.all-contributorsrc
.flake8
.gitignore
CODE_OF_CONDUCT.md
CONTRIBUTING.md
CONTRIBUTORS.md
GOVERNANCE.md
LICENSE
MANIFEST.in
README.md
pytest.ini
requirements.optional.txt
requirements.txt
setup.cfg
setup.py
.github/pull_request_template.md
.github/workflows/ci.yml
biosimulators_utils/__init__.py
biosimulators_utils/__main__.py
biosimulators_utils/_version.py
biosimulators_utils/config.py
biosimulators_utils/data_model.py
biosimulators_utils/exceptions.py
biosimulators_utils/image.py
biosimulators_utils/warnings.py
biosimulators_utils.egg-info/PKG-INFO
biosimulators_utils.egg-info/SOURCES.txt
biosimulators_utils.egg-info/dependency_links.txt
biosimulators_utils.egg-info/entry_points.txt
biosimulators_utils.egg-info/requires.txt
biosimulators_utils.egg-info/top_level.txt
biosimulators_utils/archive/__init__.py
biosimulators_utils/archive/data_model.py
biosimulators_utils/archive/io.py
biosimulators_utils/archive/utils.py
biosimulators_utils/biosimulations/__init__.py
biosimulators_utils/biosimulations/data_model.py
biosimulators_utils/biosimulations/utils.py
biosimulators_utils/combine/__init__.py
biosimulators_utils/combine/data_model.py
biosimulators_utils/combine/exceptions.py
biosimulators_utils/combine/exec.py
biosimulators_utils/combine/io.py
biosimulators_utils/combine/utils.py
biosimulators_utils/combine/validation.py
biosimulators_utils/gh_action/__init__.py
biosimulators_utils/gh_action/core.py
biosimulators_utils/gh_action/data_model.py
biosimulators_utils/kisao/__init__.py
biosimulators_utils/kisao/utils.py
biosimulators_utils/licensing/__init__.py
biosimulators_utils/licensing/core.py
biosimulators_utils/licensing/gurobi.py
biosimulators_utils/log/__init__.py
biosimulators_utils/log/data_model.py
biosimulators_utils/log/utils.py
biosimulators_utils/log/warnings.py
biosimulators_utils/model_lang/__init__.py
biosimulators_utils/model_lang/bngl/__init__.py
biosimulators_utils/model_lang/bngl/utils.py
biosimulators_utils/model_lang/bngl/validation.py
biosimulators_utils/model_lang/cellml/__init__.py
biosimulators_utils/model_lang/cellml/cellml1.0.rnc
biosimulators_utils/model_lang/cellml/cellml1.0.rng
biosimulators_utils/model_lang/cellml/mathml2.rnc
biosimulators_utils/model_lang/cellml/mathml2.rng
biosimulators_utils/model_lang/cellml/utils.py
biosimulators_utils/model_lang/cellml/validation.py
biosimulators_utils/model_lang/lems/__init__.py
biosimulators_utils/model_lang/lems/validation.py
biosimulators_utils/model_lang/neuroml/__init__.py
biosimulators_utils/model_lang/neuroml/validation.py
biosimulators_utils/model_lang/rba/__init__.py
biosimulators_utils/model_lang/rba/utils.py
biosimulators_utils/model_lang/rba/validation.py
biosimulators_utils/model_lang/sbml/__init__.py
biosimulators_utils/model_lang/sbml/utils.py
biosimulators_utils/model_lang/sbml/validation.py
biosimulators_utils/model_lang/smoldyn/__init__.py
biosimulators_utils/model_lang/smoldyn/utils.py
biosimulators_utils/model_lang/smoldyn/validation.py
biosimulators_utils/model_lang/xpp/__init__.py
biosimulators_utils/model_lang/xpp/data_model.py
biosimulators_utils/model_lang/xpp/utils.py
biosimulators_utils/model_lang/xpp/validation.py
biosimulators_utils/omex_meta/__init__.py
biosimulators_utils/omex_meta/data_model.py
biosimulators_utils/omex_meta/io.py
biosimulators_utils/omex_meta/utils.py
biosimulators_utils/omex_meta/validation.py
biosimulators_utils/ref/__init__.py
biosimulators_utils/ref/data_model.py
biosimulators_utils/ref/utils.py
biosimulators_utils/report/__init__.py
biosimulators_utils/report/data_model.py
biosimulators_utils/report/io.py
biosimulators_utils/report/warnings.py
biosimulators_utils/sedml/__init__.py
biosimulators_utils/sedml/data_model.py
biosimulators_utils/sedml/exceptions.py
biosimulators_utils/sedml/exec.py
biosimulators_utils/sedml/io.py
biosimulators_utils/sedml/math.py
biosimulators_utils/sedml/model_utils.py
biosimulators_utils/sedml/utils.py
biosimulators_utils/sedml/validation.py
biosimulators_utils/sedml/warnings.py
biosimulators_utils/simulator/__init__.py
biosimulators_utils/simulator/cli.py
biosimulators_utils/simulator/data_model.py
biosimulators_utils/simulator/environ.py
biosimulators_utils/simulator/exceptions.py
biosimulators_utils/simulator/exec.py
biosimulators_utils/simulator/io.py
biosimulators_utils/simulator/specs.py
biosimulators_utils/simulator/utils.py
biosimulators_utils/simulator_registry/__init__.py
biosimulators_utils/simulator_registry/data_model.py
biosimulators_utils/simulator_registry/process_submission.py
biosimulators_utils/simulator_registry/query.py
biosimulators_utils/simulator_registry/submit.py
biosimulators_utils/utils/__init__.py
biosimulators_utils/utils/core.py
biosimulators_utils/utils/identifiers_org.py
biosimulators_utils/utils/logging.py
biosimulators_utils/viz/__init__.py
biosimulators_utils/viz/data_model.py
biosimulators_utils/viz/io.py
biosimulators_utils/viz/utils.py
biosimulators_utils/viz/warnings.py
biosimulators_utils/viz/vega/__init__.py
biosimulators_utils/viz/vega/utils.py
biosimulators_utils/viz/vega/escher/__init__.py
biosimulators_utils/viz/vega/escher/core.py
biosimulators_utils/viz/vega/escher/template.json
biosimulators_utils/viz/vega/ginml/__init__.py
biosimulators_utils/viz/vega/ginml/core.py
biosimulators_utils/viz/vega/ginml/template.json
biosimulators_utils/viz/vega/sbgn/__init__.py
biosimulators_utils/viz/vega/sbgn/core.py
biosimulators_utils/viz/vega/sbgn/pd.template.json
biosimulators_utils/xml/__init__.py
biosimulators_utils/xml/utils.py
docs/.nojekyll
docs/about.html
docs/genindex.html
docs/index.html
docs/installation.html
docs/py-modindex.html
docs/search.html
docs/searchindex.js
docs/tutorial_api.html
docs/tutorial_cli.html
docs-src/about.rst
docs-src/conf.py
docs-src/genindex.rst
docs-src/index.rst
docs-src/installation.rst
docs-src/requirements.txt
docs-src/_static/biosimulators-logo.svg
docs-src/_static/css/biosimulators.css
docs/_static/alabaster.css
docs/_static/basic.css
docs/_static/biosimulators-logo.svg
docs/_static/custom.css
docs/_static/doctools.js
docs/_static/documentation_options.js
docs/_static/file.png
docs/_static/jquery-3.5.1.js
docs/_static/jquery.js
docs/_static/language_data.js
docs/_static/minus.png
docs/_static/plus.png
docs/_static/pygments.css
docs/_static/searchtools.js
docs/_static/underscore-1.12.0.js
docs/_static/underscore-1.13.1.js
docs/_static/underscore-1.3.1.js
docs/_static/underscore.js
docs/_static/webpack-macros.html
docs/_static/css/biosimulators.css
docs/_static/css/blank.css
docs/_static/css/index.c5995385ac14fb8791e8eb36b4908be2.css
docs/_static/css/index.ff1ffe594081f20da1ef19478df9384b.css
docs/_static/css/theme.css
docs/_static/js/index.1c5a1a01449ed65a7b51.js
docs/_static/js/index.be7d3bbb2ef33a8344ce.js
docs/_static/vendor/fontawesome/5.13.0/LICENSE.txt
docs/_static/vendor/fontawesome/5.13.0/css/all.min.css
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.eot
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.svg
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.ttf
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-regular-400.eot
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-regular-400.svg
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-regular-400.ttf
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-regular-400.woff
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-regular-400.woff2
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.eot
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.svg
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.ttf
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff
docs/_static/vendor/fontawesome/5.13.0/webfonts/fa-solid-900.woff2
docs/source/biosimulators_utils.archive.html
docs/source/biosimulators_utils.biosimulations.html
docs/source/biosimulators_utils.cellml.html
docs/source/biosimulators_utils.combine.html
docs/source/biosimulators_utils.exec_status.html
docs/source/biosimulators_utils.gh_action.html
docs/source/biosimulators_utils.html
docs/source/biosimulators_utils.kisao.html
docs/source/biosimulators_utils.lems.html
docs/source/biosimulators_utils.licensing.html
docs/source/biosimulators_utils.log.html
docs/source/biosimulators_utils.model_lang.bngl.html
docs/source/biosimulators_utils.model_lang.cellml.html
docs/source/biosimulators_utils.model_lang.html
docs/source/biosimulators_utils.model_lang.lems.html
docs/source/biosimulators_utils.model_lang.neuroml.html
docs/source/biosimulators_utils.model_lang.rba.html
docs/source/biosimulators_utils.model_lang.sbml.html
docs/source/biosimulators_utils.model_lang.smoldyn.html
docs/source/biosimulators_utils.model_lang.xpp.html
docs/source/biosimulators_utils.neuroml.html
docs/source/biosimulators_utils.omex_meta.html
docs/source/biosimulators_utils.plot.html
docs/source/biosimulators_utils.ref.html
docs/source/biosimulators_utils.report.html
docs/source/biosimulators_utils.sbml.html
docs/source/biosimulators_utils.sedml.html
docs/source/biosimulators_utils.simulator.html
docs/source/biosimulators_utils.simulator_registry.html
docs/source/biosimulators_utils.utils.html
docs/source/biosimulators_utils.viz.html
docs/source/biosimulators_utils.viz.vega.escher.html
docs/source/biosimulators_utils.viz.vega.ginml.html
docs/source/biosimulators_utils.viz.vega.html
docs/source/biosimulators_utils.viz.vega.sbgn.html
docs/source/biosimulators_utils.xml.html
tests/requirements.txt
tests/test_config.py
tests/test_image.py
tests/test_main.py
tests/archive/test_archive_data_model.py
tests/archive/test_archive_io.py
tests/biosimulations/test_biosimulations_data_model.py
tests/biosimulations/test_biosimulations_utils.py
tests/combine/test_combine_data_model.py
tests/combine/test_combine_exec.py
tests/combine/test_combine_io.py
tests/combine/test_combine_utils.py
tests/combine/test_combine_validation.py
tests/fixtures/BIOMD0000000075.xml
tests/fixtures/BIOMD0000000297-params-vars.xml
tests/fixtures/BIOMD0000000297.omex
tests/fixtures/BIOMD0000000297.xml
tests/fixtures/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling-params-vars.xml
tests/fixtures/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling.xml
tests/fixtures/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.omex
tests/fixtures/combine-formats.csv
tests/fixtures/invalid-parent-format-in-manifest.omex
tests/fixtures/kisao-2.13.owl
tests/fixtures/kisao-2.14.owl
tests/fixtures/manifest-in-manifest.omex
tests/fixtures/missing-parent-in-manifest.omex
tests/fixtures/multiple-manifests.omex
tests/fixtures/multiple-updated-dates.omex
tests/fixtures/no-metadata.omex
tests/fixtures/sbml-fbc-textbook.xml
tests/fixtures/sbml-invalid-model.xml
tests/fixtures/sbml-list-of-species.xml
tests/fixtures/sbml-three-species.xml
tests/fixtures/tellurium.json
tests/fixtures/bngl/LR_comp.bngl
tests/fixtures/bngl/empty-sample-times.bngl
tests/fixtures/bngl/insufficient-action-args-2.bngl
tests/fixtures/bngl/insufficient-action-args.bngl
tests/fixtures/bngl/invalid-syntax.bngl
tests/fixtures/bngl/invalid.bngl
tests/fixtures/bngl/invalid.bngl2
tests/fixtures/bngl/multiple-actions.bngl
tests/fixtures/bngl/no-actions.bngl
tests/fixtures/bngl/non-uniform-sample-times.bngl
tests/fixtures/bngl/sample-times.bngl
tests/fixtures/bngl/step-action-args.bngl
tests/fixtures/bngl/valid.bngl
tests/fixtures/cellml/albrecht_colegrove_friel_2002-error.xml
tests/fixtures/cellml/albrecht_colegrove_friel_2002.xml
tests/fixtures/cellml/invalid_cellml_2.0.xml
tests/fixtures/cellml/invalid_namespace.xml
tests/fixtures/cellml/level2-imported-model.xml
tests/fixtures/cellml/missing-attribute.xml
tests/fixtures/cellml/parameters-1.1.cellml
tests/fixtures/cellml/version2-missing-imports.xml
tests/fixtures/cellml/version2-with-imports.xml
tests/fixtures/cellml/version2.xml
tests/fixtures/escher/e_coli_core.Core metabolism.json
tests/fixtures/ginml/ginsim-35-regulatoryGraph.ginml
tests/fixtures/ginml/ginsim-79-regulatoryGraph-expanded comments.ginml
tests/fixtures/images/Johnrogershousemay2020.webp
tests/fixtures/images/Jpegvergroessert.jpg
tests/fixtures/images/PNG_transparency_demonstration_1.png
tests/fixtures/images/Rotating_earth_(large).gif
tests/fixtures/images/Tif.tif
tests/fixtures/images/all_gray.bmp
tests/fixtures/lems/KConductance.channel.nml
tests/fixtures/lems/LEMS_NML2_Ex5_DetCell.xml
tests/fixtures/lems/LeakConductance.channel.nml
tests/fixtures/lems/NML2_SingleCompHHCell.nml
tests/fixtures/lems/NaConductance.channel.nml
tests/fixtures/lems/invalid.xml
tests/fixtures/lems/missing-include.xml
tests/fixtures/lems/no-simulation.xml
tests/fixtures/lems/undefined-target.xml
tests/fixtures/neuroml/IM.channel.nml
tests/fixtures/neuroml/invalid-model.nml
tests/fixtures/omex-metadata/abbrev.rdf
tests/fixtures/omex-metadata/adh-model.xml
tests/fixtures/omex-metadata/biosimulations-abbrev-third-a.rdf
tests/fixtures/omex-metadata/biosimulations-abbrev-third-b.rdf
tests/fixtures/omex-metadata/biosimulations-abbrev-third-c.rdf
tests/fixtures/omex-metadata/biosimulations-abbrev.rdf
tests/fixtures/omex-metadata/biosimulations-with-file-annotations.rdf
tests/fixtures/omex-metadata/biosimulations.rdf
tests/fixtures/omex-metadata/demo1.xml
tests/fixtures/omex-metadata/glucose-transport.xml
tests/fixtures/omex-metadata/invalid-thumbnail-uri.rdf
tests/fixtures/omex-metadata/invalid.rdf
tests/fixtures/omex-metadata/libcombine.rdf
tests/fixtures/omex-metadata/malformed.rdf
tests/fixtures/omex-metadata/michaelis-menten.xml
tests/fixtures/omex-metadata/missing-label-2.rdf
tests/fixtures/omex-metadata/missing-label.rdf
tests/fixtures/omex-metadata/missing-required.rdf
tests/fixtures/omex-metadata/missing-thumbnail-uri.rdf
tests/fixtures/omex-metadata/missing-uri.rdf
tests/fixtures/omex-metadata/multiple-roots.rdf
tests/fixtures/omex-metadata/multiple-thumbnails.rdf
tests/fixtures/omex-metadata/no-root.rdf
tests/fixtures/omex-metadata/simple-regulation.xml
tests/fixtures/omex-metadata/smad-nuclear-transport.xml
tests/fixtures/omex-metadata/too-many-objects.rdf
tests/fixtures/omex-metadata/toy-model.xml
tests/fixtures/omex-metadata/warning.rdf
tests/fixtures/rba/Escherichia-coli-K12-WT-invalid.zip
tests/fixtures/rba/Escherichia-coli-K12-WT.zip
tests/fixtures/sbgn/Repressilator_PD_v6_color-modified.sbgn
tests/fixtures/sedml/BIOMD0000000673_sim.sedml
tests/fixtures/sedml/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-invalid-model.sedml
tests/fixtures/sedml/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-invalid-target.sedml
tests/fixtures/sedml/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-invalid-xpath.sedml
tests/fixtures/sedml/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.sedml
tests/fixtures/sedml/add-xml.sedml
tests/fixtures/sedml/data-description-with-variable.sedml
tests/fixtures/sedml/data-description.sedml
tests/fixtures/sedml/duplicate-data-generator-task-ids.sedml
tests/fixtures/sedml/duplicate-ids.sedml
tests/fixtures/sedml/duplicate-model-ids.sedml
tests/fixtures/sedml/duplicate-simulation-ids.sedml
tests/fixtures/sedml/initialTime-more-than-outputStartTime.sedml
tests/fixtures/sedml/invalid-task-model-reference.sedml
tests/fixtures/sedml/invalid-task-simulation-reference.sedml
tests/fixtures/sedml/new-xml-with-top-level-namespace.sedml
tests/fixtures/sedml/no-id.sedml
tests/fixtures/sedml/outputStartTime-more-than-outputEndTime.sedml
tests/fixtures/sedml/repeated-task.sedml
tests/fixtures/sedml-validation/invalid-omex-manifest-missing-attribute.omex
tests/fixtures/sedml-validation/invalid-sedml-missing-attribute.omex
tests/fixtures/sedml-validation/invalid-sedml-missing-namespace.omex
tests/fixtures/sedml-validation/invalid-sedml-multiple-errors.omex
tests/fixtures/sedml-validation/valid-sedml-bngl.omex
tests/fixtures/sedml-validation/valid-sedml-sbml-qual.omex
tests/fixtures/sedml-validation/warnings-sedml-sbml.omex
tests/fixtures/smoldyn/bounce1.txt
tests/fixtures/smoldyn/compart-2.txt
tests/fixtures/smoldyn/compart.txt
tests/fixtures/smoldyn/invalid.txt
tests/fixtures/xpp/BIOMD0000000001.ode
tests/fixtures/xpp/wilson-cowan-auxiliary-variables.ode
tests/fixtures/xpp/wilson-cowan-invalid.ode
tests/fixtures/xpp/wilson-cowan-modified-2.ode
tests/fixtures/xpp/wilson-cowan-modified-3.ode
tests/fixtures/xpp/wilson-cowan-modified-4.ode
tests/fixtures/xpp/wilson-cowan-modified-5.ode
tests/fixtures/xpp/wilson-cowan-modified.ode
tests/fixtures/xpp/wilson-cowan-with-sets.ode
tests/fixtures/xpp/wilson-cowan.ode
tests/fixtures/xpp/wilson-cowan/ics.ic
tests/fixtures/xpp/wilson-cowan/params.par
tests/fixtures/xpp/wilson-cowan/wilson-cowan.ode
tests/fixtures/xpp/wilson-cowan-2/wilson-cowan.ode
tests/fixtures/xpp/wilson-cowan-2/wilson-cowan.ode.set
tests/gh_action/test_gh_action_core.py
tests/kisao/test_kisao_utils.py
tests/licensing/test_licensing_gurobi.py
tests/log/test_log_data_model.py
tests/log/test_log_utils.py
tests/model_lang/bngl/test_bngl_utils.py
tests/model_lang/bngl/test_bngl_validation.py
tests/model_lang/cellml/test_cellml_utils.py
tests/model_lang/cellml/test_cellml_validation.py
tests/model_lang/lems/test_lems_validation.py
tests/model_lang/neuroml/test_neuroml_validation.py
tests/model_lang/rba/test_rba_utils.py
tests/model_lang/rba/test_rba_validation.py
tests/model_lang/sbml/test_sbml_utils.py
tests/model_lang/sbml/test_sbml_validation.py
tests/model_lang/smoldyn/test_smoldyn_utils.py
tests/model_lang/smoldyn/test_smoldyn_validation.py
tests/model_lang/xpp/test_xpp_utils.py
tests/model_lang/xpp/test_xpp_validation.py
tests/omex_meta/test_omex_meta_io.py
tests/omex_meta/test_omex_meta_utils.py
tests/omex_meta/test_omex_meta_validation.py
tests/ref/test_ref_data_model.py
tests/ref/test_ref_utils.py
tests/report/test_report_io.py
tests/sedml/test_sedml_data_model.py
tests/sedml/test_sedml_exec.py
tests/sedml/test_sedml_io.py
tests/sedml/test_sedml_math.py
tests/sedml/test_sedml_model_utils.py
tests/sedml/test_sedml_utils.py
tests/sedml/test_sedml_validation.py
tests/simulator/test_simulator_cli.py
tests/simulator/test_simulator_exceptions.py
tests/simulator/test_simulator_exec.py
tests/simulator/test_simulator_io.py
tests/simulator/test_simulator_specs.py
tests/simulator/test_simulator_utils.py
tests/simulator_registry/test_simulator_registry_data_model.py
tests/simulator_registry/test_simulator_registry_query.py
tests/simulator_registry/test_submit_to_simulator_registry.py
tests/utils/test_core_utils.py
tests/utils/test_identifiers_org_utils.py
tests/utils/test_logger_utils.py
tests/viz/test_viz_io.py
tests/viz/vega/test_viz_vega_escher.py
tests/viz/vega/test_viz_vega_ginml.py
tests/viz/vega/test_viz_vega_sbgn.py
tests/xml/test_xml_utils.py