├── .dockerignore ├── .env ├── .github └── workflows │ ├── pylint_on_pull_request.yml │ ├── run-integration-tests.yaml │ └── run-unit-tests.yml ├── .gitignore ├── .graphics └── stochss-logo.svg ├── .pylintrc ├── .win32.env ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── COPYRIGHT ├── Dockerfile ├── EXAMPLE_DIRECTORY.md ├── LICENSE ├── Makefile ├── README.md ├── __version__.py ├── action.yml ├── client ├── app.js ├── config.js ├── domain-view │ ├── domain-view.js │ ├── domainView.pug │ ├── templates │ │ ├── actionsView.pug │ │ ├── editAction.pug │ │ ├── editParticleView.pug │ │ ├── editShape.pug │ │ ├── editTransformation.pug │ │ ├── editType.pug │ │ ├── limitsView.pug │ │ ├── propertiesView.pug │ │ ├── quickviewType.pug │ │ ├── shapesView.pug │ │ ├── transformationsView.pug │ │ ├── typesView.pug │ │ ├── viewAction.pug │ │ ├── viewParticle.pug │ │ ├── viewShape.pug │ │ ├── viewTransformation.pug │ │ └── viewType.pug │ └── views │ │ ├── action-view.js │ │ ├── actions-view.js │ │ ├── limits-view.js │ │ ├── particle-view.js │ │ ├── properties-view.js │ │ ├── quickview-type.js │ │ ├── shape-view.js │ │ ├── shapes-view.js │ │ ├── transformation-view.js │ │ ├── transformations-view.js │ │ ├── type-view.js │ │ ├── types-view.js │ │ └── view-particle.js ├── file-config.js ├── graphics.js ├── job-view │ ├── job-view.js │ ├── jobView.pug │ ├── templates │ │ ├── gillespyResultsEnsembleView.pug │ │ ├── gillespyResultsView.pug │ │ ├── inferenceResultsView.pug │ │ ├── jobLogsView.pug │ │ ├── parameterScanResultsView.pug │ │ ├── parameterSweepResultsView.pug │ │ ├── spatialResultsView.pug │ │ └── sweepParameterRange.pug │ └── views │ │ ├── job-logs-view.js │ │ ├── job-results-view.js │ │ └── sweep-parameter-range-view.js ├── modals.js ├── model-view │ ├── model-view.js │ ├── modelView.pug │ ├── templates │ │ ├── boundaryConditionsView.pug │ │ ├── domainViewer.pug │ │ ├── editBoundaryCondition.pug │ │ ├── editEvent.pug │ │ ├── editEventAssignment.pug │ │ ├── editFunctionDefinition.pug │ │ ├── editInitialCondition.pug │ │ ├── editParameter.pug │ │ ├── editReaction.pug │ │ ├── editRule.pug │ │ ├── editSpatialSpecie.pug │ │ ├── editSpecie.pug │ │ ├── eventAssignmentsView.pug │ │ ├── eventsView.pug │ │ ├── initialConditionsView.pug │ │ ├── parametersView.pug │ │ ├── reactantProduct.pug │ │ ├── reactionRestrictTo.pug │ │ ├── reactionTypeTemplate.pug │ │ ├── reactionsView.pug │ │ ├── rulesView.pug │ │ ├── sbmlComponentsView.pug │ │ ├── spatialSpeciesView.pug │ │ ├── speciesTypeTemplate.pug │ │ ├── speciesView.pug │ │ ├── stoichSpecieView.pug │ │ ├── viewBoundaryCondition.pug │ │ ├── viewEvent.pug │ │ ├── viewEventAssignment.pug │ │ ├── viewFunctionDefinition.pug │ │ ├── viewInitialCondition.pug │ │ ├── viewParameter.pug │ │ ├── viewReaction.pug │ │ ├── viewRule.pug │ │ ├── viewSpatialSpecie.pug │ │ └── viewSpecie.pug │ └── views │ │ ├── boundary-condition-view.js │ │ ├── boundary-conditions-view.js │ │ ├── component-types.js │ │ ├── domain-viewer.js │ │ ├── event-assignment-view.js │ │ ├── event-assignments-view.js │ │ ├── event-view.js │ │ ├── events-view.js │ │ ├── function-definition-view.js │ │ ├── initial-condition-view.js │ │ ├── initial-conditions-view.js │ │ ├── parameter-view.js │ │ ├── parameters-view.js │ │ ├── reactant-product.js │ │ ├── reaction-restrict-to.js │ │ ├── reaction-view.js │ │ ├── reactions-view.js │ │ ├── rule-view.js │ │ ├── rules-view.js │ │ ├── sbml-components-view.js │ │ ├── specie-view.js │ │ ├── species-view.js │ │ └── stoich-species-view.js ├── models │ ├── action.js │ ├── actions.js │ ├── boundary-condition.js │ ├── boundary-conditions.js │ ├── creator.js │ ├── creators.js │ ├── domain-type.js │ ├── domain-types.js │ ├── domain.js │ ├── event-assignment.js │ ├── event-assignments.js │ ├── event.js │ ├── events.js │ ├── function-definition.js │ ├── function-definitions.js │ ├── inference-parameter.js │ ├── inference-parameters.js │ ├── inference-settings.js │ ├── initial-condition.js │ ├── initial-conditions.js │ ├── job.js │ ├── jobs.js │ ├── me.js │ ├── metadata.js │ ├── model.js │ ├── parameter-sweep-settings.js │ ├── parameter.js │ ├── parameters.js │ ├── particle.js │ ├── particles.js │ ├── point.js │ ├── presentation.js │ ├── project.js │ ├── reaction.js │ ├── reactions.js │ ├── results-settings.js │ ├── rule.js │ ├── rules.js │ ├── settings.js │ ├── shape.js │ ├── shapes.js │ ├── simulation-settings.js │ ├── specie.js │ ├── species.js │ ├── stoich-specie.js │ ├── stoich-species.js │ ├── summary-stat.js │ ├── summary-stats.js │ ├── sweep-parameter.js │ ├── sweep-parameters.js │ ├── timespan-settings.js │ ├── transformation.js │ ├── transformations.js │ ├── user-settings.js │ ├── workflow-group.js │ ├── workflow-groups.js │ ├── workflow.js │ └── workflows.js ├── page-help.js ├── pages │ ├── base.js │ ├── browser.js │ ├── domain-editor.js │ ├── example-library.js │ ├── home.js │ ├── job-presentation.js │ ├── loading-page.js │ ├── model-editor.js │ ├── model-presentation.js │ ├── multiple-plots.js │ ├── notebook-presentation.js │ ├── page.js │ ├── project-manager.js │ ├── quickstart.js │ ├── user-settings.js │ ├── users-home.js │ ├── workflow-manager.js │ └── workflow-selection.js ├── project-config.js ├── reaction-types.js ├── settings-view │ ├── settings-view.js │ ├── settingsView.pug │ ├── templates │ │ ├── editCustomSummaryStatView.pug │ │ ├── editCustomSummaryStats.pug │ │ ├── editIdentitySummaryStatView.pug │ │ ├── editIdentitySummaryStats.pug │ │ ├── editMinimalSummaryStats.pug │ │ ├── editSweepParameter.pug │ │ ├── editUniformParameterView.pug │ │ ├── editUniformParameters.pug │ │ ├── inferenceSettingsView.pug │ │ ├── parameterSettingsView.pug │ │ ├── spatialSettingsView.pug │ │ ├── timespanSettingsView.pug │ │ ├── viewCustomSummaryStatView.pug │ │ ├── viewCustomSummaryStats.pug │ │ ├── viewIdentitySummaryStatView.pug │ │ ├── viewIdentitySummaryStats.pug │ │ ├── viewMinimalSummaryStats.pug │ │ ├── viewSweepParameter.pug │ │ ├── viewUniformParameterView.pug │ │ ├── viewUniformParameters.pug │ │ └── wellMixedSettingsView.pug │ └── views │ │ ├── custom-summary-stat-view.js │ │ ├── identity-summary-stat-view.js │ │ ├── inference-parameters-view.js │ │ ├── inference-settings-view.js │ │ ├── parameter-settings-view.js │ │ ├── spatial-settings-view.js │ │ ├── summary-stats-view.js │ │ ├── sweep-parameter-view.js │ │ ├── timespan-settings-view.js │ │ ├── uniform-parameter-view.js │ │ └── well-mixed-settings-view.js ├── styles │ ├── bootstrap.css │ └── styles.css ├── templates │ ├── body.pug │ ├── head.pug │ ├── includes │ │ ├── archiveListing.pug │ │ ├── creatorListing.pug │ │ ├── editProject.pug │ │ ├── jobListing.pug │ │ ├── jstreeView.pug │ │ ├── metaData.pug │ │ ├── modelListing.pug │ │ ├── presentationView.pug │ │ ├── viewDomainType.pug │ │ ├── workflowGroupListing.pug │ │ ├── workflowListing.pug │ │ └── workflowStatus.pug │ └── pages │ │ ├── browser.pug │ │ ├── domainEditor.pug │ │ ├── errorTemplate.pug │ │ ├── exampleLibrary.pug │ │ ├── home.pug │ │ ├── jobPresentation.pug │ │ ├── loadingPage.pug │ │ ├── modelEditor.pug │ │ ├── modelPresentation.pug │ │ ├── multiplePlots.pug │ │ ├── multiplePlotsPresentation.pug │ │ ├── notebookPresentation.pug │ │ ├── projectManager.pug │ │ ├── quickstart.pug │ │ ├── userSettings.pug │ │ ├── usersHome.pug │ │ ├── workflowManager.pug │ │ └── workflowSelection.pug ├── tooltips.js └── views │ ├── archive-listing.js │ ├── creator-listing.js │ ├── edit-project.js │ ├── input.js │ ├── job-listing.js │ ├── jstree-view.js │ ├── main.js │ ├── meta-data.js │ ├── model-listing.js │ ├── presentation-view.js │ ├── tests.js │ ├── view-sweep-parameter.js │ ├── workflow-group-listing.js │ ├── workflow-listing.js │ └── workflow-status.js ├── custom.css ├── custom.js ├── jupyter_notebook_config.py ├── jupyterhub ├── .env ├── Dockerfile.jupyterhub ├── cull_idle_servers.py ├── custom │ ├── custom.js │ └── favicon.ico ├── docker-compose.yml ├── handlers.py ├── home_template.pug ├── job_presentation.py ├── jupyterhub_config.py ├── model_presentation.py ├── notebook_presentation.py ├── presentation_base.py ├── presentation_error.py ├── secrets │ └── .gitignore └── static │ └── stochss-logo.png ├── launch_webbrowser.py ├── log.py ├── package.json ├── page_template.pug ├── public_models ├── 3D-Cylinder.proj │ ├── 3D-Cylinder.domn │ └── 3D_cylinder.wkgp │ │ ├── 3D_cylinder.ipynb │ │ └── 3D_cylinder.smdl ├── Brusselator.proj │ ├── Brusselator.sbml │ └── Brusselator.wkgp │ │ ├── Brusselator.ipynb │ │ └── Brusselator.mdl ├── Degradation.proj │ ├── Degradation.sbml │ └── Degradation.wkgp │ │ ├── Degradation.ipynb │ │ └── Degradation.mdl ├── Dimerization.proj │ ├── Dimerization.sbml │ └── Dimerization.wkgp │ │ ├── Dimerization.ipynb │ │ └── Dimerization.mdl ├── Example SIR Epidemic Project.proj │ └── SIR Epidemic Model.wkgp │ │ ├── Example 1D Parameter Sweep Workflow Incomplete.wkfl │ │ ├── README.md │ │ └── settings.json │ │ ├── Example 2D Parameter Sweep Workflow Complete.wkfl │ │ ├── README.md │ │ ├── job_04282021_171753 │ │ │ ├── COMPLETE │ │ │ ├── RUNNING │ │ │ ├── SIR Epidemic Model.mdl │ │ │ ├── info.json │ │ │ ├── logs.txt │ │ │ ├── results │ │ │ │ ├── plots.json │ │ │ │ ├── results.json │ │ │ │ ├── results.p │ │ │ │ └── results_csv_04282021_171753 │ │ │ │ │ ├── avg-avg.csv │ │ │ │ │ ├── avg-max.csv │ │ │ │ │ ├── avg-min.csv │ │ │ │ │ ├── avg-var.csv │ │ │ │ │ ├── final-avg.csv │ │ │ │ │ ├── final-max.csv │ │ │ │ │ ├── final-min.csv │ │ │ │ │ ├── final-var.csv │ │ │ │ │ ├── max-avg.csv │ │ │ │ │ ├── max-max.csv │ │ │ │ │ ├── max-min.csv │ │ │ │ │ ├── max-var.csv │ │ │ │ │ ├── min-avg.csv │ │ │ │ │ ├── min-max.csv │ │ │ │ │ ├── min-min.csv │ │ │ │ │ ├── min-var.csv │ │ │ │ │ ├── var-avg.csv │ │ │ │ │ ├── var-max.csv │ │ │ │ │ ├── var-min.csv │ │ │ │ │ └── var-var.csv │ │ │ └── settings.json │ │ └── settings.json │ │ ├── Example Ensemble Simulation Workflow Complete.wkfl │ │ ├── README.md │ │ ├── job_03222021_190022 │ │ │ ├── COMPLETE │ │ │ ├── RUNNING │ │ │ ├── SIR Epidemic Model.mdl │ │ │ ├── info.json │ │ │ ├── logs.txt │ │ │ ├── results │ │ │ │ ├── plots.json │ │ │ │ └── results_csv_08272020_162750 │ │ │ │ │ ├── results_csv0.csv │ │ │ │ │ ├── results_csv1.csv │ │ │ │ │ ├── results_csv10.csv │ │ │ │ │ ├── results_csv11.csv │ │ │ │ │ ├── results_csv12.csv │ │ │ │ │ ├── results_csv13.csv │ │ │ │ │ ├── results_csv14.csv │ │ │ │ │ ├── results_csv15.csv │ │ │ │ │ ├── results_csv16.csv │ │ │ │ │ ├── results_csv17.csv │ │ │ │ │ ├── results_csv18.csv │ │ │ │ │ ├── results_csv19.csv │ │ │ │ │ ├── results_csv2.csv │ │ │ │ │ ├── results_csv3.csv │ │ │ │ │ ├── results_csv4.csv │ │ │ │ │ ├── results_csv5.csv │ │ │ │ │ ├── results_csv6.csv │ │ │ │ │ ├── results_csv7.csv │ │ │ │ │ ├── results_csv8.csv │ │ │ │ │ └── results_csv9.csv │ │ │ └── settings.json │ │ └── settings.json │ │ └── SIR Epidemic Model.mdl ├── Gene-Regulatory-Network.proj │ ├── Gene_Regulatory_Network_1.domn │ ├── Gene_Regulatory_Network_1.wkgp │ │ ├── Gene_Regulatory_Network_1.ipynb │ │ └── Gene_Regulatory_Network_1.smdl │ ├── Gene_Regulatory_Network_2.wkgp │ │ ├── Gene_Regulatory_Network_2.ipynb │ │ └── Gene_Regulatory_Network_2.smdl │ └── Gene_Regulatory_network_2.domn ├── Genetic-Toggle-Switch.proj │ ├── Genetic_Toggle_Switch.sbml │ └── Genetic_Toggle_Switch.wkgp │ │ ├── Genetic_Toggle_Switch.ipynb │ │ ├── Genetic_Toggle_Switch.mdl │ │ ├── Toggle_Switch_1D_Parameter_Sweep.ipynb │ │ ├── Toggle_Switch_2D_Parameter_Sweep.ipynb │ │ ├── Toggle_Switch_SCIOPE_Model_Exploration.ipynb │ │ └── Toggle_Switch_SCIOPE_Model_Inference.ipynb ├── Lotkavolterra-Oscillator.proj │ ├── Lotkavolterra_Oscillator.sbml │ └── Lotkavolterra_Oscillator.wkgp │ │ ├── Lotkavolterra_Oscillator.ipynb │ │ └── Lotkavolterra_Oscillator.mdl ├── Michaelis-Menten.proj │ ├── Michaelis_Menten.sbml │ └── Michaelis_Menten.wkgp │ │ ├── Michaelis_Menten.ipynb │ │ └── Michaelis_Menten.mdl ├── Opioid.proj │ ├── Opioid.sbml │ └── Opioid.wkgp │ │ ├── Opioid.ipynb │ │ └── Opioid.mdl ├── Oregonator.proj │ ├── Oregonator.sbml │ └── Oregonator.wkgp │ │ ├── Oregonator.ipynb │ │ └── Oregonator.mdl ├── Schlogl.proj │ ├── Schlogl.sbml │ └── Schlogl.wkgp │ │ ├── Schlogl.ipynb │ │ └── Schlogl.mdl ├── Spatial-Birth-Death.proj │ ├── Spatial_Birth_Death.domn │ └── Spatial_Birth_Death.wkgp │ │ ├── Spatial_Birth_Death.ipynb │ │ └── Spatial_Birth_Death.smdl ├── Tyson-Oscillator.proj │ ├── Tyson_2_State_Oscillator.sbml │ └── Tyson_2_State_Oscillator.wkgp │ │ ├── Tyson_2_State_Oscillator.ipynb │ │ └── Tyson_2_State_Oscillator.mdl ├── Vilar-Oscillator.proj │ ├── Vilar_Oscillator.sbml │ └── Vilar_Oscillator.wkgp │ │ ├── Vilar_Oscillator.ipynb │ │ ├── Vilar_Oscillator.mdl │ │ ├── Vilar_Oscillator_SCIOPE_Model_Exploration.ipynb │ │ └── Vilar_Oscillator_SCIOPE_Model_Inference.ipynb └── Yeast-Polarization.proj │ ├── Polarization_In_Yeast.domn │ └── Polarization_In_Yeast.wkgp │ ├── Polarization_In_Yeast.ipynb │ └── Polarization_In_Yeast.smdl ├── requirements.txt ├── setup.bat ├── setup.py ├── stochss-logo.png ├── stochss ├── dist │ ├── favicon.ico │ ├── file-browser-create-model-dropdown.png │ ├── file-browser-new-model-dropdown (copy).png │ ├── file-browser-new-model-dropdown.png │ ├── model-editor-preview-results.png │ ├── model-editor-reaction-editor.png │ ├── model-editor-select-default-species-mode.png │ ├── stochss-logo.png │ ├── workflow-editor-ensemble-simulation.png │ └── workflow-results-std-deviation-plot.png ├── handlers │ ├── __init__.py │ ├── file_browser.py │ ├── log.py │ ├── models.py │ ├── pages.py │ ├── project.py │ ├── util │ │ ├── __init__.py │ │ ├── ensemble_simulation.py │ │ ├── model_inference.py │ │ ├── parameter_scan.py │ │ ├── parameter_sweep.py │ │ ├── parameter_sweep_1d.py │ │ ├── parameter_sweep_2d.py │ │ ├── parameter_sweep_notebook.py │ │ ├── sciope_notebook.py │ │ ├── scripts │ │ │ ├── __init__.py │ │ │ ├── aws_compute.py │ │ │ ├── run_preview.py │ │ │ ├── start_job.py │ │ │ └── upload_remote_file.py │ │ ├── spatial_simulation.py │ │ ├── stochss_base.py │ │ ├── stochss_errors.py │ │ ├── stochss_file.py │ │ ├── stochss_folder.py │ │ ├── stochss_job.py │ │ ├── stochss_model.py │ │ ├── stochss_notebook.py │ │ ├── stochss_project.py │ │ ├── stochss_sbml.py │ │ ├── stochss_spatial_model.py │ │ └── stochss_workflow.py │ └── workflows.py └── tests │ ├── __init__.py │ ├── example_models.py │ ├── integration_tests │ ├── __init__.py │ └── test_gillespy2.py │ ├── run_all_tests.py │ ├── run_integration_tests.py │ ├── run_unit_tests.py │ └── unit_tests │ ├── __init__.py │ ├── test_model_template.py │ ├── test_settings_template.py │ ├── test_stochss_base.py │ └── test_stochss_file.py ├── stochss_templates ├── domainPlotTemplate.json ├── instance_types.txt ├── modelTemplate.json ├── userSettingTemplate.json └── workflowSettingsTemplate.json ├── webpack.config.js └── webpack.hub.config.js /.dockerignore: 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