Submit PySceS 0.9.9

[biosimulators-daemon]

---

id: pysces version: 0.9.9 specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_PySCeS/440ee6e2dd9805af428bd21bdc6998f68d48ff61/biosimulators.json specificationsPatch: version: 0.9.9 validateImage: true commitSimulator: true

---

[biosimulators-daemon]

Thank you @biosimulators-daemon 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 is available here.

[biosimulators-daemon]

The specifications of your simulator is valid!

[biosimulators-daemon]

Summary of tests

• Executed 13 test cases

• Passed 6 test cases:

  • docker_image.BioContainersLabelsTestCase
  • docker_image.OciLabelsTestCase
  • published_project.PublishedProjectTestCase:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
  • published_project.PublishedProjectTestCase:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
  • published_project.PublishedProjectTestCase:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
  • sedml.MultipleTasksPerSedDocumentTestCase

• Failed 0 test cases

• Skipped 7 test cases:

  • published_project.PublishedProjectTestCase:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
  • published_project.PublishedProjectTestCase:bngl/test-bngl
  • published_project.PublishedProjectTestCase:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint
  • published_project.PublishedProjectTestCase:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
  • published_project.PublishedProjectTestCase:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
  • published_project.PublishedProjectTestCase:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
  • published_project.PublishedProjectTestCase:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock

Warnings

published_project.PublishedProjectTestCase:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (3.3 s)

Required model formats and simulation algorithms for SED tasks:

• Format: format_2585 Algorithm: KISAO_0000019

  Warnings:

  Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

  Log:

  Matplotlib created a temporary config/cache directory at /tmp/matplotlib-kf5udty5 because the default path (/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Matplotlib interface not available
  Attempting alternate pitcon import ...
  Attempting alternate nleq2 import ...
  /opt/conda/envs/py/lib/python3.7/site-packages/assimulo/solvers/odepack.py:717: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray
  38892959/120069679,11804845./141497517]])]
  Found 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:
  BIOMD0000000912_sim.sedml:
    Tasks (1):
      BIOMD0000000912_sim
    Reports (1):
      BIOMD0000000912_sim: 4 data sets
    Plots (1):
      plot_1: 3 curves
  
  Executing SED-ML file 0: BIOMD0000000912_sim.sedml
  Found 1 tasks
    BIOMD0000000912_sim
  Executing task 1: BIOMD0000000912_sim
  Info: single compartment model: locating "Induction_of_tumor" in default compartment
  Info: single compartment model: locating "Removal_of_tumor_from_the_system_by_the_action_of_immune_response" in default compartment
  Info: single compartment model: locating "Activation_and_transfer_of_effector_cells_to_the_action_site" in default compartment
  Info: single compartment model: locating "Deactivation_and_removal_of_effector_cells_from_the_site_of_tumor" in default compartment
  Info: single compartment model: locating "Activation_of_interleukin_2" in default compartment
  Info: single compartment model: locating "Deactivation_of_interleukin2" in default compartment
  Writing file: /tmp/tmp224qas_3.psc
  
  SBML2PSC
  in : /tmp/tmps9xn1gwr/./Caravagna2010.xml
  out: /tmp/tmp224qas_3.psc
  Using model directory: /tmp/Pysces/psc
  /tmp/tmp224qas_3.psc loading ..... 
  Parsing file: /tmp/tmp224qas_3.psc
  Info: No reagents have been fixed
  
  Calculating L matrix . . . . . . .  done.
  Calculating K matrix . . . . . . .  done.
  
  CVODE time for 5001 points: 0.48885655403137207
  /opt/conda/envs/py/lib/python3.7/site-packages/tables/path.py:155: NaturalNameWarning: object name is not a valid Python identifier: 'BIOMD0000000912_sim.sedml'; it does not match the pattern ``^[a-zA-Z_][a-zA-Z0-9_]*$``; you will not be able to use natural naming to access this object; using ``getattr()`` will still work, though
  check_attribute_name(name)
  /opt/conda/envs/py/lib/python3.7/site-packages/biosimulators_utils/sedml/exec.py:213: SedmlFeatureNotSupportedWarning: Output plot_1 skipped because outputs of type Plot2D are not yet supported
  output.id, output.__class__.__name__), SedmlFeatureNotSupportedWarning)

[biosimulators-daemon]

The image for your simulator is valid!

[biosimulators-daemon]

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

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