{"sedDocuments":[{"outputs":[{"dataSets":[{"status":"SUCCEEDED","id":"data_set_time"},{"status":"SUCCEEDED","id":"data_set_NFAT_dephosphorylated"},{"status":"SUCCEEDED","id":"data_set_NFAT_phosphorylated"},{"status":"SUCCEEDED","id":"data_set_NFAT_transported"},{"status":"SUCCEEDED","id":"data_set_stimulus"}],"duration":0.081006,"output":"","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"report"},{"curves":[{"status":"SUCCEEDED","id":"curve_NFAT_dephosphorylated"},{"status":"SUCCEEDED","id":"curve_NFAT_transported"}],"duration":0.221586,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: IllogicalVizWarning: \u001b[33mA title could not be inferred for the Y axis because the Y data generators have inconsistent names.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"Figure_3c"}],"tasks":[{"simulatorDetails":[{"value":"deterministic","key":"methodName"},{"value":22,"key":"methodCode"},{"key":"parameters"}],"algorithm":"KISAO_0000560","duration":0.127412,"output":"/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33m- Variable `var_NFAT_transported` may be invalid.\r\n  - XPath could not be validated.\r\n- Variable `var_NFAT_dephosphorylated` may be invalid.\r\n  - XPath could not be validated.\r\n- Variable `var_stimulus` may be invalid.\r\n  - XPath could not be validated.\r\n- Variable `var_NFAT_phosphorylated` may be invalid.\r\n  - XPath could not be validated.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mModel `BIOMD0000000678` may be invalid.\r\n  - The model file `/tmp/tmppi3sfbdr.xml` may be invalid.\r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <initialAssignment> <math> expression 'stim_duration' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <initialAssignment> <math> expression 'stim_frequency' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <assignmentRule> <math> expression '1 - NFAT_phosphorylated - NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <assignmentRule> <math> expression '100 * NFAT_phosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <assignmentRule> <math> expression '100 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <assignmentRule> <math> expression '100 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <assignmentRule> <math> expression 'piecewise(1, lt(time - floor(time / ModelValue_13) * ModelValue_13, ModelValue_17), 0)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <kineticLaw> <math> expression 'Jurkat_cell * function_for_modified_reaction_1(NFAT_phosphorylated, k1, stimulus)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <kineticLaw> <math> expression 'Jurkat_cell * k2 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <kineticLaw> <math> expression 'Jurkat_cell * k3 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n       The units of the <kineticLaw> <math> expression 'Jurkat_cell * k4 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'k1' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'k2' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'k3' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'k4' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'stim_frequency' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'dNFAT' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'pNFAT' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'tNFAT' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'stim_duration' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'ModelValue_17' does not have a 'units' attribute.\r\n      \r\n    - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n       The <parameter> with the id 'ModelValue_13' does not have a 'units' attribute.\r\n      \u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n","skipReason":null,"exception":null,"status":"SUCCEEDED","id":"BIOMD0000000678_task"}],"duration":0.576045,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  BIOMD0000000678_sim.sedml:\r\n    Tasks (1):\r\n      BIOMD0000000678_task\r\n    Reports (1):\r\n      report: 5 data sets\r\n    Plots (1):\r\n      Figure_3c: 2 curves\r\n\r\nExecuting SED-ML file 1: BIOMD0000000678_sim.sedml ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `BIOMD0000000678_task`\r\n    Outputs:\r\n      `Figure_3c`\r\n      `report`\r\n  Executing task 1: `BIOMD0000000678_task`\r\n    Executing simulation ... \u001b[34msucceeded\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `report` ... \u001b[34msucceeded\u001b[0m\r\n      Generating output 2: `Figure_3c` ...","skipReason":null,"exception":null,"status":"SUCCEEDED","location":"BIOMD0000000678_sim.sedml"}],"duration":0.875171,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m============================================ Downloading COMBINE archive ============================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    463      0 --:--:-- --:--:-- --:--:--   464\n\r100 78393  100 78393    0     0   185k      0 --:--:-- --:--:-- --:--:--  185k\n\n\u001b[0;36m============================================= Executing COMBINE archive =============================================\u001b[0m\nINFO:    Using cached SIF image\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `BIOMD0000000678` may be invalid.\r\n    - The model file `BIOMD0000000678_url.xml` may be invalid.\r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <initialAssignment> <math> expression 'stim_duration' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <initialAssignment> <math> expression 'stim_frequency' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <assignmentRule> <math> expression '1 - NFAT_phosphorylated - NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <assignmentRule> <math> expression '100 * NFAT_phosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <assignmentRule> <math> expression '100 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <assignmentRule> <math> expression '100 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <assignmentRule> <math> expression 'piecewise(1, lt(time - floor(time / ModelValue_13) * ModelValue_13, ModelValue_17), 0)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <kineticLaw> <math> expression 'Jurkat_cell * function_for_modified_reaction_1(NFAT_phosphorylated, k1, stimulus)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <kineticLaw> <math> expression 'Jurkat_cell * k2 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <kineticLaw> <math> expression 'Jurkat_cell * k3 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n         The units of the <kineticLaw> <math> expression 'Jurkat_cell * k4 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'k1' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'k2' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'k3' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'k4' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'stim_frequency' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'dNFAT' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'pNFAT' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'tNFAT' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'stim_duration' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'ModelValue_17' does not have a 'units' attribute.\r\n        \r\n      - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n         The <parameter> with the id 'ModelValue_13' does not have a 'units' attribute.\r\n        \r\n    - The changes of the model may be invalid.\r\n      - Change 1 may be invalid.\r\n        - XPath could not be validated.\r\n  - Data generator `data_gen_NFAT_phosphorylated` may be invalid.\r\n    - Variable `var_NFAT_phosphorylated` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_gen_NFAT_dephosphorylated` may be invalid.\r\n    - Variable `var_NFAT_dephosphorylated` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_gen_NFAT_transported` may be invalid.\r\n    - Variable `var_NFAT_transported` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_gen_stimulus` may be invalid.\r\n    - Variable `var_stimulus` may be invalid.\r\n      - XPath could not be validated.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe COMBINE/OMEX archive may be invalid.\r\n  - The SED-ML file at location `./BIOMD0000000678_sim.sedml` may be invalid.\r\n    - Model `BIOMD0000000678` may be invalid.\r\n      - The model file `BIOMD0000000678_url.xml` may be invalid.\r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <initialAssignment> <math> expression 'stim_duration' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <initialAssignment> <math> expression 'stim_frequency' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <assignmentRule> <math> expression '1 - NFAT_phosphorylated - NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <assignmentRule> <math> expression '100 * NFAT_phosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <assignmentRule> <math> expression '100 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <assignmentRule> <math> expression '100 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <assignmentRule> <math> expression 'piecewise(1, lt(time - floor(time / ModelValue_13) * ModelValue_13, ModelValue_17), 0)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <kineticLaw> <math> expression 'Jurkat_cell * function_for_modified_reaction_1(NFAT_phosphorylated, k1, stimulus)' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <kineticLaw> <math> expression 'Jurkat_cell * k2 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <kineticLaw> <math> expression 'Jurkat_cell * k3 * NFAT_dephosphorylated' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - In situations where a mathematical expression contains literal numbers or parameters whose units have not been declared, it is not possible to verify accurately the consistency of the units in the expression. \r\n           The units of the <kineticLaw> <math> expression 'Jurkat_cell * k4 * NFAT_transported' cannot be fully checked. Unit consistency reported as either no errors or further unit errors related to this object may not be accurate.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'k1' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'k2' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'k3' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'k4' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'stim_frequency' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'dNFAT' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'pNFAT' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'tNFAT' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'stim_duration' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'ModelValue_17' does not have a 'units' attribute.\r\n          \r\n        - As a principle of best modeling practice, the units of a <parameter> should be declared rather than be left undefined. Doing so improves the ability of software to check the consistency of units and helps make it easier to detect potential errors in models.\r\n           The <parameter> with the id 'ModelValue_13' does not have a 'units' attribute.\r\n          \r\n      - The changes of the model may be invalid.\r\n        - Change 1 may be invalid.\r\n          - XPath could not be validated.\r\n    - Data generator `data_gen_NFAT_phosphorylated` may be invalid.\r\n      - Variable `var_NFAT_phosphorylated` may be invalid.\r\n        - XPath could not be validated.\r\n    - Data generator `data_gen_NFAT_dephosphorylated` may be invalid.\r\n      - Variable `var_NFAT_dephosphorylated` may be invalid.\r\n        - XPath could not be validated.\r\n    - Data generator `data_gen_NFAT_transported` may be invalid.\r\n      - Variable `var_NFAT_transported` may be invalid.\r\n        - XPath could not be validated.\r\n    - Data generator `data_gen_stimulus` may be invalid.\r\n      - Variable `var_stimulus` may be invalid.\r\n        - XPath could not be validated.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n/usr/local/lib/python3.9/site-packages/biosimulators_utils/warnings.py:31: BioSimulatorsWarning: \u001b[33mThe SED document is potentially incorrect.\r\n  - Model `BIOMD0000000678` may be invalid.\r\n    - The changes of the model may be invalid.\r\n      - Change 1 may be invalid.\r\n        - XPath could not be validated.\r\n  - Data generator `data_gen_NFAT_phosphorylated` may be invalid.\r\n    - Variable `var_NFAT_phosphorylated` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_gen_NFAT_dephosphorylated` may be invalid.\r\n    - Variable `var_NFAT_dephosphorylated` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_gen_NFAT_transported` may be invalid.\r\n    - Variable `var_NFAT_transported` may be invalid.\r\n      - XPath could not be validated.\r\n  - Data generator `data_gen_stimulus` may be invalid.\r\n    - Variable `var_stimulus` may be invalid.\r\n      - XPath could not be validated.\u001b[0m\r\n  warnings.warn(termcolor.colored(message, Colors.warning.value), category)\r\n \u001b[34msucceeded\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 1\n      Skipped: 0\n      Failed: 0\n    Outputs:\n      Succeeded: 2\n      Skipped: 0\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Tasks (1):\n    Succeeded: 1\n    Skipped: 0\n    Failed: 0\n  Outputs (2):\n    Succeeded: 2\n    Skipped: 0\n    Failed: 0\n\n\n\u001b[0;36m=================================================== Saving results ==================================================\u001b[0m\ncreating group /BIOMD0000000678_sim.sedml\ncreating dataset /BIOMD0000000678_sim.sedml/Figure_3c, shape: (3, 1001), type: float64\ndataset created, uuid: d-c60a5a18-a3f2e0b3-85c6-f71df4-dbc88f, chunk_size: (3, 1001)\ncreating dataset /BIOMD0000000678_sim.sedml/report, shape: (5, 1001), type: float64\ndataset created, uuid: d-c60a5a18-a3f2e0b3-6380-b97049-362217, chunk_size: (5, 1001)\ncreating attribute combineArchiveLocation in /BIOMD0000000678_sim.sedml\ncreating attribute uri in /BIOMD0000000678_sim.sedml\ncreating attribute _type in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute sedmlDataSetIds in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute sedmlDataSetLabels in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute sedmlDataSetNames in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute sedmlDataSetShapes in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute sedmlId in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute sedmlName in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute uri in /BIOMD0000000678_sim.sedml/Figure_3c\ncreating attribute _type in /BIOMD0000000678_sim.sedml/report\ncreating attribute sedmlDataSetDataTypes in /BIOMD0000000678_sim.sedml/report\ncreating attribute sedmlDataSetIds in /BIOMD0000000678_sim.sedml/report\ncreating attribute sedmlDataSetLabels in /BIOMD0000000678_sim.sedml/report\ncreating attribute sedmlDataSetNames in /BIOMD0000000678_sim.sedml/report\ncreating attribute sedmlDataSetShapes in /BIOMD0000000678_sim.sedml/report\ncreating attribute sedmlId in /BIOMD0000000678_sim.sedml/report\ncreating attribute uri in /BIOMD0000000678_sim.sedml/report\ncreate_links: /\ngot link: BIOMD0000000678_sim.sedml\ncreate_links: /BIOMD0000000678_sim.sedml\ngot link: Figure_3c\ngot link: report\nwrite_dataset src: /BIOMD0000000678_sim.sedml/Figure_3c to tgt: /BIOMD0000000678_sim.sedml/Figure_3c, shape: (3, 1001), type: float64\niterating over chunks for /BIOMD0000000678_sim.sedml/Figure_3c\nwriting dataset data for slice: (slice(0, 3, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000678_sim.sedml/Figure_3c\nwrite_dataset src: /BIOMD0000000678_sim.sedml/report to tgt: /BIOMD0000000678_sim.sedml/report, shape: (5, 1001), type: float64\niterating over chunks for /BIOMD0000000678_sim.sedml/report\nwriting dataset data for slice: (slice(0, 5, 1), slice(0, 1001, 1))\ndone with dataload for /BIOMD0000000678_sim.sedml/report\nload_file complete\nFile outputs/reports.h5 uploaded to domain: /results/61fea497f499ccf25faafc68\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 91%)\n  adding: outputs/BIOMD0000000678_sim.sedml/ (stored 0%)\n  adding: outputs/BIOMD0000000678_sim.sedml/Figure_3c.pdf (deflated 24%)\n  adding: outputs/reports.h5 (deflated 36%)\n  adding: rawLog.txt (deflated 92%)\n\n\u001b[0;36m=================================================== Saving outputs ==================================================\u001b[0m\nCompleted 25.7 KiB/116.3 KiB (337.0 KiB/s) with 4 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/61fea497f499ccf25faafc68/rawLog.txt\nCompleted 25.7 KiB/116.3 KiB (337.0 KiB/s) with 3 file(s) remaining\rCompleted 42.6 KiB/116.3 KiB (349.3 KiB/s) with 3 file(s) remaining\rupload: outputs/BIOMD0000000678_sim.sedml/Figure_3c.pdf to s3://files.biosimulations.org/simulations/61fea497f499ccf25faafc68/outputs/BIOMD0000000678_sim.sedml/Figure_3c.pdf\nCompleted 42.6 KiB/116.3 KiB (349.3 KiB/s) with 2 file(s) remaining\rCompleted 55.2 KiB/116.3 KiB (430.8 KiB/s) with 2 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/61fea497f499ccf25faafc68/outputs/plots.zip\nCompleted 55.2 KiB/116.3 KiB (430.8 KiB/s) with 1 file(s) remaining\rCompleted 116.3 KiB/116.3 KiB (872.9 KiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/61fea497f499ccf25faafc68/output.zip\nCompleted 65.7 KiB/65.7 KiB (754.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/61fea497f499ccf25faafc68/outputs/reports.h5\nCompleted 36.0 KiB/36.0 KiB (253.4 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/61fea497f499ccf25faafc68/outputs/log.yml\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\n\u001b[0;32mPost thumbnails to the API.....Succeeded\nCreate thumbnails from the images specified in the manifest.....Succeeded\nRead the manifest and post the files to the API.....Succeeded\nProcess the manifest file in the combine archive.....Succeeded\nExtract the files in the combine archive.....Succeeded\nPost the SED-ML file to the API.....Succeeded\nProcess the SED-ML file in the combine archive.....Succeeded\nPost the Metadata to the API.....Succeeded\nProcess the Metadata in the combine archive.....Succeeded\nPost the logs to the API.....Succeeded\nRetrieve the logs of the simulation run.....Succeeded\nProcess and upload the outputs of the simulation run.....Succeeded\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","skipReason":null,"exception":null,"status":"SUCCEEDED"}