Integration_COMBINE

Integration into COMBINE Archive

All SED-ML files (including the associated Colab notebooks, output files (plots and tables) and validation results were stored in a fully featured COMBINE archive using the Webcat tool.

List of SED-ML files (./experiment)

• DefaultSimulation.sedml
• Fig3.sedml (created with SEDML_Fig3_v2.ipynb)
• Fig4.sedml (created with SEDML_Fig4_v3.ipynb)
• Fig5.sedml (created with SEDML_Fig5_v2.ipynb)
• SuppFig9.sedml (created with SEDML_SuppFig9_v3.ipynb)
• SuppFig9_COPASI.sedml

List of outputs (subfolders in ./result)

• DefaultSimulation (Tellurium v2.2.0: model data (.csv), plot (.png); SED-ML WebTools v2.4: plot (.pdf))
• Fig3 (Tellurium v2.2.0: model data (.csv), plots (.png); Adobe Illustrator: plots (.pdf))
• Fig4 (Tellurium v2.2.0: model data (.csv), plots (.png); Adobe Illustrator: plots (.pdf))
• Fig5 (Tellurium v2.2.0: model data (.csv), plots (.png); Adobe Illustrator: plots (.pdf))
• SuppFig9 (Tellurium v2.2.0: model data (.csv), plots (.png); Adobe Illustrator: plots (.pdf))
• SuppFig9_COPASI (COPASI v4.33: model data (.txt), plots (.png), COPASI file (.cps); Adobe Illustrator: plots (.pdf))
• Validation
  • Test_COPASI_2021-06-28 (COPASI v4.33: model data (.txt), plots (.png), COPASI files (.cps); Adobe Illustrator: plots (.pdf))
    • Fig3
    • SuppFig9
  • Test_SWT_2021-06-28 (SED-ML WebTools v2.4: model data (.xml), plots (.png); ; Adobe Illustrator: plots (.pdf))
    • Fig3
    • Fig4
    • Fig5
    • SuppFig9