├── .gitattributes ├── .gitignore ├── .readthedocs.yaml ├── .travis.yml ├── CONTRIBUTING.rst ├── LICENSE.txt ├── MANIFEST.in ├── NEWS.txt ├── NOTICE.txt ├── README.md ├── VirtualEnv.md ├── bld.bat ├── clean.sh ├── docs ├── API.rst ├── Makefile ├── README.md ├── _apidoc │ ├── modules.rst │ ├── tellurium.analysis.rst │ ├── tellurium.dev.deprecated.rst │ ├── tellurium.dev.oven.ndarray.rst │ ├── tellurium.dev.oven.rst │ ├── tellurium.dev.rst │ ├── tellurium.notebooks.rst │ ├── tellurium.plotting.rst │ ├── tellurium.roadrunner.rst │ ├── tellurium.rst │ ├── tellurium.sedml.rst │ ├── tellurium.sedml.templates.rst │ ├── tellurium.teconverters.rst │ ├── tellurium.teio.rst │ ├── tellurium.tests.rst │ ├── tellurium.tests.sedml.rst │ ├── tellurium.tests.testdata.rst │ ├── tellurium.tests.testdata.sedml.data.rst │ ├── tellurium.tests.testdata.sedml.rst │ ├── tellurium.tests.testdata.sedml.sed-ml.cellml.rst │ ├── tellurium.tests.testdata.sedml.sed-ml.rst │ ├── tellurium.utils.rst │ └── tellurium.visualization.rst ├── _notebooks │ └── core │ │ ├── _notebooks │ │ └── core │ │ │ ├── antimonyExample_files │ │ │ ├── antimonyExample_2_1.png │ │ │ ├── antimonyExample_2_10.png │ │ │ ├── antimonyExample_2_2.png │ │ │ ├── antimonyExample_2_3.png │ │ │ ├── antimonyExample_2_5.png │ │ │ ├── antimonyExample_2_6.png │ │ │ ├── antimonyExample_2_7.png │ │ │ ├── antimonyExample_2_8.png │ │ │ └── antimonyExample_2_9.png │ │ │ ├── combineExample_files │ │ │ ├── combineExample_2_0.png │ │ │ └── combineExample_3_0.png │ │ │ ├── introduction_files │ │ │ ├── introduction_2_0.png │ │ │ └── introduction_4_0.png │ │ │ ├── model_consecutiveUniUniReactions_files │ │ │ └── model_consecutiveUniUniReactions_2_0.png │ │ │ ├── model_feedback_oscillations_files │ │ │ ├── model_feedback_oscillations_2_0.png │ │ │ └── model_feedback_oscillations_2_1.png │ │ │ ├── model_generatingDifferentWaveforms_files │ │ │ └── model_generatingDifferentWaveforms_2_0.png │ │ │ ├── model_modelFromBioModels_files │ │ │ └── model_modelFromBioModels_2_0.png │ │ │ ├── model_normalizedSpecies_files │ │ │ └── model_normalizedSpecies_3_0.png │ │ │ ├── parameter_scan_files │ │ │ ├── parameter_scan_2_0.png │ │ │ └── parameter_scan_3_0.png │ │ │ ├── phrasedmlExample_files │ │ │ ├── phrasedmlExample_10_0.png │ │ │ ├── phrasedmlExample_10_1.png │ │ │ ├── phrasedmlExample_12_0.png │ │ │ ├── phrasedmlExample_12_1.png │ │ │ ├── phrasedmlExample_14_0.png │ │ │ ├── phrasedmlExample_2_0.png │ │ │ ├── phrasedmlExample_4_0.png │ │ │ ├── phrasedmlExample_4_1.png │ │ │ ├── phrasedmlExample_6_0.png │ │ │ ├── phrasedmlExample_8_0.png │ │ │ └── phrasedmlExample_8_1.png │ │ │ ├── plot2DParameterScan_files │ │ │ ├── plot2DParameterScan_0_0.png │ │ │ └── plot2DParameterScan_0_1.png │ │ │ ├── roadrunnerBasics_files │ │ │ ├── roadrunnerBasics_4_0.png │ │ │ └── roadrunnerBasics_6_1.png │ │ │ ├── steadystate_scan_files │ │ │ └── steadystate_scan_2_0.png │ │ │ ├── tellurium_examples_files │ │ │ ├── tellurium_examples_11_0.png │ │ │ ├── tellurium_examples_13_0.png │ │ │ ├── tellurium_examples_15_1.png │ │ │ ├── tellurium_examples_17_0.png │ │ │ ├── tellurium_examples_19_0.png │ │ │ ├── tellurium_examples_21_0.png │ │ │ ├── tellurium_examples_23_0.png │ │ │ ├── tellurium_examples_25_0.png │ │ │ ├── tellurium_examples_27_0.png │ │ │ ├── tellurium_examples_29_0.png │ │ │ ├── tellurium_examples_31_0.png │ │ │ ├── tellurium_examples_3_0.png │ │ │ ├── tellurium_examples_3_1.png │ │ │ ├── tellurium_examples_5_0.png │ │ │ ├── tellurium_examples_7_1.png │ │ │ └── tellurium_examples_9_0.png │ │ │ ├── tellurium_model_loading_files │ │ │ ├── tellurium_model_loading_2_1.png │ │ │ └── tellurium_model_loading_2_3.png │ │ │ ├── tellurium_plotting_files │ │ │ ├── tellurium_plotting_1_0.png │ │ │ ├── tellurium_plotting_2_0.png │ │ │ ├── tellurium_plotting_2_1.png │ │ │ ├── tellurium_plotting_3_0.png │ │ │ ├── tellurium_plotting_4_0.png │ │ │ ├── tellurium_plotting_6_0.png │ │ │ ├── tellurium_plotting_6_1.png │ │ │ ├── tellurium_plotting_extendedplotting.png │ │ │ ├── tellurium_plotting_parameter_scans.png │ │ │ └── tellurium_plotting_parameter_uncertainty.png │ │ │ ├── tellurium_reset_files │ │ │ ├── tellurium_reset_2_1.png │ │ │ ├── tellurium_reset_2_3.png │ │ │ ├── tellurium_reset_2_5.png │ │ │ ├── tellurium_reset_2_6.png │ │ │ └── tellurium_reset_2_7.png │ │ │ ├── tellurium_stochastic_files │ │ │ ├── tellurium_stochastic_2_0.png │ │ │ ├── tellurium_stochastic_4_0.png │ │ │ └── tellurium_stochastic_6_0.png │ │ │ └── tesedmlExample_files │ │ │ ├── tesedmlExample_4_1.png │ │ │ ├── tesedmlExample_6_0.png │ │ │ ├── tesedmlExample_6_1.png │ │ │ └── tesedmlExample_6_2.png │ │ ├── antimonyExample.rst │ │ ├── antimonyExample_files │ │ ├── antimonyExample_2_1.png │ │ ├── antimonyExample_2_2.png │ │ ├── antimonyExample_2_3.png │ │ └── antimonyExample_2_5.png │ │ ├── combineExample.rst │ │ ├── combineExample_files │ │ ├── combineExample_2_0.png │ │ └── combineExample_3_0.png │ │ ├── computeSteadyState.rst │ │ ├── introduction.rst │ │ ├── introduction_files │ │ ├── introduction_2_0.png │ │ └── introduction_4_0.png │ │ ├── methods_installing_packages.rst │ │ ├── model_consecutiveUniUniReactions.rst │ │ ├── model_consecutiveUniUniReactions_files │ │ └── model_consecutiveUniUniReactions_2_0.png │ │ ├── model_feedback_oscillations.rst │ │ ├── model_feedback_oscillations_files │ │ ├── model_feedback_oscillations_2_0.png │ │ └── model_feedback_oscillations_2_1.png │ │ ├── model_generatingDifferentWaveforms.rst │ │ ├── model_generatingDifferentWaveforms_files │ │ └── model_generatingDifferentWaveforms_2_0.png │ │ ├── model_modelFromBioModels.rst │ │ ├── model_modelFromBioModels_files │ │ └── model_modelFromBioModels_2_0.png │ │ ├── model_nonUnitStoichiometries.rst │ │ ├── model_normalizedSpecies.rst │ │ ├── model_normalizedSpecies_files │ │ └── model_normalizedSpecies_3_0.png │ │ ├── parameter_scan.rst │ │ ├── parameter_scan_files │ │ ├── parameter_scan_2_0.png │ │ └── parameter_scan_3_0.png │ │ ├── phrasedmlExample.rst │ │ ├── phrasedmlExample_files │ │ ├── phrasedmlExample_10_0.png │ │ ├── phrasedmlExample_10_1.png │ │ ├── phrasedmlExample_12_0.png │ │ ├── phrasedmlExample_12_1.png │ │ ├── phrasedmlExample_14_0.png │ │ ├── phrasedmlExample_2_0.png │ │ ├── phrasedmlExample_4_0.png │ │ ├── phrasedmlExample_4_1.png │ │ ├── phrasedmlExample_6_0.png │ │ ├── phrasedmlExample_8_0.png │ │ └── phrasedmlExample_8_1.png │ │ ├── plot2DParameterScan.rst │ │ ├── plot2DParameterScan_files │ │ ├── plot2DParameterScan_0_0.png │ │ └── plot2DParameterScan_0_1.png │ │ ├── roadrunnerBasics.rst │ │ ├── roadrunnerBasics_files │ │ ├── roadrunnerBasics_4_0.png │ │ └── roadrunnerBasics_6_1.png │ │ ├── steadystate_scan.rst │ │ ├── steadystate_scan_files │ │ └── steadystate_scan_2_0.png │ │ ├── tellurium_examples.rst │ │ ├── tellurium_examples_files │ │ ├── tellurium_examples_11_0.png │ │ ├── tellurium_examples_13_0.png │ │ ├── tellurium_examples_15_1.png │ │ ├── tellurium_examples_17_0.png │ │ ├── tellurium_examples_19_0.png │ │ ├── tellurium_examples_21_0.png │ │ ├── tellurium_examples_23_0.png │ │ ├── tellurium_examples_25_0.png │ │ ├── tellurium_examples_27_0.png │ │ ├── tellurium_examples_29_0.png │ │ ├── tellurium_examples_31_0.png │ │ ├── tellurium_examples_3_0.png │ │ ├── tellurium_examples_3_1.png │ │ ├── tellurium_examples_5_0.png │ │ ├── tellurium_examples_7_1.png │ │ └── tellurium_examples_9_0.png │ │ ├── tellurium_export.rst │ │ ├── tellurium_interconversion.rst │ │ ├── tellurium_model_loading.rst │ │ ├── tellurium_model_loading_files │ │ ├── tellurium_model_loading_2_1.png │ │ └── tellurium_model_loading_2_3.png │ │ ├── tellurium_plotting.rst │ │ ├── tellurium_plotting_files │ │ ├── tellurium_plotting_1_0.png │ │ ├── tellurium_plotting_2_0.png │ │ ├── tellurium_plotting_2_1.png │ │ ├── tellurium_plotting_3_0.png │ │ ├── tellurium_plotting_4_0.png │ │ ├── tellurium_plotting_6_0.png │ │ ├── tellurium_plotting_6_1.png │ │ ├── tellurium_plotting_extendedplotting.png │ │ ├── tellurium_plotting_parameter_scans.png │ │ └── tellurium_plotting_parameter_uncertainty.png │ │ ├── tellurium_reset.rst │ │ ├── tellurium_reset_files │ │ ├── tellurium_reset_2_1.png │ │ ├── tellurium_reset_2_3.png │ │ ├── tellurium_reset_2_5.png │ │ ├── tellurium_reset_2_6.png │ │ └── tellurium_reset_2_7.png │ │ ├── tellurium_stochastic.rst │ │ ├── tellurium_stochastic_files │ │ ├── tellurium_stochastic_2_0.png │ │ ├── tellurium_stochastic_4_0.png │ │ └── tellurium_stochastic_6_0.png │ │ ├── tellurium_test.rst │ │ ├── tellurium_utility.rst │ │ ├── template.rst │ │ ├── tesedmlExample.rst │ │ └── tesedmlExample_files │ │ ├── tesedmlExample_4_1.png │ │ ├── tesedmlExample_6_0.png │ │ ├── tesedmlExample_6_1.png │ │ └── tesedmlExample_6_2.png ├── antimony.rst ├── appendix.rst ├── conf.py ├── images │ ├── antimony_0.png │ ├── antimony_1.png │ ├── antimony_2.png │ ├── antimony_3.png │ ├── antimony_4.png │ ├── favicon.ico │ ├── jupyter1_example.png │ ├── linux.png │ ├── macos.png │ ├── new-kernel-python-3.png │ ├── notebook-autocompletion.png │ ├── notebook-example-quickstart.png │ ├── notebook-failed-to-load-kernel.png │ ├── notebook-found-kernels.png │ ├── notebook-import-sbml.png │ ├── notebook-kernel-spec-mouse-over.png │ ├── notebook-markdown.png │ ├── notebook-new-markdown-cell.png │ ├── notebook-omex-longer-pulse.png │ ├── notebook-omex-pulse.png │ ├── notebook-open-example-notebook.png │ ├── notebook-python-cell.png │ ├── notebook-r-demo.png │ ├── notebook-reset-clear.png │ ├── notebook-run-sb-cell.png │ ├── notebook-save-omex.png │ ├── notebook-sb-cell-change-name.png │ ├── notebook-sb-cell.png │ ├── notebook-search-replace-demo-whole-words.png │ ├── notebook-simulate-sb-cell.png │ ├── notebook-word-boundary.png │ ├── notebook_screenshot.png │ ├── spyder-filemenu.png │ ├── spyder-help.png │ ├── spyder-overview.png │ ├── spyder-ratelaw.png │ ├── spyderFrontEndExample.png │ ├── tellurium-front-page-image.png │ ├── tellurium │ │ ├── Tellurium.icns │ │ ├── Tellurium.ico │ │ ├── Tellurium.pptx │ │ ├── Tellurium_filled.png │ │ ├── Tellurium_filled_small.png │ │ ├── Tellurium_light.ico │ │ └── Tellurium_splash.pdn │ ├── tellurium_logo.png │ ├── tellurium_logo_50.png │ ├── tellurium_screenshot.png │ ├── tellurium_screenshot2.png │ └── windows.png ├── index.rst ├── installation.rst ├── latex.rst ├── make.bat ├── make_docs.log ├── make_docs.sh ├── make_notebooks_rst.log ├── make_notebooks_rst.sh ├── notebooks.rst ├── paramscan.rst ├── quickstart.rst ├── requirements.txt ├── sedml.md ├── tellurium_methods.rst ├── testing.rst └── walkthrough.rst ├── examples ├── __init__.py ├── notebooks-py │ ├── antimonyExample.py │ ├── combineExample.py │ ├── computeSteadyState.py │ ├── introduction.py │ ├── model_consecutiveUniUniReactions.py │ ├── model_feedback_oscillations.py │ ├── model_generatingDifferentWaveforms.py │ ├── model_modelFromBioModels.py │ ├── model_nonUnitStoichiometries.py │ ├── model_normalizedSpecies.py │ ├── parameter_scan.py │ ├── phrasedmlExample.py │ ├── plot2DParameterScan.py │ ├── roadrunnerBasics.py │ ├── steadystate_scan.py │ ├── tellurium_examples.py │ ├── tellurium_export.py │ ├── tellurium_interconversion.py │ ├── tellurium_model_loading.py │ ├── tellurium_plotting.py │ ├── tellurium_reset.py │ ├── tellurium_stochastic.py │ ├── tellurium_test.py │ ├── tellurium_utility.py │ ├── template.py │ └── tesedmlExample.py ├── notebooks │ ├── README.md │ ├── core │ │ ├── _te_BIOMD0000000003 │ │ │ ├── BIOMD0000000003.sedx.xml │ │ │ ├── model1.xml │ │ │ └── plot1.png │ │ ├── antimonyExample.ipynb │ │ ├── combineExample.ipynb │ │ ├── computeSteadyState.ipynb │ │ ├── introduction.ipynb │ │ ├── methods_installing_packages.ipynb │ │ ├── model_consecutiveUniUniReactions.ipynb │ │ ├── model_feedback_oscillations.ipynb │ │ ├── model_generatingDifferentWaveforms.ipynb │ │ ├── model_modelFromBioModels.ipynb │ │ ├── model_nonUnitStoichiometries.ipynb │ │ ├── model_normalizedSpecies.ipynb │ │ ├── parameter_scan.ipynb │ │ ├── phrasedmlExample.ipynb │ │ ├── plot2DParameterScan.ipynb │ │ ├── roadrunnerBasics.ipynb │ │ ├── steadystate_scan.ipynb │ │ ├── tellurium_examples.ipynb │ │ ├── tellurium_export.ipynb │ │ ├── tellurium_interconversion.ipynb │ │ ├── tellurium_model_loading.ipynb │ │ ├── tellurium_plotting.ipynb │ │ ├── tellurium_reset.ipynb │ │ ├── tellurium_stochastic.ipynb │ │ ├── tellurium_test.ipynb │ │ ├── tellurium_utility.ipynb │ │ ├── template.ipynb │ │ └── tesedmlExample.ipynb │ ├── docstrings │ │ └── docstring_examples.ipynb │ ├── index.ipynb │ ├── models │ │ ├── .ipynb_checkpoints │ │ │ └── Gillespie_test-checkpoint.ipynb │ │ ├── Gillespie_test.ipynb │ │ ├── Koenig_demo_10.xml │ │ ├── modelCompositionAndChange.ipynb │ │ ├── phrasedml.ipynb │ │ ├── yeast_glycolysis.html │ │ ├── yeast_glycolysis.ipynb │ │ └── yeast_glycolysis.xml │ └── widgets │ │ ├── widgets_lorenz.ipynb │ │ ├── widgets_ontology_search.ipynb │ │ ├── widgets_parameter_slider.ipynb │ │ └── widgets_species_search.ipynb └── tellurium-files │ ├── SBMLfromBioModelsDB.py │ ├── __init__.py │ ├── computeSteadyState.py │ ├── consecutiveUniUniReactions.py │ ├── events │ ├── 00026-sbml-l3v1.xml │ ├── 00952-sbml-l3v1.xml │ ├── events.py │ └── feedback.xml │ ├── export │ └── latex_export.py │ ├── exportToMatlab.py │ ├── generatingDifferentWaveforms.py │ ├── linearChain.py │ ├── nonUnitStoichiometries.py │ ├── omex │ ├── CombineArchiveShowCase.py │ ├── README.md │ └── __init__.py │ ├── parameterscan │ ├── create_colormap.py │ ├── parameter_scan.py │ ├── plot_array.py │ ├── plot_multi_array.py │ └── steadystatescan.py │ ├── parameterscanExample.py │ ├── phrasedml │ ├── case_01.py │ ├── case_02.py │ ├── case_03.py │ ├── case_04.py │ ├── case_05.py │ ├── case_06.py │ ├── case_07.py │ ├── case_08.py │ ├── case_09.py │ ├── case_10.py │ ├── case_11.py │ ├── case_12.py │ ├── lorenz.py │ ├── models │ │ ├── BIOMD0000000010.xml │ │ └── lorenz.xml │ ├── omex │ │ └── repressilator.omex │ ├── oneStep.py │ ├── parameterScan1D.py │ ├── parameterScan2D.py │ ├── repeatedStochastic.py │ ├── repressilator.py │ └── simpletimecourse.py │ ├── phrasedmlExample.py │ ├── settingBoundarySpecies.py │ ├── simpleUniUniReaction.py │ └── singleGeneExpressingProteinAndProteinDegradation.py ├── installer ├── cp_tellurium_to_install.sh ├── linux │ └── README.md └── windows │ ├── README.txt │ ├── Tellurium-Winpython-3.12.10.0-2.4.2-win64-setup.iss │ ├── Tellurium-Winpython-3.7.4.0-2.3.0-win64-setup.iss │ ├── Tellurium_splash_installer_updated.bmp │ ├── favicon.ico │ ├── installer_small_updated.bmp │ ├── settings3.3.6 │ ├── .pyzo │ │ └── config.ssdf │ ├── pydistutils.cfg │ └── winpython.ini │ ├── settings4.1.3 │ ├── .pyzo │ │ └── config.ssdf │ ├── pydistutils.cfg │ └── winpython.ini │ ├── settings6.0.4 │ └── winpython.ini │ ├── tellurium-Python-2.7-win32-superpack-setup.iss │ ├── tellurium-spyder-bdist_wininst.bmp │ ├── tellurium_icon_64x64.ico │ └── tellurium_icon_small.ico ├── meta.yaml ├── misc ├── schema │ └── level1 │ │ ├── version1 │ │ ├── sed-ml-L1-V1.xsd │ │ └── sedml-mathml.xsd │ │ ├── version2 │ │ ├── sed-ml-L1-V2.xsd │ │ └── sedml-mathml.xsd │ │ └── version3 │ │ ├── sed-ml-L1-V3.xsd │ │ └── sedml-mathml.xsd └── specifications │ ├── sed-ml-L1V2.pdf │ └── sed-ml-L1V3-draft1.pdf ├── requirements.txt ├── roadrunner.conf ├── scripts ├── download_count.py └── tellurium_github_downloads.png ├── setup.py ├── spyder_mod ├── Spyder 3.2.2 │ ├── favicon.ico │ ├── favicon.png │ ├── scripts │ │ └── env.bat │ └── spyder │ │ ├── app │ │ ├── mainwindow.py │ │ └── restart.py │ │ ├── config │ │ └── main.py │ │ ├── images │ │ ├── Tellurium_splash.png │ │ ├── Tellurium_splash_whiteout.png │ │ ├── te_64_1.svg │ │ ├── tellurium-spyder-bdist_wininst.bmp │ │ └── tellurium_icon_big.ico │ │ └── plugins │ │ └── editor.py ├── Spyder 3.3.0 │ ├── favicon.ico │ ├── favicon.png │ ├── libcombine.pth │ ├── libnuml.pth │ ├── libsbml.pth │ ├── libsedml.pth │ ├── scripts │ │ └── env.bat │ └── spyder │ │ ├── app │ │ ├── mainwindow.py │ │ └── restart.py │ │ ├── config │ │ └── main.py │ │ ├── images │ │ ├── Tellurium_splash.png │ │ ├── Tellurium_splash_whiteout.png │ │ ├── te_64_1.svg │ │ ├── tellurium-spyder-bdist_wininst.bmp │ │ └── tellurium_icon_big.ico │ │ └── plugins │ │ └── editor.py ├── Spyder 3.3.6 │ ├── scripts │ │ └── env.bat │ └── site-packages │ │ ├── libcombine.pth │ │ ├── libnuml.pth │ │ ├── libsbml.pth │ │ ├── libsedml.pth │ │ └── spyder │ │ ├── app │ │ ├── mainwindow.py │ │ └── restart.py │ │ ├── config │ │ └── main.py │ │ ├── images │ │ ├── Tellurium_splash.png │ │ ├── Tellurium_splash_whiteout.png │ │ ├── favicon.ico │ │ ├── favicon.png │ │ ├── te_64_1.svg │ │ ├── tellurium-spyder-bdist_wininst.bmp │ │ └── tellurium_icon_big.ico │ │ └── plugins │ │ └── editor.py ├── Spyder 4.1.3 │ ├── scripts │ │ └── env.bat │ └── site-packages │ │ └── spyder │ │ ├── app │ │ ├── mainwindow.py │ │ ├── restart.py │ │ └── utils.py │ │ ├── config │ │ └── main.py │ │ ├── images │ │ ├── Tellurium_splash.png │ │ ├── Tellurium_splash_whiteout.png │ │ ├── favicon.ico │ │ ├── favicon.png │ │ ├── te_64_1.svg │ │ ├── tellurium-spyder-bdist_wininst.bmp │ │ └── tellurium_icon_big.ico │ │ └── plugins │ │ └── editor │ │ └── plugin.py ├── Spyder 4.2.1 │ ├── scripts │ │ └── env.bat │ └── site-packages │ │ └── spyder │ │ ├── app │ │ ├── mainwindow.py │ │ ├── restart.py │ │ └── utils.py │ │ ├── config │ │ └── main.py │ │ ├── images │ │ ├── Tellurium_splash.png │ │ ├── Tellurium_splash_whiteout.png │ │ ├── favicon.ico │ │ ├── favicon.png │ │ ├── te_64_1.svg │ │ ├── tellurium-spyder-bdist_wininst.bmp │ │ └── tellurium_icon_big.ico │ │ └── plugins │ │ └── editor │ │ └── plugin.py ├── Spyder 5.1.5 │ ├── scripts │ │ └── env.bat │ └── site-packages │ │ └── spyder │ │ ├── app │ │ ├── mainwindow.py │ │ ├── restart.py │ │ └── utils.py │ │ ├── config │ │ └── main.py │ │ ├── images │ │ ├── Tellurium_splash.png │ │ ├── Tellurium_splash.svg │ │ ├── Tellurium_splash_whiteout.png │ │ ├── favicon.ico │ │ ├── favicon.png │ │ ├── te_64_1.svg │ │ ├── tellurium-spyder-bdist_wininst.bmp │ │ └── tellurium_icon_big.ico │ │ └── plugins │ │ └── editor │ │ └── plugin.py └── Spyder 6.0.4 │ ├── scripts │ └── env.bat │ └── site-packages │ └── spyder │ ├── app │ ├── mainwindow.py │ ├── restart.py │ └── utils.py │ ├── config │ └── main.py │ ├── images │ ├── Tellurium_splash.png │ ├── Tellurium_splash.svg │ ├── Tellurium_splash_whiteout.png │ ├── favicon.ico │ ├── favicon.png │ ├── te_64_1.svg │ ├── tellurium-spyder-bdist_wininst.bmp │ └── tellurium_icon_big.ico │ └── plugins │ └── editor │ └── widgets │ └── main_widget.py ├── tellurium ├── VERSION.txt ├── __init__.py ├── analysis │ ├── __init__.py │ ├── annotations.py │ ├── bifurcation.py │ ├── parameterestimation.py │ ├── parameterscan.py │ ├── sensitivityanalysis.py │ ├── simulator.py │ ├── stochasticmodel.py │ └── test.py ├── dev │ ├── __init__.py │ ├── deprecated │ │ ├── README.md │ │ ├── __init__.py │ │ ├── tecombine.py │ │ └── tephrasedml.py │ └── oven │ │ ├── README.md │ │ ├── __init__.py │ │ ├── archive_plots.ipynb │ │ ├── libnuml_import.py │ │ ├── ndarray │ │ ├── __init__.py │ │ └── ndarray.py │ │ └── omex │ │ ├── L1V3_ikappab.omex │ │ ├── L1V3_leloup-sbml.omex │ │ ├── L1V3_lorenz-sbml.omex │ │ ├── L1V3_oscli-nested-pulse.omex │ │ ├── L1V3_parameter-scan-2d.omex │ │ ├── L1V3_plotting-data-csv.omex │ │ ├── L1V3_plotting-data-numl.omex │ │ ├── L1V3_repeated-scan-oscli.omex │ │ ├── L1V3_repeated-steady-scan-oscli.omex │ │ ├── L1V3_repeated-stochastic-runs.omex │ │ ├── L1V3_repressilator.omex │ │ └── L1V3_vanderpol-sbml.omex ├── notebooks │ ├── __init__.py │ ├── notebooktools.py │ ├── ontologysearch.py │ ├── parameterslider.py │ └── speciessearch.py ├── plotting │ ├── __init__.py │ ├── api.py │ ├── engine.py │ ├── engine_mpl.py │ ├── engine_null.py │ ├── engine_plotly.py │ └── factory.py ├── roadrunner │ ├── __init__.py │ └── extended_roadrunner.py ├── sedml │ ├── __init__.py │ ├── data.py │ ├── mathml.py │ ├── templates │ │ ├── __init__.py │ │ ├── macros_helpers.template │ │ └── tesedml_template.template │ ├── tesedml.py │ ├── utils.py │ └── xpath.py ├── teconverters │ ├── __init__.py │ ├── antimony_regex.py │ ├── antimony_sbo.py │ ├── convert_antimony.py │ ├── convert_omex.py │ ├── convert_phrasedml.py │ └── inline_omex.py ├── teio │ ├── __init__.py │ └── latex.py ├── tellurium.py ├── temiriam.py ├── testcases.py ├── tests │ ├── README.md │ ├── __init__.py │ ├── helpers.py │ ├── run_tests.sh │ ├── sedml │ │ ├── __init__.py │ │ ├── test_archive.py │ │ ├── test_data.py │ │ ├── test_kisao.py │ │ ├── test_omex.py │ │ ├── test_phrasedml.py │ │ ├── test_sedml.py │ │ └── test_tesedml.py │ ├── test_API.py │ ├── test_analysis.py │ ├── test_examples.py │ ├── test_inline_omex.py │ ├── test_io.py │ ├── test_omex.py │ ├── test_plotting.py │ ├── test_runner.py │ ├── test_tellurium.py │ ├── test_temiriam.py │ └── testdata │ │ ├── __init__.py │ │ ├── models │ │ ├── example1 │ │ ├── example1.cellml │ │ ├── example1.xml │ │ └── feedback.xml │ │ ├── sedml │ │ ├── __init__.py │ │ ├── data.zip │ │ ├── data │ │ │ ├── __init__.py │ │ │ ├── data_creator.py │ │ │ ├── numlData1D.xml │ │ │ ├── numlData2D.xml │ │ │ ├── numlData2D2RC.xml │ │ │ ├── omex │ │ │ │ ├── jws_adlung2017_fig2g.omex │ │ │ │ ├── jws_adlung2017_fig2g │ │ │ │ │ ├── data │ │ │ │ │ │ ├── Fig2G_BaF3data.tsv │ │ │ │ │ │ ├── Fig2G_BaF3data.xlsx │ │ │ │ │ │ ├── Fig2G_mCFUEdata.tsv │ │ │ │ │ │ └── Fig2G_mCFUEdata.xlsx │ │ │ │ │ ├── manifest.xml │ │ │ │ │ ├── metadata.rdf │ │ │ │ │ ├── models │ │ │ │ │ │ ├── adlung1.sbml │ │ │ │ │ │ └── adlung2.sbml │ │ │ │ │ └── sedml │ │ │ │ │ │ └── adlung2017_fig2g.sedml │ │ │ │ ├── parameter_from_data_csv.omex │ │ │ │ ├── parameter_from_data_csv │ │ │ │ │ ├── parameter-from-data-csv.xml │ │ │ │ │ ├── parameters.csv │ │ │ │ │ └── vanderpol-sbml.xml │ │ │ │ ├── plot_csv.omex │ │ │ │ ├── plot_csv │ │ │ │ │ ├── manifest.xml │ │ │ │ │ ├── oscli.csv │ │ │ │ │ └── plot_csv.xml │ │ │ │ ├── plot_csv_with_model.omex │ │ │ │ ├── plot_csv_with_model │ │ │ │ │ ├── manifest.xml │ │ │ │ │ ├── oscli.csv │ │ │ │ │ ├── oscli.xml │ │ │ │ │ └── plot_csv_with_model.xml │ │ │ │ ├── plot_numl.omex │ │ │ │ ├── plot_numl │ │ │ │ │ ├── manifest.xml │ │ │ │ │ ├── oscli.numl │ │ │ │ │ └── plot_numl.xml │ │ │ │ ├── plot_numl_with_model.omex │ │ │ │ ├── plot_numl_with_model │ │ │ │ │ ├── manifest.xml │ │ │ │ │ ├── oscli.numl │ │ │ │ │ ├── oscli.xml │ │ │ │ │ └── plot_numl_with_model.xml │ │ │ │ └── zip_archives.py │ │ │ ├── oscli.csv │ │ │ ├── oscli.tsv │ │ │ ├── oscli.xml │ │ │ ├── parameter-from-data-csv.xml │ │ │ ├── parameters.csv │ │ │ ├── reading-numlData1D.xml │ │ │ ├── reading-numlData2D.xml │ │ │ ├── reading-numlData2DRC.xml │ │ │ ├── reading-oscli-csv.xml │ │ │ ├── reading-oscli-numl.xml │ │ │ └── reading-oscli-tsv.xml │ │ ├── models │ │ │ ├── BioModel1_repressor_activator_oscillations.xml │ │ │ ├── BorisEJB.xml │ │ │ ├── app2sim.xml │ │ │ ├── asedml3repeat.xml │ │ │ ├── asedmlComplex.xml │ │ │ ├── curien.xml │ │ │ ├── example1.ant │ │ │ ├── example1.cellml │ │ │ ├── example1.xml │ │ │ ├── leloup_gonze_goldbeter_1999_a.cellml │ │ │ ├── lorenz.xml │ │ │ ├── model1.xml │ │ │ └── oscli.xml │ │ ├── omex │ │ │ ├── CombineArchiveShowCase.omex │ │ │ ├── README.md │ │ │ ├── biomodels │ │ │ │ ├── README.md │ │ │ │ ├── create_omex.py │ │ │ │ ├── omex │ │ │ │ │ ├── BIOMD0000000003_fig4_sedml.omex │ │ │ │ │ ├── BIOMD0000000003_sedml.omex │ │ │ │ │ ├── BIOMD0000000004_sedml.omex │ │ │ │ │ ├── BIOMD0000000005_sedml.omex │ │ │ │ │ ├── BIOMD0000000007_fig_2a_b_sedml.omex │ │ │ │ │ ├── BIOMD0000000007_fig_2a_sedml.omex │ │ │ │ │ ├── BIOMD0000000008_sedml.omex │ │ │ │ │ ├── BIOMD0000000056_fig2_sedml.omex │ │ │ │ │ ├── BIOMD0000000087_fig5_sedml.omex │ │ │ │ │ ├── BIOMD0000000107_fig13_sedml.omex │ │ │ │ │ ├── BIOMD0000000107_fig9_sedml.omex │ │ │ │ │ ├── BIOMD0000000109_sf2a_sedml.omex │ │ │ │ │ ├── BIOMD0000000110_fig6B_sedml.omex │ │ │ │ │ ├── BIOMD0000000111_fi4_sedml.omex │ │ │ │ │ ├── BIOMD0000000144_fig1b_sedml.omex │ │ │ │ │ ├── BIOMD0000000150_fig1b_sedml.omex │ │ │ │ │ ├── BIOMD0000000168_fig3a_sedml.omex │ │ │ │ │ ├── BIOMD0000000169_fig5c_sedml.omex │ │ │ │ │ ├── BIOMD0000000181_fig12_sedml.omex │ │ │ │ │ ├── BIOMD0000000186_fig3a_sedml.omex │ │ │ │ │ ├── BIOMD0000000187_fig3b_sedml.omex │ │ │ │ │ ├── BIOMD0000000193_fig2b_sedml.omex │ │ │ │ │ ├── BIOMD0000000194_fig2b_sedml.omex │ │ │ │ │ ├── BIOMD0000000195_fig8a_sedml.omex │ │ │ │ │ ├── BIOMD0000000207_ab_sedml.omex │ │ │ │ │ ├── BIOMD0000000207_c_sedml.omex │ │ │ │ │ ├── BIOMD0000000208_fig3a_sedml.omex │ │ │ │ │ ├── BIOMD0000000216_fig2c_sedml.omex │ │ │ │ │ ├── BIOMD0000000228_fig4_sedml.omex │ │ │ │ │ ├── BIOMD0000000242_fig2_sedml.omex │ │ │ │ │ ├── BIOMD0000000265_fig2_sedml.omex │ │ │ │ │ ├── BIOMD0000000297_fig3_sedml.omex │ │ │ │ │ ├── BIOMD0000000370_fig2_sedml.omex │ │ │ │ │ ├── BIOMD0000000406_fig7c_sedml.omex │ │ │ │ │ ├── BIOMD0000000409_fig7b_sedml.omex │ │ │ │ │ └── MODEL3897771820_fig8_sedml.omex │ │ │ │ └── sedml │ │ │ │ │ ├── BIOMD0000000003_fig4_sedml.xml │ │ │ │ │ ├── BIOMD0000000003_sedml.xml │ │ │ │ │ ├── BIOMD0000000004_sedml.xml │ │ │ │ │ ├── BIOMD0000000005_sedml.xml │ │ │ │ │ ├── BIOMD0000000007_fig_2a_b_sedml.xml │ │ │ │ │ ├── BIOMD0000000007_fig_2a_sedml.xml │ │ │ │ │ ├── BIOMD0000000008_sedml.xml │ │ │ │ │ ├── BIOMD0000000056_fig2_sedml.xml │ │ │ │ │ ├── BIOMD0000000087_fig5_sedml.xml │ │ │ │ │ ├── BIOMD0000000107_fig13_sedml.xml │ │ │ │ │ ├── BIOMD0000000107_fig9_sedml.xml │ │ │ │ │ ├── BIOMD0000000109_sf2a_sedml.xml │ │ │ │ │ ├── BIOMD0000000110_fig6B_sedml.xml │ │ │ │ │ ├── BIOMD0000000111_fi4_sedml.xml │ │ │ │ │ ├── BIOMD0000000144_fig1b_sedml.xml │ │ │ │ │ ├── BIOMD0000000150_fig1b_sedml.xml │ │ │ │ │ ├── BIOMD0000000168_fig3a_sedml.xml │ │ │ │ │ ├── BIOMD0000000169_fig5c_sedml.xml │ │ │ │ │ ├── BIOMD0000000181_fig12_sedml.xml │ │ │ │ │ ├── BIOMD0000000186_fig3a_sedml.xml │ │ │ │ │ ├── BIOMD0000000187_fig3b_sedml.xml │ │ │ │ │ ├── BIOMD0000000193_fig2b_sedml.xml │ │ │ │ │ ├── BIOMD0000000194_fig2b_sedml.xml │ │ │ │ │ ├── BIOMD0000000195_fig8a_sedml.xml │ │ │ │ │ ├── BIOMD0000000196_sedml.xml │ │ │ │ │ ├── BIOMD0000000207_ab_sedml.xml │ │ │ │ │ ├── BIOMD0000000207_c_sedml.xml │ │ │ │ │ ├── BIOMD0000000208_fig3a_sedml.xml │ │ │ │ │ ├── BIOMD0000000216_fig2c_sedml.xml │ │ │ │ │ ├── BIOMD0000000228_fig4_sedml.xml │ │ │ │ │ ├── BIOMD0000000242_fig2_sedml.xml │ │ │ │ │ ├── BIOMD0000000265_fig2_sedml.xml │ │ │ │ │ ├── BIOMD0000000297_fig3_sedml.xml │ │ │ │ │ ├── BIOMD0000000370_fig2_sedml.xml │ │ │ │ │ ├── BIOMD0000000406_fig7c_sedml.xml │ │ │ │ │ ├── BIOMD0000000409_fig7b_sedml.xml │ │ │ │ │ └── MODEL3897771820_fig8_sedml.xml │ │ │ ├── cellml │ │ │ │ ├── README.md │ │ │ │ └── lorenz-cellml.omex │ │ │ ├── jws │ │ │ │ ├── README.md │ │ │ │ ├── download_omex.py │ │ │ │ └── omex │ │ │ │ │ ├── adlung2017_fig2bto2e.sedx │ │ │ │ │ ├── adlung2017_fig2f.sedx │ │ │ │ │ ├── adlung2017_fig2g.sedx │ │ │ │ │ ├── alsheihk2011_fig3-user.sedx │ │ │ │ │ ├── alsheihk2011_fig4-user.sedx │ │ │ │ │ ├── alsheihk2011_fig5-user.sedx │ │ │ │ │ ├── alsheihk2011_fig6-user.sedx │ │ │ │ │ ├── alsheihk2011_fig7-user.sedx │ │ │ │ │ ├── arnaout2000_fig1-user.sedx │ │ │ │ │ ├── bachar2004_fig1-user.sedx │ │ │ │ │ ├── bachmann2011.sedx │ │ │ │ │ ├── bajaria2002_fig2.sedx │ │ │ │ │ ├── beuke2017_fig6.sedx │ │ │ │ │ ├── cai2009_fig2and3-user.sedx │ │ │ │ │ ├── callaway2002_fig4-user.sedx │ │ │ │ │ ├── callaway2002_fig5-user.sedx │ │ │ │ │ ├── callaway2002_fig8-user.sedx │ │ │ │ │ ├── chan2004_fig3.sedx │ │ │ │ │ ├── dixit2005_fig2-user.sedx │ │ │ │ │ ├── essunger1994_fig2-2.sedx │ │ │ │ │ ├── essunger1994_fig4.sedx │ │ │ │ │ ├── essunger1994_fig5.sedx │ │ │ │ │ ├── essunger1994_fig6-user.sedx │ │ │ │ │ ├── essunger1994_fig8.sedx │ │ │ │ │ ├── fan2014_fig1a.sedx │ │ │ │ │ ├── fisher2006_fig3a.sedx │ │ │ │ │ ├── fraser2002_fig1a_1b_2a_2b.sedx │ │ │ │ │ ├── hernandezvargas2013.sedx │ │ │ │ │ ├── ho1995_fig3.sedx │ │ │ │ │ ├── huo2013_fig2-user.sedx │ │ │ │ │ ├── iwami2012_fig3.sedx │ │ │ │ │ ├── jansen2005_fig1-user.sedx │ │ │ │ │ ├── jones2002_fig2.sedx │ │ │ │ │ ├── kirschner1998_fig2-user.sedx │ │ │ │ │ ├── kolodkin2010_figure2b.sedx │ │ │ │ │ ├── kouril3_experiment-user.sedx │ │ │ │ │ ├── landi2008_fig2-user.sedx │ │ │ │ │ ├── levering2012_fig2-user.sedx │ │ │ │ │ ├── levering2012_fig5-user.sedx │ │ │ │ │ ├── li2014_fig3-user.sedx │ │ │ │ │ ├── lou2009_fig2-user.sedx │ │ │ │ │ ├── martins2016_fig4b.sedx │ │ │ │ │ ├── martins2016_fig6.sedx │ │ │ │ │ ├── martins2016_figev3a.sedx │ │ │ │ │ ├── miao2008_fig1.sedx │ │ │ │ │ ├── naresh2005_fig2to3-user.sedx │ │ │ │ │ ├── naresh2011_fig11to13-user.sedx │ │ │ │ │ ├── naresh2011_fig6to7-user.sedx │ │ │ │ │ ├── naresh2011_fig8to10-user.sedx │ │ │ │ │ ├── nyabadza2013_fig1b-user.sedx │ │ │ │ │ ├── ouattara2008_fig3.sedx │ │ │ │ │ ├── pankavich2016_fig1.sedx │ │ │ │ │ ├── pankavich2016_fig2.sedx │ │ │ │ │ ├── penkler2aa_experiment-user.sedx │ │ │ │ │ ├── perelson1993_fig11-user.sedx │ │ │ │ │ ├── perelson1993_fig2and3-user.sedx │ │ │ │ │ ├── perelson1993_fig8-user.sedx │ │ │ │ │ ├── perelson1996_fig1a-user.sedx │ │ │ │ │ ├── perelson1996_fig1b_top.sedx │ │ │ │ │ ├── revilla2003_fig2a-user.sedx │ │ │ │ │ ├── revilla2003_fig2bandc-user.sedx │ │ │ │ │ ├── ribeiro2008_fig4-user.sedx │ │ │ │ │ ├── rong2007a_fig2aandb-user.sedx │ │ │ │ │ ├── rong2007b_fig1-user.sedx │ │ │ │ │ ├── rong2008_fig2-user.sedx │ │ │ │ │ ├── roy2010_fig2-user.sedx │ │ │ │ │ ├── roy2010_fig3.sedx │ │ │ │ │ ├── sedaghat2008_fig4-user.sedx │ │ │ │ │ ├── shu2014_fig3-user.sedx │ │ │ │ │ ├── speirs2005_fig4-user.sedx │ │ │ │ │ ├── srivastava2012_fig2-user.sedx │ │ │ │ │ ├── srivastava2012_fig3and4-user.sedx │ │ │ │ │ ├── stafford2000_fig2.sedx │ │ │ │ │ ├── tripathi2007_fig7_10to7_11-user.sedx │ │ │ │ │ ├── tripathi2007_fig7_4-user.sedx │ │ │ │ │ ├── tripathi2007_fig7_5to7_7-user.sedx │ │ │ │ │ ├── tripathi2007_fig7_8to7_9-user.sedx │ │ │ │ │ ├── wahl2000_fig6-user.sedx │ │ │ │ │ ├── wang2012_fig1and2-user.sedx │ │ │ │ │ ├── wang2015_fig9-user.sedx │ │ │ │ │ ├── wodarz2000_fig2-user.sedx │ │ │ │ │ ├── wodarz2007_fig1-user.sedx │ │ │ │ │ └── zhao2013_fig3a-user.sedx │ │ │ ├── specification │ │ │ │ ├── L1V3 │ │ │ │ │ ├── L1V3_ikappab.omex │ │ │ │ │ ├── L1V3_leloup-sbml.omex │ │ │ │ │ ├── L1V3_lorenz-cellml.omex │ │ │ │ │ ├── L1V3_lorenz-sbml.omex │ │ │ │ │ ├── L1V3_oscli-nested-pulse.omex │ │ │ │ │ ├── L1V3_parameter-scan-2d.omex │ │ │ │ │ ├── L1V3_plotting-data-csv.omex │ │ │ │ │ ├── L1V3_plotting-data-numl.omex │ │ │ │ │ ├── L1V3_repeated-scan-oscli.omex │ │ │ │ │ ├── L1V3_repeated-steady-scan-oscli.omex │ │ │ │ │ ├── L1V3_repeated-stochastic-runs.omex │ │ │ │ │ ├── L1V3_repressilator.omex │ │ │ │ │ ├── L1V3_vanderpol-cellml.omex │ │ │ │ │ └── L1V3_vanderpol-sbml.omex │ │ │ │ └── README.md │ │ │ └── tellurium │ │ │ │ ├── BIOMD0000000003.sedx │ │ │ │ ├── BIOMD0000000012.sedx │ │ │ │ ├── BIOMD0000000139.sedx │ │ │ │ ├── BIOMD0000000140.sedx │ │ │ │ ├── BM12.sedx │ │ │ │ ├── BorisEJB-test.sedx │ │ │ │ ├── BorisEJB.sedx │ │ │ │ ├── BorisEJBos.sedx │ │ │ │ ├── BorisEJBsteady.sedx │ │ │ │ ├── ClockSedML.sedx │ │ │ │ ├── EllowitzRepressilator.sedx │ │ │ │ ├── JanaWolf.sedx │ │ │ │ ├── README.md │ │ │ │ ├── brusselator.sedx │ │ │ │ ├── case_01.omex │ │ │ │ ├── case_02.omex │ │ │ │ ├── case_03.omex │ │ │ │ ├── case_04.omex │ │ │ │ ├── case_05.omex │ │ │ │ ├── case_06.omex │ │ │ │ ├── case_07.omex │ │ │ │ ├── case_08.omex │ │ │ │ ├── case_09.omex │ │ │ │ ├── case_10.omex │ │ │ │ ├── case_11.omex │ │ │ │ ├── case_12.omex │ │ │ │ ├── lorenz.omex │ │ │ │ ├── miase.sedx │ │ │ │ ├── oneStep.omex │ │ │ │ ├── oscli-computeChange.sedx │ │ │ │ ├── parameterScan1D.omex │ │ │ │ ├── parameterScan2D.omex │ │ │ │ ├── repeatedStochastic.omex │ │ │ │ ├── repressilator.omex │ │ │ │ ├── sedMLBIOM21.sedx │ │ │ │ ├── sedmlCurienJWS.sedx │ │ │ │ └── specificationL1V2.sedx │ │ └── sed-ml │ │ │ ├── BIOMD0000000003.sedml │ │ │ ├── BIOMD0000000012.sedml │ │ │ ├── BIOMD0000000021.sedml │ │ │ ├── BIOMD0000000139.sedml │ │ │ ├── BIOMD0000000140.sedml │ │ │ ├── BM12.sedml │ │ │ ├── BioModel1_repressor_activator_oscillations.sedml │ │ │ ├── BorisEJB-os.sedml │ │ │ ├── BorisEJB-steady.sedml │ │ │ ├── BorisEJB-test.sedml │ │ │ ├── __init__.py │ │ │ ├── app2sim.sedml │ │ │ ├── asedml3repeat.sedml │ │ │ ├── asedmlComplex.sedml │ │ │ ├── brusselator.sedml │ │ │ ├── cellml │ │ │ ├── BR-INa-variants.sedml │ │ │ ├── __init__.py │ │ │ └── leloup.sedml │ │ │ ├── lorenz.sedml │ │ │ ├── miase.sedml │ │ │ ├── miaseBioModels21.sedml │ │ │ ├── oscli-computeChange.sedml │ │ │ ├── sedMLBIOM21.sedml │ │ │ └── sedmlCurienJWS.sedml │ │ └── utils │ │ └── omex_from_zip │ │ ├── lorenz-model.xml │ │ ├── lorenz.xml │ │ ├── manifest.json │ │ └── results │ │ ├── sedml_webtools │ │ ├── plot1.pdf │ │ ├── plot2.pdf │ │ └── plot3.pdf │ │ └── tellurium │ │ ├── plot1.pdf │ │ ├── plot2.pdf │ │ └── plot3.pdf ├── utils │ ├── __init__.py │ ├── matrix.py │ ├── misc.py │ ├── omex.py │ 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