search

biosimulators / Biosimulators

Registry of containerized biosimulation tools that support a standard command-line interface
https://biosimulators.org
MIT License
13 stars 0 forks source link

Submit VCell 7.4.0.26 #465

Closed vcdaemon closed 2 years ago

vcdaemon commented 2 years ago

id: vcell version: 7.4.0.26 specificationsUrl: https://github.com/virtualcell/vcell/releases/download/7.4.0.26/biosimulators.json specificationsPatch: version: 7.4.0.26 image: url: ghcr.io/virtualcell/biosimulators_vcell:7.4.0.26 digest: "sha256:9777aa903ee1cde473fcdf2121679d5f4425a90b175db45385c35171dbeeda6f" 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

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

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.4 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_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 (2.5 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 (1.9 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 (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - '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_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 (0.3 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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (15.7 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) Warnings: ``` Unexpected reports were produced: BIOMD0000000912_sim.sedml/Figure_1_bottom_left ``` Log: ``` Nov 11, 2021 5:37:12 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_d23171d6-4ab4-4da3-a4fc-d014060ca7756992468439708205083 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 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] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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/temp3510147063070003177.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 158 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`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv 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 (31.8 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) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 11, 2021 5:37:28 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_d1e9ab36-533f-4ae2-b7b3-8dbbf520c2fc2088516982545221780 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 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] 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@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, 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/temp630255161296455990.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, 837 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`. report : /tmp/out/./simulation_1.sedml/report.csv 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 (31.3 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) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 11, 2021 5:38:00 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_8ddca928-c5ce-48bb-8ea6-2884adc2b54d4699173555905722850 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 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] 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@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, 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/temp7468375968450099889.xml /tmp/out/simulation_1.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@74834afd 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, 188 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`. report : /tmp/out/./simulation_1.sedml/report.csv 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 (16.2 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_1c ``` Log: ``` Nov 11, 2021 5:38:32 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_c72e39a9-2762-4932-a61a-16cb220c11ab9054547496679941302 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 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] 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@146dfe6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@4716be8b, name=LacI protein, getId()=data_gen_px] DataGenerator [math=org.jmathml.ASTRootNode@1fc32e4f, name=TetR protein, getId()=data_gen_py] DataGenerator [math=org.jmathml.ASTRootNode@2f67b837, name=cI protein, getId()=data_gen_pz] DataGenerator [math=org.jmathml.ASTRootNode@1869fbd2, name=LacI mRNA, getId()=data_gen_x] DataGenerator [math=org.jmathml.ASTRootNode@6af9fcb2, name=TetR mRNA, getId()=data_gen_y] DataGenerator [math=org.jmathml.ASTRootNode@6cce16f4, 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/temp196473845212518169.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@64f16277 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Elowitz-Nature-2000-Repressilator__model' Task 'task'. Running simulation task_task, 118 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_1c` while CSV generation. Generating report `report`. Generating report `__plot__Figure_1c`. report : /tmp/out/simulation.sedml/report.csv 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 (80.6 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) * 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) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Warnings: ``` Unexpected reports were produced: simulation.sedml/plot2d_Euler_default simulation.sedml/plot2d_Euler_small_step_size simulation.sedml/plot2d_Fig_1_c simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det simulation.sedml/plot2d_low_delta_R_stoch ``` Log: ``` Nov 11, 2021 5:39:53 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_05dc64dc-efbd-4735-8208-9d37df3819bb5854181139415134145 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), 6 simulation(s), 6 task(s), 6 report(s), 6 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation 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] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_stochastic, name=ODE stochastic, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] Model [id=ODE_stochastic_0, name=ODE stochastic modified, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] 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=0.1] ], getId()=Euler_default] 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_2, simulationReference=Euler_default, getId()=tsk_0_2] 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@635572a7, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@79d94571, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4dd02341, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3212a8d7, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@7a1a3478, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@495b0487, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@55dfcc6, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@222eb8aa, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@93cf163, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@1852a3ff, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@7203c7ff, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@25bfcafd, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4b6690c0, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@46268f08, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@2a76840c, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@71454b9d, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@eda25e5, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@7cf6a5f9, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@623e088f, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@39fcbef6, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@66565121, name=time_tsk_0_2, getId()=time_tsk_0_2] DataGenerator [math=org.jmathml.ASTRootNode@2fc6f97f, name=dataGen_tsk_0_2_mRNA_R, getId()=dataGen_tsk_0_2_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@3d2ee678, name=dataGen_tsk_0_2_A, getId()=dataGen_tsk_0_2_A] DataGenerator [math=org.jmathml.ASTRootNode@6179e425, name=dataGen_tsk_0_2_R, getId()=dataGen_tsk_0_2_R] DataGenerator [math=org.jmathml.ASTRootNode@35f26e72, name=dataGen_tsk_0_2_PrmA, getId()=dataGen_tsk_0_2_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@2d6764b2, name=dataGen_tsk_0_2_PrmR, getId()=dataGen_tsk_0_2_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@67304a40, name=dataGen_tsk_0_2_C, getId()=dataGen_tsk_0_2_C] DataGenerator [math=org.jmathml.ASTRootNode@49c6c24f, name=dataGen_tsk_0_2_PrmA_bound, getId()=dataGen_tsk_0_2_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@6fe1b4fb, name=dataGen_tsk_0_2_PrmR_bound, getId()=dataGen_tsk_0_2_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@79351f41, name=dataGen_tsk_0_2_mRNA_A_, getId()=dataGen_tsk_0_2_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@1c32386d, name=time_tsk_0_3, getId()=time_tsk_0_3] DataGenerator [math=org.jmathml.ASTRootNode@6399551e, name=dataGen_tsk_0_3_mRNA_R, getId()=dataGen_tsk_0_3_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@13d73fa, name=dataGen_tsk_0_3_A, getId()=dataGen_tsk_0_3_A] DataGenerator [math=org.jmathml.ASTRootNode@5023bb8b, name=dataGen_tsk_0_3_R, getId()=dataGen_tsk_0_3_R] DataGenerator [math=org.jmathml.ASTRootNode@5d5f10b2, name=dataGen_tsk_0_3_PrmA, getId()=dataGen_tsk_0_3_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@74c79fa2, name=dataGen_tsk_0_3_PrmR, getId()=dataGen_tsk_0_3_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1e0f9063, name=dataGen_tsk_0_3_C, getId()=dataGen_tsk_0_3_C] DataGenerator [math=org.jmathml.ASTRootNode@53bd8fca, name=dataGen_tsk_0_3_PrmA_bound, getId()=dataGen_tsk_0_3_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@7642df8f, name=dataGen_tsk_0_3_PrmR_bound, getId()=dataGen_tsk_0_3_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@3e30646a, name=dataGen_tsk_0_3_mRNA_A_, getId()=dataGen_tsk_0_3_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@5cde6747, name=time_tsk_1_0, getId()=time_tsk_1_0] DataGenerator [math=org.jmathml.ASTRootNode@63a270c9, name=dataGen_tsk_1_0_mRNA_R, getId()=dataGen_tsk_1_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@37c7595, name=dataGen_tsk_1_0_A, getId()=dataGen_tsk_1_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3ed242a4, name=dataGen_tsk_1_0_R, getId()=dataGen_tsk_1_0_R] DataGenerator [math=org.jmathml.ASTRootNode@1199fe66, name=dataGen_tsk_1_0_PrmA, getId()=dataGen_tsk_1_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@614df0a4, name=dataGen_tsk_1_0_PrmR, getId()=dataGen_tsk_1_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1fdf1c5, name=dataGen_tsk_1_0_C, getId()=dataGen_tsk_1_0_C] DataGenerator [math=org.jmathml.ASTRootNode@2d96543c, name=dataGen_tsk_1_0_PrmA_bound, getId()=dataGen_tsk_1_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@73a2e526, name=dataGen_tsk_1_0_PrmR_bound, getId()=dataGen_tsk_1_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@7d64e326, name=dataGen_tsk_1_0_mRNA_A_, getId()=dataGen_tsk_1_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@13f95696, name=time_tsk_1_1, getId()=time_tsk_1_1] DataGenerator [math=org.jmathml.ASTRootNode@cd1d761, name=dataGen_tsk_1_1_mRNA_R, getId()=dataGen_tsk_1_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@68be8808, name=dataGen_tsk_1_1_A, getId()=dataGen_tsk_1_1_A] DataGenerator [math=org.jmathml.ASTRootNode@32193bea, name=dataGen_tsk_1_1_R, getId()=dataGen_tsk_1_1_R] DataGenerator [math=org.jmathml.ASTRootNode@6b8d96d9, name=dataGen_tsk_1_1_PrmA, getId()=dataGen_tsk_1_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@69653e16, name=dataGen_tsk_1_1_PrmR, getId()=dataGen_tsk_1_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@758705fa, name=dataGen_tsk_1_1_C, getId()=dataGen_tsk_1_1_C] DataGenerator [math=org.jmathml.ASTRootNode@ebaa6cb, name=dataGen_tsk_1_1_PrmA_bound, getId()=dataGen_tsk_1_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@906d29b, name=dataGen_tsk_1_1_PrmR_bound, getId()=dataGen_tsk_1_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@49d3c823, 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_default_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_R], Curve [id=plot2d_Euler_default_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_A], Curve [id=plot2d_Euler_default_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_R], Curve [id=plot2d_Euler_default_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA], Curve [id=plot2d_Euler_default_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR], Curve [id=plot2d_Euler_default_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_C], Curve [id=plot2d_Euler_default_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA_bound], Curve [id=plot2d_Euler_default_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR_bound], Curve [id=plot2d_Euler_default_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_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@2d86479f org.jlibsedml.Report@e0c6e6ba org.jlibsedml.Report@4f95fd0e org.jlibsedml.Report@8fa06b88 org.jlibsedml.Report@64458c95 org.jlibsedml.Report@b2ac9b88 org.jlibsedml.Report@7c222d1f 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/temp9052593165540672128.xml Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp6202222232887778506.xml Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler 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/temp8303860888566004394.xml Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson Succesful model import: SBML file /tmp/temp2362451184279349980.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@7dee835 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, 123 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_2'. Running simulation for 23 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 Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 255, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML ----------------------------------------------------------------------------------------------------- final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000) Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'. Running simulation tsk_0_3_tsk_0_3, 805 ms ----------------------------------------------------------------------------------------------------- /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@43471a7e 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, 53 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@4b56b031 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, 286 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@733e6df7 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, 187 ms ----------------------------------------------------------------------------------------------------- Ran 6 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_default` 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_default`. 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_default`. Generating report `__plot__plot2d_Euler_small_step_size`. Generating report `__plot__plot2d_Fig_1_c`. Generating report `__plot__plot2d_low_delta_R_stoch`. report : /tmp/out/simulation.sedml/report_Euler_default.csv report : /tmp/out/simulation.sedml/report_Fig_1_c.csv report : /tmp/out/simulation.sedml/report_low_delta_R_stoch.csv report : /tmp/out/simulation.sedml/report_Fig_1a.csv report : /tmp/out/simulation.sedml/report_Euler_small_step_size.csv report : /tmp/out/simulation.sedml/report_low_delta_R_det.csv 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 (32.7 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_2ab simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det ``` Log: ``` Nov 11, 2021 5:38:48 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_4bcff4af-4f1d-4d03-8939-5ad6ce2b24fc7063814984677509648 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 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] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] 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@7fb95505, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@58be6e8, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@7331196b, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3f9342d4, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@ab7395e, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@50d13246, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@2bd08376, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@e70f13a, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@3d3e5463, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@64a40280, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@4b40f651, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@42b02722, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@d62fe5b, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@49964d75, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@528c868, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@466276d8, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@5ce8d869, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@27eedb64, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@64c63c79, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@31c7528f, 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], ...
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 (7.2 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 11, 2021 5:30:52 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2807188b-5802-449f-bbda-c27d53607fe559604921516919912 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 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__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 247, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML All sedml documents in this archive failed to execute ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (7.2 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: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 11, 2021 5:30:59 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_0ab3243b-9b04-4a3c-b0b5-91830e4163623802268182511304338 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 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__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 247, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML All sedml documents in this archive failed to execute ```
sedml.SimulatorProducesLinear3DPlots (0.4 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 (0.4 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 (0.4 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 (12.5 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 11, 2021 5:32:30 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1d0c1a7c-e0c1-4b87-beb2-d885bb1687312744166650965399614 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 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] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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/temp1333423497302090278.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 83 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (14.1 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 11, 2021 5:32:56 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5e85ecb3-7119-4c10-971b-735b487b9e987954226986388584410 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 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] 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@7ca33c24, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@fade1fc, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@67c2e933, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@41dd05a, 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/temp763206626543631184.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@6f952d6c Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 88 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (13.9 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/tmps1fmk329/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:33:25 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_6d5601d7-85ce-4a98-ae98-9236139f98a77538213561599275447 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 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] 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@291a7e3c, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@ca30bc1, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@1046d517, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@3b7d3a38, name=I, getId()=data_gen_I] DataGenerator [math=org.jmathml.ASTRootNode@416c58f5, name=null, getId()=data_gen_time__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@5505ae1a, name=null, getId()=data_gen_T__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@73cd37c0, name=null, getId()=data_gen_E__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@21337f7b, 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/temp1720140376313324588.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@3c818ac4 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 90 ms ----------------------------------------------------------------------------------------------------- /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@2aa27288 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 42 ms ----------------------------------------------------------------------------------------------------- Ran 2 simulations for 1 biomodels. Generating report `report`. 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 421, 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 155, 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 586, in read_csv return _read(filepath_or_buffer, kwds) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1047, 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 223, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, 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 Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 247, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML ```
sedml.SimulatorSupportsModelAttributeChanges (14.1 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 11, 2021 5:33:39 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_788bf9bd-5f03-4908-99fd-cff7b0925a1c8901911078794957017 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 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] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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/temp4396218200548261938.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@75b3673 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 87 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (9.2 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/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:34:34 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_2e7a6900-283f-4cbf-b033-2e2e8123e3f7407563666027037800 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_2e7a6900-283f-4cbf-b033-2e2e8123e3f7407563666027037800/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute Nov 11, 2021 5:34:39 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_14994681-3a62-415b-af01-225236fc5dc26172964669003566963 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_14994681-3a62-415b-af01-225236fc5dc26172964669003566963/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (9.6 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/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:34:44 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_c9c9c01b-833c-44c6-9140-85f1700ff6c65176553789698698727 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_c9c9c01b-833c-44c6-9140-85f1700ff6c65176553789698698727/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute Nov 11, 2021 5:34:48 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_c331545a-c553-4a57-a87f-9b5199d4f98d3008332026088695910 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_c331545a-c553-4a57-a87f-9b5199d4f98d3008332026088695910/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (4.6 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:34:53 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_62461d76-a1e6-4ba5-aa94-5d21651dae694017014004333295752 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_62461d76-a1e6-4ba5-aa94-5d21651dae694017014004333295752/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (4.6 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:34:58 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_3944c618-d22a-4a8c-a768-a69f13238f6d1224434417448811376 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_3944c618-d22a-4a8c-a768-a69f13238f6d1224434417448811376/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (4.7 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:35:02 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_f126729a-9532-4852-a00b-cc8315f3f63e1967277300721900132 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_f126729a-9532-4852-a00b-cc8315f3f63e1967277300721900132/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.6 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/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:35:07 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_3d6c5013-45f0-465b-9ba3-e7a6090502786474989528634986978 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_3d6c5013-45f0-465b-9ba3-e7a6090502786474989528634986978/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.5 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/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:35:12 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_6624e5af-c9e0-4c35-af2e-c7a1f1f47e203042323528214996391 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_6624e5af-c9e0-4c35-af2e-c7a1f1f47e203042323528214996391/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.5 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmps1fmk329/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:35:16 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_004849cf-1760-4bdc-aec6-1dd11c60c7316124013692624722347 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( ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of VCell to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.

biosimulators-daemon commented 2 years ago

Summary of tests

biosimulators-daemon commented 2 years ago

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.3 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_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 (2.6 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 (2.0 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 (0.3 s)
Test if a Docker image declares the environment variables that is supports Warnings: ``` Docker images for simulation tools should declare the environment variables that they support. The Docker image does not declare the following standard environment variables recognized by BioSimulators: - '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_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 (0.3 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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (16.9 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) Warnings: ``` Unexpected reports were produced: BIOMD0000000912_sim.sedml/Figure_1_bottom_left ``` Log: ``` Nov 11, 2021 5:40:28 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1d3cbed2-0729-46ad-8c2e-46f6cae604c48393851103599960722 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 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] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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/temp5563569307175084006.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 188 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`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv 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 (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_0000086`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000086) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 11, 2021 5:40:45 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5a929464-f526-4227-9ea3-ad51e685ac1d1098670421569920384 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 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] 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@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, 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/temp1493413889589878188.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, 873 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`. report : /tmp/out/./simulation_1.sedml/report.csv 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 (33.4 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) Warnings: ``` Unexpected reports were produced: simulation_1.sedml/Figure_3a simulation_1.sedml/Figure_3b simulation_1.sedml/Figure_3c simulation_1.sedml/Figure_3d ``` Log: ``` Nov 11, 2021 5:41:19 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1c1e0ef4-20fa-454e-b0a3-2c6dfadff13f2778828067192565306 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 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] 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@1b955cac, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@676cf48, name=Trim, getId()=data_gen_Trim] DataGenerator [math=org.jmathml.ASTRootNode@5a1de7fb, name=Clb, getId()=data_gen_Clb] DataGenerator [math=org.jmathml.ASTRootNode@335b5620, name=Sic, getId()=data_gen_Sic] DataGenerator [math=org.jmathml.ASTRootNode@29a0cdb, name=PTrim, getId()=data_gen_PTrim] DataGenerator [math=org.jmathml.ASTRootNode@32a68f4f, name=PClb, getId()=data_gen_PClb] DataGenerator [math=org.jmathml.ASTRootNode@73194df, name=SBF, getId()=data_gen_SBF] DataGenerator [math=org.jmathml.ASTRootNode@6eb2384f, name=IE, getId()=data_gen_IE] DataGenerator [math=org.jmathml.ASTRootNode@3c9c0d96, name=Cdc20a, getId()=data_gen_Cdc20a] DataGenerator [math=org.jmathml.ASTRootNode@3a4621bd, name=Cdc20, getId()=data_gen_Cdc20] DataGenerator [math=org.jmathml.ASTRootNode@31dadd46, name=Cdh1, getId()=data_gen_Cdh1] DataGenerator [math=org.jmathml.ASTRootNode@4ed5eb72, name=Swe1, getId()=data_gen_Swe1] DataGenerator [math=org.jmathml.ASTRootNode@12f9af83, name=Swe1M, getId()=data_gen_Swe1M] DataGenerator [math=org.jmathml.ASTRootNode@19b93fa8, name=PSwe1, getId()=data_gen_PSwe1] DataGenerator [math=org.jmathml.ASTRootNode@7e6ef134, name=PSwe1M, getId()=data_gen_PSwe1M] DataGenerator [math=org.jmathml.ASTRootNode@1f010bf0, name=Mih1a, getId()=data_gen_Mih1a] DataGenerator [math=org.jmathml.ASTRootNode@40db2a24, name=Mcm, getId()=data_gen_Mcm] DataGenerator [math=org.jmathml.ASTRootNode@10cf09e8, name=BE, getId()=data_gen_BE] DataGenerator [math=org.jmathml.ASTRootNode@1921ad94, name=Cln, getId()=data_gen_Cln] DataGenerator [math=org.jmathml.ASTRootNode@ee86bcb, name=mass, getId()=data_gen_mass] DataGenerator [math=org.jmathml.ASTRootNode@177bea38, 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/temp6443096623102550505.xml /tmp/out/simulation_1.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@74834afd 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, 167 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`. report : /tmp/out/./simulation_1.sedml/report.csv 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 (17.4 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_1c ``` Log: ``` Nov 11, 2021 5:41:52 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Elowitz-Nature-2000-Repressilator.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_1829adcf-753f-4f01-ba0d-cf64a8d5f6404891237113367299167 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 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] 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@146dfe6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@4716be8b, name=LacI protein, getId()=data_gen_px] DataGenerator [math=org.jmathml.ASTRootNode@1fc32e4f, name=TetR protein, getId()=data_gen_py] DataGenerator [math=org.jmathml.ASTRootNode@2f67b837, name=cI protein, getId()=data_gen_pz] DataGenerator [math=org.jmathml.ASTRootNode@1869fbd2, name=LacI mRNA, getId()=data_gen_x] DataGenerator [math=org.jmathml.ASTRootNode@6af9fcb2, name=TetR mRNA, getId()=data_gen_y] DataGenerator [math=org.jmathml.ASTRootNode@6cce16f4, 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/temp7831083420136270533.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@64f16277 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'Elowitz-Nature-2000-Repressilator__model' Task 'task'. Running simulation task_task, 162 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Ignoring unsupported output `Figure_1c` while CSV generation. Generating report `report`. Generating report `__plot__Figure_1c`. report : /tmp/out/simulation.sedml/report.csv 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 (85.1 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) * Format: [`format_2585`](https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fformat_2585) Algorithm: [`KISAO_0000030`](https://www.ebi.ac.uk/ols/ontologies/kisao/terms?iri=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000030) Warnings: ``` Unexpected reports were produced: simulation.sedml/plot2d_Euler_default simulation.sedml/plot2d_Euler_small_step_size simulation.sedml/plot2d_Fig_1_c simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det simulation.sedml/plot2d_low_delta_R_stoch ``` Log: ``` Nov 11, 2021 5:43:19 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_f6cb39c4-d8b7-4213-80c5-82b7ebdec1c56258458668500298382 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), 6 simulation(s), 6 task(s), 6 report(s), 6 plot2D(s), and 0 plot3D(s) Successful translation of SED-ML file : simulation.sedml ----------------------------------------------------------------------------------------------------- name: simulation 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] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] Model [id=ODE_stochastic, name=ODE stochastic, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] Model [id=ODE_stochastic_0, name=ODE stochastic modified, language=urn:sedml:language:sbml, src=model_ODE_stochastic.xml] 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=0.1] ], getId()=Euler_default] 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_2, simulationReference=Euler_default, getId()=tsk_0_2] 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@635572a7, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@79d94571, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4dd02341, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3212a8d7, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@7a1a3478, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@495b0487, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@55dfcc6, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@222eb8aa, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@93cf163, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@1852a3ff, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@7203c7ff, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@25bfcafd, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@4b6690c0, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@46268f08, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@2a76840c, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@71454b9d, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@eda25e5, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@7cf6a5f9, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@623e088f, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@39fcbef6, name=dataGen_tsk_0_1_mRNA_A_, getId()=dataGen_tsk_0_1_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@66565121, name=time_tsk_0_2, getId()=time_tsk_0_2] DataGenerator [math=org.jmathml.ASTRootNode@2fc6f97f, name=dataGen_tsk_0_2_mRNA_R, getId()=dataGen_tsk_0_2_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@3d2ee678, name=dataGen_tsk_0_2_A, getId()=dataGen_tsk_0_2_A] DataGenerator [math=org.jmathml.ASTRootNode@6179e425, name=dataGen_tsk_0_2_R, getId()=dataGen_tsk_0_2_R] DataGenerator [math=org.jmathml.ASTRootNode@35f26e72, name=dataGen_tsk_0_2_PrmA, getId()=dataGen_tsk_0_2_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@2d6764b2, name=dataGen_tsk_0_2_PrmR, getId()=dataGen_tsk_0_2_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@67304a40, name=dataGen_tsk_0_2_C, getId()=dataGen_tsk_0_2_C] DataGenerator [math=org.jmathml.ASTRootNode@49c6c24f, name=dataGen_tsk_0_2_PrmA_bound, getId()=dataGen_tsk_0_2_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@6fe1b4fb, name=dataGen_tsk_0_2_PrmR_bound, getId()=dataGen_tsk_0_2_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@79351f41, name=dataGen_tsk_0_2_mRNA_A_, getId()=dataGen_tsk_0_2_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@1c32386d, name=time_tsk_0_3, getId()=time_tsk_0_3] DataGenerator [math=org.jmathml.ASTRootNode@6399551e, name=dataGen_tsk_0_3_mRNA_R, getId()=dataGen_tsk_0_3_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@13d73fa, name=dataGen_tsk_0_3_A, getId()=dataGen_tsk_0_3_A] DataGenerator [math=org.jmathml.ASTRootNode@5023bb8b, name=dataGen_tsk_0_3_R, getId()=dataGen_tsk_0_3_R] DataGenerator [math=org.jmathml.ASTRootNode@5d5f10b2, name=dataGen_tsk_0_3_PrmA, getId()=dataGen_tsk_0_3_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@74c79fa2, name=dataGen_tsk_0_3_PrmR, getId()=dataGen_tsk_0_3_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1e0f9063, name=dataGen_tsk_0_3_C, getId()=dataGen_tsk_0_3_C] DataGenerator [math=org.jmathml.ASTRootNode@53bd8fca, name=dataGen_tsk_0_3_PrmA_bound, getId()=dataGen_tsk_0_3_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@7642df8f, name=dataGen_tsk_0_3_PrmR_bound, getId()=dataGen_tsk_0_3_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@3e30646a, name=dataGen_tsk_0_3_mRNA_A_, getId()=dataGen_tsk_0_3_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@5cde6747, name=time_tsk_1_0, getId()=time_tsk_1_0] DataGenerator [math=org.jmathml.ASTRootNode@63a270c9, name=dataGen_tsk_1_0_mRNA_R, getId()=dataGen_tsk_1_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@37c7595, name=dataGen_tsk_1_0_A, getId()=dataGen_tsk_1_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3ed242a4, name=dataGen_tsk_1_0_R, getId()=dataGen_tsk_1_0_R] DataGenerator [math=org.jmathml.ASTRootNode@1199fe66, name=dataGen_tsk_1_0_PrmA, getId()=dataGen_tsk_1_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@614df0a4, name=dataGen_tsk_1_0_PrmR, getId()=dataGen_tsk_1_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@1fdf1c5, name=dataGen_tsk_1_0_C, getId()=dataGen_tsk_1_0_C] DataGenerator [math=org.jmathml.ASTRootNode@2d96543c, name=dataGen_tsk_1_0_PrmA_bound, getId()=dataGen_tsk_1_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@73a2e526, name=dataGen_tsk_1_0_PrmR_bound, getId()=dataGen_tsk_1_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@7d64e326, name=dataGen_tsk_1_0_mRNA_A_, getId()=dataGen_tsk_1_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@13f95696, name=time_tsk_1_1, getId()=time_tsk_1_1] DataGenerator [math=org.jmathml.ASTRootNode@cd1d761, name=dataGen_tsk_1_1_mRNA_R, getId()=dataGen_tsk_1_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@68be8808, name=dataGen_tsk_1_1_A, getId()=dataGen_tsk_1_1_A] DataGenerator [math=org.jmathml.ASTRootNode@32193bea, name=dataGen_tsk_1_1_R, getId()=dataGen_tsk_1_1_R] DataGenerator [math=org.jmathml.ASTRootNode@6b8d96d9, name=dataGen_tsk_1_1_PrmA, getId()=dataGen_tsk_1_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@69653e16, name=dataGen_tsk_1_1_PrmR, getId()=dataGen_tsk_1_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@758705fa, name=dataGen_tsk_1_1_C, getId()=dataGen_tsk_1_1_C] DataGenerator [math=org.jmathml.ASTRootNode@ebaa6cb, name=dataGen_tsk_1_1_PrmA_bound, getId()=dataGen_tsk_1_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@906d29b, name=dataGen_tsk_1_1_PrmR_bound, getId()=dataGen_tsk_1_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@49d3c823, 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_default_curve_0, logX=false, logY=false, name=curve_0, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_mRNA_R], Curve [id=plot2d_Euler_default_curve_1, logX=false, logY=false, name=curve_1, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_A], Curve [id=plot2d_Euler_default_curve_2, logX=false, logY=false, name=curve_2, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_R], Curve [id=plot2d_Euler_default_curve_3, logX=false, logY=false, name=curve_3, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA], Curve [id=plot2d_Euler_default_curve_4, logX=false, logY=false, name=curve_4, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR], Curve [id=plot2d_Euler_default_curve_5, logX=false, logY=false, name=curve_5, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_C], Curve [id=plot2d_Euler_default_curve_6, logX=false, logY=false, name=curve_6, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmA_bound], Curve [id=plot2d_Euler_default_curve_7, logX=false, logY=false, name=curve_7, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_PrmR_bound], Curve [id=plot2d_Euler_default_curve_8, logX=false, logY=false, name=curve_8, xDataReference=time_tsk_0_2, yDataReference=dataGen_tsk_0_2_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@2d86479f org.jlibsedml.Report@e0c6e6ba org.jlibsedml.Report@4f95fd0e org.jlibsedml.Report@8fa06b88 org.jlibsedml.Report@64458c95 org.jlibsedml.Report@b2ac9b88 org.jlibsedml.Report@7c222d1f 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/temp1929381953618144929.xml Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE Succesful model import: SBML file /tmp/temp989980827199069782.xml Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler 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/temp2179315603967045481.xml Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson Succesful model import: SBML file /tmp/temp7504842111153493250.xml /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@7dee835 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, 126 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_2'. Running simulation for 27 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 Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 255, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML ----------------------------------------------------------------------------------------------------- final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000) Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'. Running simulation tsk_0_3_tsk_0_3, 861 ms ----------------------------------------------------------------------------------------------------- /tmp/out/simulation.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@43471a7e 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, 51 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@4b56b031 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, 269 ms ----------------------------------------------------------------------------------------------------- cbit.vcell.solver.stoch.GibsonSolver@740fefc6 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, 206 ms ----------------------------------------------------------------------------------------------------- Ran 6 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_default` 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_default`. 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_default`. Generating report `__plot__plot2d_Euler_small_step_size`. Generating report `__plot__plot2d_Fig_1_c`. Generating report `__plot__plot2d_low_delta_R_stoch`. report : /tmp/out/simulation.sedml/report_Euler_default.csv report : /tmp/out/simulation.sedml/report_Fig_1_c.csv report : /tmp/out/simulation.sedml/report_low_delta_R_stoch.csv report : /tmp/out/simulation.sedml/report_Fig_1a.csv report : /tmp/out/simulation.sedml/report_Euler_small_step_size.csv report : /tmp/out/simulation.sedml/report_low_delta_R_det.csv 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 (34.9 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) Warnings: ``` Unexpected reports were produced: simulation.sedml/Figure_2ab simulation.sedml/plot2d_Fig_1a simulation.sedml/plot2d_low_delta_R_det ``` Log: ``` Nov 11, 2021 5:42:10 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_7b0d367e-7b34-40f5-8aa8-caf7b43a35877577223053257356931 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 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] Model [id=ODE_deterministic_0, name=ODE deterministic modified, language=urn:sedml:language:sbml, src=model_ODE_deterministic.xml] 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@7fb95505, name=time_tsk_0_0, getId()=time_tsk_0_0] DataGenerator [math=org.jmathml.ASTRootNode@58be6e8, name=dataGen_tsk_0_0_mRNA_R, getId()=dataGen_tsk_0_0_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@7331196b, name=dataGen_tsk_0_0_A, getId()=dataGen_tsk_0_0_A] DataGenerator [math=org.jmathml.ASTRootNode@3f9342d4, name=dataGen_tsk_0_0_R, getId()=dataGen_tsk_0_0_R] DataGenerator [math=org.jmathml.ASTRootNode@ab7395e, name=dataGen_tsk_0_0_PrmA, getId()=dataGen_tsk_0_0_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@50d13246, name=dataGen_tsk_0_0_PrmR, getId()=dataGen_tsk_0_0_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@2bd08376, name=dataGen_tsk_0_0_C, getId()=dataGen_tsk_0_0_C] DataGenerator [math=org.jmathml.ASTRootNode@e70f13a, name=dataGen_tsk_0_0_PrmA_bound, getId()=dataGen_tsk_0_0_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@3d3e5463, name=dataGen_tsk_0_0_PrmR_bound, getId()=dataGen_tsk_0_0_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@64a40280, name=dataGen_tsk_0_0_mRNA_A_, getId()=dataGen_tsk_0_0_mRNA_A_] DataGenerator [math=org.jmathml.ASTRootNode@4b40f651, name=time_tsk_0_1, getId()=time_tsk_0_1] DataGenerator [math=org.jmathml.ASTRootNode@42b02722, name=dataGen_tsk_0_1_mRNA_R, getId()=dataGen_tsk_0_1_mRNA_R] DataGenerator [math=org.jmathml.ASTRootNode@d62fe5b, name=dataGen_tsk_0_1_A, getId()=dataGen_tsk_0_1_A] DataGenerator [math=org.jmathml.ASTRootNode@49964d75, name=dataGen_tsk_0_1_R, getId()=dataGen_tsk_0_1_R] DataGenerator [math=org.jmathml.ASTRootNode@528c868, name=dataGen_tsk_0_1_PrmA, getId()=dataGen_tsk_0_1_PrmA] DataGenerator [math=org.jmathml.ASTRootNode@466276d8, name=dataGen_tsk_0_1_PrmR, getId()=dataGen_tsk_0_1_PrmR] DataGenerator [math=org.jmathml.ASTRootNode@5ce8d869, name=dataGen_tsk_0_1_C, getId()=dataGen_tsk_0_1_C] DataGenerator [math=org.jmathml.ASTRootNode@27eedb64, name=dataGen_tsk_0_1_PrmA_bound, getId()=dataGen_tsk_0_1_PrmA_bound] DataGenerator [math=org.jmathml.ASTRootNode@64c63c79, name=dataGen_tsk_0_1_PrmR_bound, getId()=dataGen_tsk_0_1_PrmR_bound] DataGenerator [math=org.jmathml.ASTRootNode@31c7528f, 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] ...
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 (7.9 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., ``#model1``). Reason for skip: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 11, 2021 5:33:42 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_aca44101-bc3f-4aad-8b7c-5af8ef9f3d5a6512298253209749826 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 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__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@7b205dbd, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@106cc338, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@7a67e3c6, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 247, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML All sedml documents in this archive failed to execute ```
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (7.5 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: ``` Simulator did not produce the following reports: - `BIOMD0000000912_sim.sedml/report` ``` Log: ``` Nov 11, 2021 5:33:50 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_b163fba8-8a8a-4126-8956-5de933563bd27181667903393636376 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 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__] Model [id=__source__, name=null, language=urn:sedml:language:sbml, src=Caravagna2010.xml] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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 [Fatal Error] :1:1: Content is not allowed in prolog. [Fatal Error] :1:1: Content is not allowed in prolog. java.lang.RuntimeException: Error importing from SBML : no SBML source. at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:449) at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:704) at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:71) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:286) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection Error importing from SBML : no SBML source. Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 247, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML All sedml documents in this archive failed to execute ```
sedml.SimulatorProducesLinear3DPlots (0.5 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 (0.4 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 (0.4 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 (13.3 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements. Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 11, 2021 5:35:28 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_6c755fe4-1f3e-4da0-b71d-482452fc484d2411884629879193858 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 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] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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/temp5986887769886573490.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@63a5d002 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 85 ms ----------------------------------------------------------------------------------------------------- Ran 1 simulations for 1 biomodels. Generating report `report`. report : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsComputeModelChanges (14.8 s)
Test that a simulator supports compute model changes Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 11, 2021 5:35:55 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_0edaa626-2084-4011-bd3d-75c79a4697348662024303798661756 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 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] 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@7ca33c24, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@fade1fc, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@67c2e933, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@41dd05a, 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/temp4232925488456701832.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@6f952d6c 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 : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsDataSetsWithDifferentShapes (15.2 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/tmpwzdaunhr/sedml/sedml.SimulatorSupportsDataSetsWithDifferentShapes/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:36:26 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_0430648a-7c2b-4d93-8f9f-6553459326ef1146984658937179306 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 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] 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@291a7e3c, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@ca30bc1, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@1046d517, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@3b7d3a38, name=I, getId()=data_gen_I] DataGenerator [math=org.jmathml.ASTRootNode@416c58f5, name=null, getId()=data_gen_time__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@5505ae1a, name=null, getId()=data_gen_T__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@73cd37c0, name=null, getId()=data_gen_E__copy_2] DataGenerator [math=org.jmathml.ASTRootNode@21337f7b, 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/temp1397533722440971695.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@3c818ac4 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'. Running simulation BIOMD0000000912_task_Caravagna2010, 98 ms ----------------------------------------------------------------------------------------------------- /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@2aa27288 Finished: SOLVER_FINISHED:completed Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'. Running simulation BIOMD0000000912_task__copy_2_BIOMD0000000912_task__copy_2, 43 ms ----------------------------------------------------------------------------------------------------- Ran 2 simulations for 1 biomodels. Generating report `report`. 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 421, 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 155, 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 586, in read_csv return _read(filepath_or_buffer, kwds) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 488, in _read return parser.read(nrows) File "/usr/local/lib/python3.8/dist-packages/pandas/io/parsers/readers.py", line 1047, 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 223, in read chunks = self._reader.read_low_memory(nrows) File "pandas/_libs/parsers.pyx", line 801, in pandas._libs.parsers.TextReader.read_low_memory File "pandas/_libs/parsers.pyx", line 857, in pandas._libs.parsers.TextReader._read_rows File "pandas/_libs/parsers.pyx", line 843, in pandas._libs.parsers.TextReader._tokenize_rows File "pandas/_libs/parsers.pyx", line 1925, 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 Traceback (most recent call last): File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/status.py", line 263, 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/status.py", line 247, in set_exception_message exc['type'] = type TypeError: 'NoneType' object does not support item assignment Failed updating task status YAML ```
sedml.SimulatorSupportsModelAttributeChanges (14.7 s)
Test that a simulator supports changes to the attributes of model elements Reason for skip: ``` The execution of the COMBINE/OMEX archive did not fail as expected ``` Log: ``` Nov 11, 2021 5:36:42 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ceee7d5e-8e41-4bb1-85e1-68e6015e8f7f958174719569134571 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 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] 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@7a67e3c6, name=time, getId()=data_gen_time] DataGenerator [math=org.jmathml.ASTRootNode@6cc558c6, name=T, getId()=data_gen_T] DataGenerator [math=org.jmathml.ASTRootNode@15713d56, name=E, getId()=data_gen_E] DataGenerator [math=org.jmathml.ASTRootNode@63f259c3, 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/temp8809250431689236386.xml /tmp/out/BIOMD0000000912_sim.sedml false cbit.vcell.solver.ode.CVodeSolverStandalone@75b3673 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 : /tmp/out/./BIOMD0000000912_sim.sedml/report.csv HDF conversion successful No PDF files found, skipping archiving `plots.zip` files Archiving resultant CSV files to `reports.zip`. ```
sedml.SimulatorSupportsRepeatedTasksWithChanges (10.0 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/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithChanges/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:37:40 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_aab11fc6-54ed-4401-a695-a2f19b5f2c401735620808435224025 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_aab11fc6-54ed-4401-a695-a2f19b5f2c401735620808435224025/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute Nov 11, 2021 5:37:45 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_7e504dcb-d8a7-43ca-a593-06e84495c8937696991419374222037 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_7e504dcb-d8a7-43ca-a593-06e84495c8937696991419374222037/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (10.0 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/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables/2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:37:50 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_ad4a5f81-50eb-4f71-8645-df02af6165ab8226696304645411763 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_ad4a5f81-50eb-4f71-8645-df02af6165ab8226696304645411763/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute Nov 11, 2021 5:37:55 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_c03e2efa-80d6-42b1-a26b-65cdb9da321c5415458911748597869 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_c03e2efa-80d6-42b1-a26b-65cdb9da321c5415458911748597869/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (5.0 s)
Test that a simulator supports repeated tasks over functional ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:38:00 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_f2dc0057-10a4-461a-bbc5-eb2c3fd7110c2530832145506496574 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_f2dc0057-10a4-461a-bbc5-eb2c3fd7110c2530832145506496574/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (5.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:38:05 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_63f2dd47-90ef-4973-b61f-48781af4def53886346192119197971 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_63f2dd47-90ef-4973-b61f-48781af4def53886346192119197971/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (5.0 s)
Test that a simulator supports repeated tasks over uniform ranges Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:38:10 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_5cda2841-e9a0-4183-ab50-1d991d6142fc6708766858402679879 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_5cda2841-e9a0-4183-ab50-1d991d6142fc6708766858402679879/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (4.9 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/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:38:15 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_54ca19eb-b4c8-485e-a5aa-428f9bbf910f550961913865452227 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_54ca19eb-b4c8-485e-a5aa-428f9bbf910f550961913865452227/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (4.9 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/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:38:20 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_374523bd-5ffe-49ea-bbe9-a874963a93791343786735003682091 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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) SED-ML processing for /tmp/vcell_temp_374523bd-5ffe-49ea-bbe9-a874963a93791343786735003682091/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:360) at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92) at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:214) at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:88) All sedml documents in this archive failed to execute ```
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (4.8 s)
Test that a simulator supports nested repeated tasks Reason for skip: ``` [Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpwzdaunhr/sedml/sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks/1/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0) ``` Log: ``` Nov 11, 2021 5:38:25 AM java.util.prefs.FileSystemPreferences$1 run INFO: Created user preferences directory. VCell CLI input archive /tmp/in/archive.omex ----------------------------------------------------------------------------------------------------- TempPath Created: /tmp/vcell_temp_0bcf2437-50b4-4c47-b956-cba719bf217b2664694353848678800 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.getRepeatedT ...
biosimulators-daemon commented 2 years ago

The image for your simulator is valid!

biosimulators-daemon commented 2 years ago

Your submission was committed to the BioSimulators registry. Thank you!

Future submissions of subsequent versions of VCell to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.