├── .github ├── dependabot.yml └── workflows │ └── Documentation.yml ├── .gitignore ├── CITATION.bib ├── LICENSE.md ├── Project.toml ├── README.md ├── dev ├── Testing │ └── test │ │ └── index.html ├── assets │ ├── documenter.js │ ├── favicon.ico │ ├── logo.png │ ├── search.js │ ├── themes │ │ ├── documenter-dark.css │ │ └── documenter-light.css │ ├── themeswap.js │ └── warner.js ├── index.html ├── search │ └── index.html ├── search_index.js ├── siteinfo.js └── test │ └── index.html ├── docs ├── Project.toml ├── extrasrc │ └── assets │ │ ├── favicon.ico │ │ └── logo.png ├── make.jl └── pages.jl ├── html ├── DiffEqUncertainty │ ├── 01-expectation_introduction.html │ ├── 02-AD_and_optimization.html │ └── 03-GPU_Bayesian_Koopman.html ├── Testing │ └── test.html ├── advanced │ ├── 01-beeler_reuter.html │ ├── 02-advanced_ODE_solving.html │ ├── 03-kolmogorov_equations.html │ └── 04-diffusion_implicit_heat_equation.html ├── exercises │ ├── 01-workshop_exercises.html │ └── 02-workshop_solutions.html ├── introduction │ ├── 01-ode_introduction.html │ ├── 02-choosing_algs.html │ ├── 03-optimizing_diffeq_code.html │ ├── 04-callbacks_and_events.html │ └── 05-formatting_plots.html ├── jumps │ └── spatial.html ├── model_inference │ ├── 01-pendulum_bayesian_inference.html │ └── 02-monte_carlo_parameter_estim.html ├── models │ ├── 01-classical_physics.html │ ├── 02-conditional_dosing.html │ ├── 03-diffeqbio_I_introduction.html │ ├── 04-diffeqbio_II_networkproperties.html │ ├── 04b-diffeqbio_III_steadystates.html │ ├── 05-kepler_problem.html │ ├── 06-pendulum_bayesian_inference.html │ ├── 07-outer_solar_system.html │ └── 08-spiking_neural_systems.html ├── ode_extras │ ├── 01-ModelingToolkit.html │ ├── 02-feagin.html │ ├── 03-ode_minmax.html │ └── 04-monte_carlo_parameter_estim.html ├── perturbation │ ├── 01-perturbation_algebraic.html │ └── 02-perturbation_differential.html ├── test.html └── type_handling │ ├── 01-number_types.html │ ├── 02-uncertainties.html │ └── 03-unitful.html ├── index.html ├── markdown ├── Testing │ └── test.md └── test.md ├── script ├── DiffEqUncertainty │ ├── 01-expectation_introduction.jl │ └── 02-AD_and_optimization.jl ├── Testing │ └── test.jl ├── advanced │ ├── 01-beeler_reuter.jl │ ├── 02-advanced_ODE_solving.jl │ ├── 03-kolmogorov_equations.jl │ └── 04-diffusion_implicit_heat_equation.jl ├── exercises │ ├── 01-workshop_exercises.jl │ └── 02-workshop_solutions.jl ├── introduction │ ├── 01-ode_introduction.jl │ ├── 02-choosing_algs.jl │ ├── 03-optimizing_diffeq_code.jl │ ├── 04-callbacks_and_events.jl │ └── 05-formatting_plots.jl ├── jumps │ └── spatial.jl ├── model_inference │ ├── 01-pendulum_bayesian_inference.jl │ └── 02-monte_carlo_parameter_estim.jl ├── models │ ├── 01-classical_physics.jl │ ├── 02-conditional_dosing.jl │ ├── 03-diffeqbio_I_introduction.jl │ ├── 03-kepler_problem.jl │ ├── 04-diffeqbio_II_networkproperties.jl │ ├── 04-spiking_neural_systems.jl │ ├── 04b-diffeqbio_III_steadystates.jl │ ├── 05-kepler_problem.jl │ ├── 05-outer_solar_system.jl │ ├── 06-pendulum_bayesian_inference.jl │ ├── 07-outer_solar_system.jl │ └── 08-spiking_neural_systems.jl ├── ode_extras │ ├── 01-ModelingToolkit.jl │ ├── 02-feagin.jl │ ├── 03-ode_minmax.jl │ └── 04-monte_carlo_parameter_estim.jl ├── perturbation │ ├── 01-perturbation_algebraic.jl │ └── 02-perturbation_differential.jl ├── test.jl └── type_handling │ ├── 01-number_types.jl │ ├── 02-uncertainties.jl │ └── 03-unitful.jl ├── src └── SciMLTutorialsOutput.jl ├── stable ├── v0.1.0 ├── v0.1 ├── DiffEqUncertainty │ ├── 01-expectation_introduction │ │ └── index.html │ ├── 02-AD_and_optimization │ │ └── index.html │ └── figures │ │ ├── 01-expectation_introduction_23_1.png │ │ ├── 01-expectation_introduction_28_1.png │ │ ├── 01-expectation_introduction_2_1.png │ │ ├── 01-expectation_introduction_5_1.png │ │ ├── 02-AD_and_optimization_11_1.png │ │ ├── 02-AD_and_optimization_13_1.png │ │ ├── 02-AD_and_optimization_14_1.png │ │ ├── 02-AD_and_optimization_1_1.png │ │ ├── 02-AD_and_optimization_21_1.png │ │ ├── 02-AD_and_optimization_3_1.png │ │ └── 02-AD_and_optimization_4_1.png ├── Testing │ └── test │ │ └── index.html ├── advanced │ ├── 01-beeler_reuter │ │ └── index.html │ ├── 02-advanced_ODE_solving │ │ └── index.html │ ├── 03-kolmogorov_equations │ │ └── index.html │ ├── 04-diffusion_implicit_heat_equation │ │ └── index.html │ └── figures │ │ ├── 01-beeler_reuter_11_1.png │ │ ├── 01-beeler_reuter_14_1.png │ │ ├── 01-beeler_reuter_21_1.png │ │ ├── 02-advanced_ODE_solving_13_1.png │ │ ├── 02-advanced_ODE_solving_24_1.png │ │ ├── 02-advanced_ODE_solving_3_1.png │ │ └── 03-kolmogorov_equations_9_1.png ├── assets │ ├── documenter.js │ ├── search.js │ ├── themes │ │ ├── documenter-dark.css │ │ └── documenter-light.css │ ├── themeswap.js │ └── warner.js ├── exercises │ ├── 01-workshop_exercises │ │ └── index.html │ ├── 02-workshop_solutions │ │ └── index.html │ └── figures │ │ ├── 02-workshop_solutions_10_1.png │ │ ├── 02-workshop_solutions_11_1.png │ │ ├── 02-workshop_solutions_13_1.png │ │ ├── 02-workshop_solutions_14_1.png │ │ ├── 02-workshop_solutions_15_1.png │ │ ├── 02-workshop_solutions_16_1.png │ │ ├── 02-workshop_solutions_24_1.png │ │ ├── 02-workshop_solutions_25_1.png │ │ ├── 02-workshop_solutions_26_1.png │ │ ├── 02-workshop_solutions_2_1.png │ │ ├── 02-workshop_solutions_3_1.png │ │ ├── 02-workshop_solutions_6_1.png │ │ ├── 02-workshop_solutions_7_1.png │ │ └── 02-workshop_solutions_8_1.png ├── index.html ├── introduction │ ├── 01-ode_introduction │ │ └── index.html │ ├── 02-choosing_algs │ │ └── index.html │ ├── 03-optimizing_diffeq_code │ │ └── index.html │ ├── 04-callbacks_and_events │ │ └── index.html │ ├── 05-formatting_plots │ │ └── index.html │ └── figures │ │ ├── 01-ode_introduction_13_1.png │ │ ├── 01-ode_introduction_29_1.png │ │ ├── 01-ode_introduction_30_1.png │ │ ├── 01-ode_introduction_31_1.png │ │ ├── 01-ode_introduction_32_1.png │ │ ├── 01-ode_introduction_4_1.png │ │ ├── 01-ode_introduction_5_1.png │ │ ├── 01-ode_introduction_6_1.png │ │ ├── 02-choosing_algs_5_1.png │ │ ├── 02-choosing_algs_6_1.png │ │ ├── 04-callbacks_and_events_10_1.png │ │ ├── 04-callbacks_and_events_12_1.png │ │ ├── 04-callbacks_and_events_13_1.png │ │ ├── 04-callbacks_and_events_16_1.png │ │ ├── 04-callbacks_and_events_19_1.png │ │ ├── 04-callbacks_and_events_20_1.png │ │ ├── 04-callbacks_and_events_21_1.png │ │ ├── 04-callbacks_and_events_22_1.png │ │ ├── 04-callbacks_and_events_24_1.png │ │ ├── 04-callbacks_and_events_25_1.png │ │ ├── 04-callbacks_and_events_6_1.png │ │ ├── 05-formatting_plots_10_1.png │ │ ├── 05-formatting_plots_11_1.png │ │ ├── 05-formatting_plots_12_1.png │ │ ├── 05-formatting_plots_2_1.png │ │ ├── 05-formatting_plots_3_1.png │ │ ├── 05-formatting_plots_4_1.png │ │ ├── 05-formatting_plots_5_1.png │ │ ├── 05-formatting_plots_6_1.png │ │ ├── 05-formatting_plots_7_1.png │ │ ├── 05-formatting_plots_8_1.png │ │ └── 05-formatting_plots_9_1.png ├── jumps │ └── spatial │ │ └── index.html ├── model_inference │ ├── 01-pendulum_bayesian_inference │ │ └── index.html │ ├── 02-monte_carlo_parameter_estim │ │ └── index.html │ └── figures │ │ ├── 01-pendulum_bayesian_inference_3_1.png │ │ ├── 01-pendulum_bayesian_inference_5_1.png │ │ ├── 01-pendulum_bayesian_inference_8_1.png │ │ ├── 01-pendulum_bayesian_inference_9_1.png │ │ └── 02-monte_carlo_parameter_estim_3_1.png ├── models │ ├── 01-classical_physics │ │ └── index.html │ ├── 02-conditional_dosing │ │ └── index.html │ ├── 03-diffeqbio_I_introduction │ │ └── index.html │ ├── 04-diffeqbio_II_networkproperties │ │ └── index.html │ ├── 04b-diffeqbio_III_steadystates │ │ └── index.html │ ├── 05-kepler_problem │ │ └── index.html │ ├── 07-outer_solar_system │ │ └── index.html │ ├── 08-spiking_neural_systems │ │ └── index.html │ └── figures │ │ ├── 01-classical_physics_10_1.png │ │ ├── 01-classical_physics_11_1.png │ │ ├── 01-classical_physics_12_1.png │ │ ├── 01-classical_physics_14_1.png │ │ ├── 01-classical_physics_15_1.png │ │ ├── 01-classical_physics_16_1.png │ │ ├── 01-classical_physics_17_1.png │ │ ├── 01-classical_physics_1_1.png │ │ ├── 01-classical_physics_2_1.png │ │ ├── 01-classical_physics_3_1.png │ │ ├── 01-classical_physics_4_1.png │ │ ├── 01-classical_physics_6_1.png │ │ ├── 01-classical_physics_8_1.png │ │ ├── 02-conditional_dosing_2_1.png │ │ ├── 02-conditional_dosing_4_1.png │ │ ├── 02-conditional_dosing_7_1.png │ │ ├── 02-conditional_dosing_8_1.png │ │ ├── 03-diffeqbio_I_introduction_10_1.png │ │ ├── 03-diffeqbio_I_introduction_11_1.png │ │ ├── 03-diffeqbio_I_introduction_12_1.png │ │ ├── 03-diffeqbio_I_introduction_16_1.png │ │ ├── 04-diffeqbio_II_networkproperties_36_1.png │ │ ├── 04-diffeqbio_II_networkproperties_38_1.png │ │ ├── 04b-diffeqbio_III_steadystates_10_1.png │ │ ├── 04b-diffeqbio_III_steadystates_11_1.png │ │ ├── 04b-diffeqbio_III_steadystates_12_1.png │ │ ├── 04b-diffeqbio_III_steadystates_14_1.png │ │ ├── 04b-diffeqbio_III_steadystates_15_1.png │ │ ├── 04b-diffeqbio_III_steadystates_7_1.png │ │ ├── 04b-diffeqbio_III_steadystates_8_1.png │ │ ├── 04b-diffeqbio_III_steadystates_9_1.png │ │ ├── 05-kepler_problem_10_1.png │ │ ├── 05-kepler_problem_3_1.png │ │ ├── 05-kepler_problem_4_1.png │ │ ├── 05-kepler_problem_5_1.png │ │ ├── 05-kepler_problem_6_1.png │ │ ├── 05-kepler_problem_7_1.png │ │ ├── 05-kepler_problem_8_1.png │ │ ├── 05-kepler_problem_9_1.png │ │ ├── 06-pendulum_bayesian_inference_3_1.png │ │ ├── 06-pendulum_bayesian_inference_5_1.png │ │ ├── 06-pendulum_bayesian_inference_8_1.png │ │ ├── 06-pendulum_bayesian_inference_9_1.png │ │ ├── 07-outer_solar_system_4_1.png │ │ ├── 08-spiking_neural_systems_10_1.png │ │ ├── 08-spiking_neural_systems_11_1.png │ │ ├── 08-spiking_neural_systems_14_1.png │ │ ├── 08-spiking_neural_systems_15_1.png │ │ ├── 08-spiking_neural_systems_17_1.png │ │ ├── 08-spiking_neural_systems_18_1.png │ │ ├── 08-spiking_neural_systems_19_1.png │ │ ├── 08-spiking_neural_systems_20_1.png │ │ ├── 08-spiking_neural_systems_21_1.png │ │ ├── 08-spiking_neural_systems_22_1.png │ │ ├── 08-spiking_neural_systems_23_1.png │ │ ├── 08-spiking_neural_systems_24_1.png │ │ ├── 08-spiking_neural_systems_25_1.png │ │ ├── 08-spiking_neural_systems_5_1.png │ │ └── 08-spiking_neural_systems_9_1.png ├── ode_extras │ ├── 01-ModelingToolkit │ │ └── index.html │ ├── 02-feagin │ │ └── index.html │ ├── 03-ode_minmax │ │ └── index.html │ └── figures │ │ ├── 01-ModelingToolkit_1_1.png │ │ ├── 02-feagin_6_1.png │ │ ├── 03-ode_minmax_3_1.png │ │ └── 03-ode_minmax_4_1.png ├── perturbation │ ├── 01-perturbation_algebraic │ │ └── index.html │ ├── 02-perturbation_differential │ │ └── index.html │ └── figures │ │ ├── 02-perturbation_differential_12_1.png │ │ └── 02-perturbation_differential_17_1.png ├── search │ └── index.html ├── search_index.js ├── siteinfo.js ├── test │ └── index.html └── type_handling │ ├── 02-uncertainties │ └── index.html │ ├── 03-unitful │ └── index.html │ └── figures │ ├── 02-uncertainties_10_1.png │ ├── 02-uncertainties_11_1.png │ ├── 02-uncertainties_7_1.png │ ├── 02-uncertainties_9_1.png │ └── 03-unitful_9_1.png ├── v0.2 ├── v0.2.0 ├── Testing │ └── test │ │ └── index.html ├── advanced │ ├── 01-beeler_reuter │ │ └── index.html │ ├── 02-diffusion_implicit_heat_equation │ │ └── index.html │ └── figures │ │ ├── 01-beeler_reuter_11_1.png │ │ ├── 01-beeler_reuter_14_1.png │ │ └── 01-beeler_reuter_21_1.png ├── assets │ ├── documenter.js │ ├── favicon.ico │ ├── logo.png │ ├── search.js │ ├── themes │ │ ├── documenter-dark.css │ │ └── documenter-light.css │ ├── themeswap.js │ └── warner.js ├── exercises │ ├── 01-workshop_exercises │ │ └── index.html │ ├── 02-workshop_solutions │ │ └── index.html │ └── figures │ │ ├── 02-workshop_solutions_10_1.png │ │ ├── 02-workshop_solutions_11_1.png │ │ ├── 02-workshop_solutions_13_1.png │ │ ├── 02-workshop_solutions_14_1.png │ │ ├── 02-workshop_solutions_15_1.png │ │ ├── 02-workshop_solutions_16_1.png │ │ ├── 02-workshop_solutions_24_1.png │ │ ├── 02-workshop_solutions_25_1.png │ │ ├── 02-workshop_solutions_26_1.png │ │ ├── 02-workshop_solutions_2_1.png │ │ ├── 02-workshop_solutions_3_1.png │ │ ├── 02-workshop_solutions_6_1.png │ │ ├── 02-workshop_solutions_7_1.png │ │ └── 02-workshop_solutions_8_1.png ├── index.html ├── jumps │ └── spatial │ │ └── index.html ├── model_inference │ ├── 01-pendulum_bayesian_inference │ │ └── index.html │ ├── 02-monte_carlo_parameter_estim │ │ └── index.html │ └── figures │ │ ├── 01-pendulum_bayesian_inference_3_1.png │ │ ├── 01-pendulum_bayesian_inference_5_1.png │ │ ├── 01-pendulum_bayesian_inference_8_1.png │ │ ├── 01-pendulum_bayesian_inference_9_1.png │ │ └── 02-monte_carlo_parameter_estim_3_1.png ├── models │ ├── 01-classical_physics │ │ └── index.html │ ├── 02-conditional_dosing │ │ └── index.html │ ├── 03-kepler_problem │ │ └── index.html │ ├── 04-spiking_neural_systems │ │ └── index.html │ ├── 05-outer_solar_system │ │ └── index.html │ └── figures │ │ ├── 01-classical_physics_10_1.png │ │ ├── 01-classical_physics_11_1.png │ │ ├── 01-classical_physics_12_1.png │ │ ├── 01-classical_physics_14_1.png │ │ ├── 01-classical_physics_15_1.png │ │ ├── 01-classical_physics_16_1.png │ │ ├── 01-classical_physics_17_1.png │ │ ├── 01-classical_physics_1_1.png │ │ ├── 01-classical_physics_2_1.png │ │ ├── 01-classical_physics_3_1.png │ │ ├── 01-classical_physics_4_1.png │ │ ├── 01-classical_physics_6_1.png │ │ ├── 01-classical_physics_8_1.png │ │ ├── 02-conditional_dosing_2_1.png │ │ ├── 02-conditional_dosing_4_1.png │ │ ├── 02-conditional_dosing_7_1.png │ │ ├── 02-conditional_dosing_8_1.png │ │ ├── 03-diffeqbio_I_introduction_10_1.png │ │ ├── 03-diffeqbio_I_introduction_11_1.png │ │ ├── 03-diffeqbio_I_introduction_12_1.png │ │ ├── 03-diffeqbio_I_introduction_16_1.png │ │ ├── 03-kepler_problem_3_1.png │ │ ├── 03-kepler_problem_4_1.png │ │ ├── 03-kepler_problem_5_1.png │ │ ├── 03-kepler_problem_6_1.png │ │ ├── 03-kepler_problem_7_1.png │ │ ├── 04-diffeqbio_II_networkproperties_36_1.png │ │ ├── 04-diffeqbio_II_networkproperties_38_1.png │ │ ├── 04-spiking_neural_systems_10_1.png │ │ ├── 04-spiking_neural_systems_11_1.png │ │ ├── 04-spiking_neural_systems_14_1.png │ │ ├── 04-spiking_neural_systems_15_1.png │ │ ├── 04-spiking_neural_systems_17_1.png │ │ ├── 04-spiking_neural_systems_18_1.png │ │ ├── 04-spiking_neural_systems_19_1.png │ │ ├── 04-spiking_neural_systems_20_1.png │ │ ├── 04-spiking_neural_systems_21_1.png │ │ ├── 04-spiking_neural_systems_22_1.png │ │ ├── 04-spiking_neural_systems_23_1.png │ │ ├── 04-spiking_neural_systems_24_1.png │ │ ├── 04-spiking_neural_systems_25_1.png │ │ ├── 04-spiking_neural_systems_5_1.png │ │ ├── 04-spiking_neural_systems_9_1.png │ │ ├── 04b-diffeqbio_III_steadystates_10_1.png │ │ ├── 04b-diffeqbio_III_steadystates_11_1.png │ │ ├── 04b-diffeqbio_III_steadystates_12_1.png │ │ ├── 04b-diffeqbio_III_steadystates_14_1.png │ │ ├── 04b-diffeqbio_III_steadystates_15_1.png │ │ ├── 04b-diffeqbio_III_steadystates_7_1.png │ │ ├── 04b-diffeqbio_III_steadystates_8_1.png │ │ ├── 04b-diffeqbio_III_steadystates_9_1.png │ │ ├── 05-kepler_problem_10_1.png │ │ ├── 05-kepler_problem_3_1.png │ │ ├── 05-kepler_problem_4_1.png │ │ ├── 05-kepler_problem_5_1.png │ │ ├── 05-kepler_problem_6_1.png │ │ ├── 05-kepler_problem_7_1.png │ │ ├── 05-kepler_problem_8_1.png │ │ ├── 05-kepler_problem_9_1.png │ │ ├── 05-outer_solar_system_4_1.png │ │ ├── 06-pendulum_bayesian_inference_3_1.png │ │ ├── 06-pendulum_bayesian_inference_5_1.png │ │ ├── 06-pendulum_bayesian_inference_8_1.png │ │ ├── 06-pendulum_bayesian_inference_9_1.png │ │ ├── 08-spiking_neural_systems_10_1.png │ │ ├── 08-spiking_neural_systems_11_1.png │ │ ├── 08-spiking_neural_systems_14_1.png │ │ ├── 08-spiking_neural_systems_15_1.png │ │ ├── 08-spiking_neural_systems_17_1.png │ │ ├── 08-spiking_neural_systems_18_1.png │ │ ├── 08-spiking_neural_systems_19_1.png │ │ ├── 08-spiking_neural_systems_20_1.png │ │ ├── 08-spiking_neural_systems_21_1.png │ │ ├── 08-spiking_neural_systems_22_1.png │ │ ├── 08-spiking_neural_systems_23_1.png │ │ ├── 08-spiking_neural_systems_24_1.png │ │ ├── 08-spiking_neural_systems_25_1.png │ │ ├── 08-spiking_neural_systems_5_1.png │ │ └── 08-spiking_neural_systems_9_1.png ├── odes │ ├── 01-ode_minmax │ │ └── index.html │ └── figures │ │ ├── 02-feagin_6_1.png │ │ ├── 03-ode_minmax_3_1.png │ │ └── 03-ode_minmax_4_1.png ├── perturbation │ ├── 01-perturbation_algebraic │ │ └── index.html │ ├── 02-perturbation_differential │ │ └── index.html │ └── figures │ │ ├── 02-perturbation_differential_12_1.png │ │ └── 02-perturbation_differential_17_1.png ├── search │ └── index.html ├── search_index.js ├── siteinfo.js ├── test │ └── index.html └── type_handling │ ├── 02-uncertainties │ └── index.html │ ├── 03-unitful │ └── index.html │ └── figures │ ├── 02-uncertainties_10_1.png │ ├── 02-uncertainties_11_1.png │ ├── 02-uncertainties_7_1.png │ ├── 02-uncertainties_9_1.png │ └── 03-unitful_9_1.png ├── v0.3 ├── v0.3.0 ├── Testing │ └── test │ │ └── index.html ├── assets │ ├── documenter.js │ ├── favicon.ico │ ├── logo.png │ ├── search.js │ ├── themes │ │ ├── documenter-dark.css │ │ └── documenter-light.css │ ├── themeswap.js │ └── warner.js ├── index.html ├── search │ └── index.html ├── search_index.js ├── siteinfo.js └── test │ └── index.html └── versions.js /.github/dependabot.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SciML/SciMLTutorialsOutput/HEAD/.github/dependabot.yml -------------------------------------------------------------------------------- /.github/workflows/Documentation.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SciML/SciMLTutorialsOutput/HEAD/.github/workflows/Documentation.yml 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