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biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
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Submit VCell 7.4.0.48 #586

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

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 commented 2 years ago

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

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

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

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

biosimulators-daemon commented 2 years ago

The specifications of your simulator is valid!

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) 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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) 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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) 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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) 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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) 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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) 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`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000027`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000027) 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 commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.6 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports. Warnings: ``` The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports. The command-line interface does not describe the following standard environment variables recognized by BioSimulators: - 'ALGORITHM_SUBSTITUTION_POLICY' - 'BUNDLE_OUTPUTS' - 'COLLECT_COMBINE_ARCHIVE_RESULTS' - 'COLLECT_SED_DOCUMENT_RESULTS' - 'DEBUG' - 'H5_REPORTS_PATH' - 'KEEP_INDIVIDUAL_OUTPUTS' - 'LOG_PATH' - 'OMEX_METADATA_INPUT_FORMAT' - 'OMEX_METADATA_OUTPUT_FORMAT' - 'OMEX_METADATA_SCHEMA' - 'PLOTS_PATH' - 'REPORTS_PATH' - 'REPORT_FORMATS' - 'SAVE_PLOT_DATA' - 'VALIDATE_IMAGES' - 'VALIDATE_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 commented 2 years ago

Skips

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000263`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000263) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000263 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3972`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3972) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3972 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_3240`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_3240) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_3240 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9004`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9004) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Reason for skip: ``` Case requires model formats format_9004 and simulation algorithms KISAO_0000030 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9012`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9012) Algorithm: [`KISAO_0000669`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000669) Reason for skip: ``` Case requires model formats format_9012 and simulation algorithms KISAO_0000669 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000088`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000088) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000088 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_000019) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_000019 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000496`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000496) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000496 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000560`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000560) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000560 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000029`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000029) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000029 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000437`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000437) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000437 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000449`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000449) Reason for skip: ``` Case requires model formats format_2585 and simulation algorithms KISAO_0000449 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9001`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9001) Algorithm: [`KISAO_0000057`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000057) Reason for skip: ``` Case requires model formats format_9001 and simulation algorithms KISAO_0000057 ``` Log: None
published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)
Required model formats and simulation algorithms for SED tasks: * Format: [`format_9010`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_9010) Algorithm: [`KISAO_0000019`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000019) Reason for skip: ``` Case requires model formats format_9010 and simulation algorithms KISAO_0000019 ``` Log: None
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (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 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 commented 2 years ago 
- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/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 commented 2 years ago

see biosimulators/Biosimulators_test_suite#63

moraru commented 2 years ago

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