear3DPlots (0.3 s)

Test that a simulator produces linear 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.3 s)

Test that a simulator produces logarithmic 3D plots

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (26.1 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

Aug 29, 2022 4:04:57 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_76d307fe-adeb-4032-8976-d272600e70ba5928104857545753401

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 1 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@797cf65c, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp1591069369245286952.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@412c995d

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 84 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

Aug 29, 2022 4:05:10 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_22157d3c-614e-426a-a022-3b34f9a855238931893595927119549

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 2 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@a776e, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@792bbc74, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@79145d5a, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@1f2f9244, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp8051944945298975810.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3051e0b2

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 79 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (26.8 s)

Test that a simulator supports compute model changes

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

Aug 29, 2022 4:05:36 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_549d16df-c655-4c57-a843-7c0e2bbb3a526803176167301837103

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 36 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@7ec3394b, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@bff34c6, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1522d8a0, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@312ab28e, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp4475693998831194382.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@26e412ef

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 75 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

Aug 29, 2022 4:05:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_2304eb0c-f5fc-4d4b-b203-470bee5b6ee877858441161846400

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 72 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@7ec3394b, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@bff34c6, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@1522d8a0, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@312ab28e, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp7120502357610831989.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@60d1b21f

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 81 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (13.2 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

Aug 29, 2022 4:06:03 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_c68be1aa-aa6d-49b5-b27f-867babbe529f8593683219782507085

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 0 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

UniformTimeCourse [initialTime=0.0, numberOfPoints=20, outputEndTime=4.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim__copy_2]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

Task [modelReference=BIOMD0000000912, name=null, simulationReference=BIOMD0000000912_sim__copy_2, getId()=BIOMD0000000912_task__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@3da05287, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@1e636ea3, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@115667d, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@736caf7a, name=I, getId()=data_gen_I]

DataGenerator [math=org.jmathml.ASTRootNode@4ce7fffa, name=null, getId()=data_gen_time__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@497486b3, name=null, getId()=data_gen_T__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@63f8276e, name=null, getId()=data_gen_E__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@75f95314, name=null, getId()=data_gen_I__copy_2]

org.jlibsedml.Report@704e371b

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp5627735593666530374.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3d7cc3cb

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 83 ms

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5a9800f8

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 36 ms

-----------------------------------------------------------------------------------------------------

Ran 2 simulations for 1 biomodels.

Generating report `report__copy_2`.

{'report__copy_2': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report__copy_2.csv

report__copy_2

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (13.7 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpvw30eesj/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

Aug 29, 2022 4:06:16 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_31c763bc-7534-496f-acfe-8eff6fae213a7952852173741883030

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 0 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

UniformTimeCourse [initialTime=0.0, numberOfPoints=20, outputEndTime=4.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim__copy_2]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

Task [modelReference=BIOMD0000000912, name=null, simulationReference=BIOMD0000000912_sim__copy_2, getId()=BIOMD0000000912_task__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@2250b9f2, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@7e3181aa, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@253d9f73, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@142269f2, name=I, getId()=data_gen_I]

DataGenerator [math=org.jmathml.ASTRootNode@331acdad, name=null, getId()=data_gen_time__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@41d426b5, name=null, getId()=data_gen_T__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@8dbfffb, name=null, getId()=data_gen_E__copy_2]

DataGenerator [math=org.jmathml.ASTRootNode@f316aeb, name=null, getId()=data_gen_I__copy_2]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp2670051388002253594.xml

Task (id='BIOMD0000000912_task__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@40620d8e

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 106 ms

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7d151a

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 46 ms

-----------------------------------------------------------------------------------------------------

Ran 2 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 433, in <module>

    fire.Fire({

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 466, in _Fire

    component, remaining_args = _CallAndUpdateTrace(

  File "/usr/local/lib/python3.8/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py", line 166, in exec_plot_output_sed_doc

    data_set_df = pd.read_csv(report_filename, header=None).T

  File "/usr/local/lib/python3.8/dist-packages/pandas/util/_decorators.py", line 311, in wrapper

    return func(*args, **kwargs)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 680, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 581, in _read

    return parser.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1254, in read

    index, columns, col_dict = self._engine.read(nrows)

  File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/c_parser_wrapper.py", line 225, in read

    chunks = self._reader.read_low_memory(nrows)

  File "pandas/_libs/parsers.pyx", line 805, in pandas._libs.parsers.TextReader.read_low_memory

  File "pandas/_libs/parsers.pyx", line 861, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 1960, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 14 fields in line 5, saw 24



HDF conversion failed

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsModelAttributeChanges (27.9 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indices

Log:

Aug 29, 2022 4:06:30 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f3f8168a-1565-4b93-b09d-de7f88de28c76791613649783052865

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 226 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp7409261109650223699.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3b6c624

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 95 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

Aug 29, 2022 4:06:43 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_df5c52bb-f702-449e-81a9-f21bc2935db98453507927752205015

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)



Successful translation of SED-ML file : BIOMD0000000912_sim.sedml

-----------------------------------------------------------------------------------------------------

name:  BIOMD0000000912_sim

sedml_name:  BIOMD0000000912_sim

content.location:  ./BIOMD0000000912_sim.sedml

content_filename:  /tmp/out/temp/./BIOMD0000000912_sim.sedml

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Starting simulate all tasks... 

Model [id=BIOMD0000000912, name=Caravagna2010 - Tumour suppression by immune system, language=urn:sedml:language:sbml, src=Caravagna2010.xml]

There are 452 changes.

UniformTimeCourse [initialTime=0.0, numberOfPoints=10, outputEndTime=2.0, outputStartTime=0.0, Algorithm [kisaoID=KISAO:0000019], getId()=BIOMD0000000912_sim]

Task [modelReference=BIOMD0000000912, name=Caravagna2010, simulationReference=BIOMD0000000912_sim, getId()=BIOMD0000000912_task]

DataGenerator [math=org.jmathml.ASTRootNode@421bba99, name=time, getId()=data_gen_time]

DataGenerator [math=org.jmathml.ASTRootNode@5d12a356, name=T, getId()=data_gen_T]

DataGenerator [math=org.jmathml.ASTRootNode@134d26af, name=E, getId()=data_gen_E]

DataGenerator [math=org.jmathml.ASTRootNode@66ac5762, name=I, getId()=data_gen_I]

org.jlibsedml.Report@c84c5553

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

SBML Import: no assignment rules.

SBML Import: no assignment rules.

LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:

- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters. 



User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.



Succesful model import: SBML file /tmp/temp4525596298708065941.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@552ed807

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

Running simulation BIOMD0000000912_task_Caravagna2010, 77 ms

-----------------------------------------------------------------------------------------------------

Ran 1 simulations for 1 biomodels.

Generating report `report`.

{'report': 'null'}

report   :  /tmp/out/./BIOMD0000000912_sim.sedml/report.csv

report

HDF conversion successful

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (7.8 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpvw30eesj/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

Aug 29, 2022 4:07:40 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_d70fb15d-e19d-4fa8-9470-da18b68f7f211853461137931808338

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182)

SED-ML processing for /tmp/vcell_temp_d70fb15d-e19d-4fa8-9470-da18b68f7f211853461137931808338/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182)

 All sedml documents in this archive failed to execute

Aug 29, 2022 4:07:44 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell CLI input archive /tmp/in/archive.omex

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_8a4aedca-9474-4101-8962-3421cc1467ad2316230475435259896

Python 3.8.10

utilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils

cliUtilPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils

cliPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/cli.py

statusPath: /usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py

SED-ML version level not supported, import may fail

java.lang.NullPointerException

	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182)

SED-ML processing for /tmp/vcell_temp_8a4aedca-9474-4101-8962-3421cc1467ad2316230475435259896/BIOMD0000000912_sim.sedml failed with error: null

org.jlibsedml.XMLException

	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)

	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)

	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:363)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:353)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:182)

 All sedml documents in this archive failed to execute

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (8.0 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpvw30eesj/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:

Aug 29, 2022 4:07:48 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

ServerID=7.3.0.16, SoftwareVersion=unknown

VCell  ...

biosimulators-daemon · 2022-08-29T16:14:45Z

- 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/2949895266). 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/2949895266).

CodeByDrescher · 2022-09-01T21:38:40Z

see biosimulators/Biosimulators_test_suite#63

moraru · 2022-09-02T03:49:54Z

This was a test resubmission of previously validated container to confirm that failures are due to issue with test suite - which they are, see previous comment

vcdaemon added the Validate/submit simulator Validate a simulation tool or request its submission to the BioSimulators registry label Aug 29, 2022

biosimulators-daemon added the Invalid This doesn't seem right label Aug 29, 2022

moraru mentioned this issue Aug 29, 2022

Resubmit VCell 7.4.0.48: #585

Closed

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moraru closed this as completed Sep 2, 2022

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Submit VCell 7.4.0.48 #586

Submit VCell 7.4.0.48 #586

vcdaemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

CodeByDrescher commented Sep 1, 2022

moraru commented Sep 2, 2022

Submit VCell 7.4.0.48 #586

Submit VCell 7.4.0.48 #586

Comments

vcdaemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

biosimulators-daemon commented Aug 29, 2022

Summary of tests

biosimulators-daemon commented Aug 29, 2022

Failures

biosimulators-daemon commented Aug 29, 2022

Warnings

biosimulators-daemon commented Aug 29, 2022

Skips

biosimulators-daemon commented Aug 29, 2022

CodeByDrescher commented Sep 1, 2022

moraru commented Sep 2, 2022