From 6ba656907aa4b4c9b288b12a5ad43f1c0636b21d Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 9 Oct 2024 10:49:38 -0400 Subject: [PATCH 1/4] disable SI for now --- Project.toml | 10 +++++----- .../structural_identifiability.md | 0 2 files changed, 5 insertions(+), 5 deletions(-) rename docs/{src/inverse_problems => unpublished}/structural_identifiability.md (100%) diff --git a/Project.toml b/Project.toml index f6e69f55dd..c100c1b450 100644 --- a/Project.toml +++ b/Project.toml @@ -32,14 +32,14 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2" HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" -StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" +# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" [extensions] CatalystBifurcationKitExtension = "BifurcationKit" CatalystCairoMakieExtension = "CairoMakie" CatalystGraphMakieExtension = "GraphMakie" CatalystHomotopyContinuationExtension = "HomotopyContinuation" -CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability" +# CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability" [compat] BifurcationKit = "0.3" @@ -64,7 +64,7 @@ Requires = "1.0" RuntimeGeneratedFunctions = "0.5.12" SciMLBase = "2.46" Setfield = "1" -StructuralIdentifiability = "0.5.8" +# StructuralIdentifiability = "0.5.8" SymbolicUtils = "2.1.2, 3.3.0" Symbolics = "5.30.1, 6" Unitful = "1.12.4" @@ -92,9 +92,9 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" +# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [targets] -test = ["BifurcationKit", "CairoMakie", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "GraphMakie", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"] +test = ["BifurcationKit", "CairoMakie", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "GraphMakie", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"] diff --git a/docs/src/inverse_problems/structural_identifiability.md b/docs/unpublished/structural_identifiability.md similarity index 100% rename from docs/src/inverse_problems/structural_identifiability.md rename to docs/unpublished/structural_identifiability.md From 26d361006aecb589d41b38b76b5e7fff30f97eab Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 9 Oct 2024 11:16:17 -0400 Subject: [PATCH 2/4] up --- docs/pages.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pages.jl b/docs/pages.jl index 7f6181a11d..e426f46594 100644 --- a/docs/pages.jl +++ b/docs/pages.jl @@ -47,7 +47,7 @@ pages = Any[ "inverse_problems/optimization_ode_param_fitting.md", # "inverse_problems/petab_ode_param_fitting.md", "inverse_problems/behaviour_optimisation.md", - "inverse_problems/structural_identifiability.md", + # "inverse_problems/structural_identifiability.md", "inverse_problems/global_sensitivity_analysis.md", "Inverse problem examples" => Any[ "inverse_problems/examples/ode_fitting_oscillation.md" From b5c6195027d8f173fa382f249f94979550b8fe84 Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 9 Oct 2024 14:07:03 -0400 Subject: [PATCH 3/4] refstring fix --- docs/src/index.md | 4 ++-- docs/src/inverse_problems/optimization_ode_param_fitting.md | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/src/index.md b/docs/src/index.md index 5e03723904..40001a997b 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -41,7 +41,7 @@ etc). - Model steady states can be [computed through homotopy continuation](@ref homotopy_continuation) using [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl) (which can find *all* steady states of systems with multiple ones), by [forward ODE simulations](@ref steady_state_solving_simulation) using [SteadyStateDiffEq.jl)](https://github.com/SciML/SteadyStateDiffEq.jl), or by [numerically solving steady-state nonlinear equations](@ref steady_state_solving_nonlinear) using [NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl). - [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) can be used to [compute bifurcation diagrams](@ref bifurcation_diagrams) of model steady states (including finding periodic orbits). - [DynamicalSystems.jl](https://github.com/JuliaDynamics/DynamicalSystems.jl) can be used to compute model [basins of attraction](@ref dynamical_systems_basins_of_attraction), [Lyapunov spectrums](@ref dynamical_systems_lyapunov_exponents), and other dynamical system properties. -- [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to [perform structural identifiability analysis](@ref structural_identifiability). + - [Optimization.jl](https://github.com/SciML/Optimization.jl), [DiffEqParamEstim.jl](https://github.com/SciML/DiffEqParamEstim.jl), and [PEtab.jl](https://github.com/sebapersson/PEtab.jl) can all be used to [fit model parameters to data](https://sebapersson.github.io/PEtab.jl/stable/Define_in_julia/). - [GlobalSensitivity.jl](https://github.com/SciML/GlobalSensitivity.jl) can be used to perform [global sensitivity analysis](@ref global_sensitivity_analysis) of model behaviors. - [SciMLSensitivity.jl](https://github.com/SciML/SciMLSensitivity.jl) can be used to compute local sensitivities of functions containing forward model simulations. @@ -233,4 +233,4 @@ versioninfo() # hide ``` ```@raw html -``` \ No newline at end of file +``` diff --git a/docs/src/inverse_problems/optimization_ode_param_fitting.md b/docs/src/inverse_problems/optimization_ode_param_fitting.md index 5834b96823..08cb8adf05 100644 --- a/docs/src/inverse_problems/optimization_ode_param_fitting.md +++ b/docs/src/inverse_problems/optimization_ode_param_fitting.md @@ -78,7 +78,7 @@ plot!(fitted_sol; idxs = :P, label = "Fitted solution", linestyle = :dash, lw = ``` !!! note - Here, a good exercise is to check the resulting parameter set and note that, while it creates a good fit to the data, it does not actually correspond to the original parameter set. [Identifiability](@ref structural_identifiability) is a concept that studies how to deal with this problem. + Here, a good exercise is to check the resulting parameter set and note that, while it creates a good fit to the data, it does not actually correspond to the original parameter set. Identifiability is a concept that studies how to deal with this problem. Say that we instead would like to use the [Broyden–Fletcher–Goldfarb–Shannon](https://en.wikipedia.org/wiki/Broyden%E2%80%93Fletcher%E2%80%93Goldfarb%E2%80%93Shanno_algorithm) algorithm, as implemented by the [Optim.jl](https://github.com/JuliaNLSolvers/Optim.jl) package. In this case we would run: ```@example diffeq_param_estim_1 @@ -187,4 +187,4 @@ If you use this functionality in your research, please cite the following paper --- ## References -[^1]: [Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga, *A protocol for dynamic model calibration*, Briefings in Bioinformatics (2023).](https://academic.oup.com/bib/article/23/1/bbab387/6383562?login=false) \ No newline at end of file +[^1]: [Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga, *A protocol for dynamic model calibration*, Briefings in Bioinformatics (2023).](https://academic.oup.com/bib/article/23/1/bbab387/6383562?login=false) From ad50b95333bd6b727aec49a7aa9e2920a6a83e36 Mon Sep 17 00:00:00 2001 From: vyudu Date: Wed, 9 Oct 2024 17:05:33 -0400 Subject: [PATCH 4/4] up --- docs/src/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/src/index.md b/docs/src/index.md index 40001a997b..1db58e8c6d 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -41,7 +41,7 @@ etc). - Model steady states can be [computed through homotopy continuation](@ref homotopy_continuation) using [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl) (which can find *all* steady states of systems with multiple ones), by [forward ODE simulations](@ref steady_state_solving_simulation) using [SteadyStateDiffEq.jl)](https://github.com/SciML/SteadyStateDiffEq.jl), or by [numerically solving steady-state nonlinear equations](@ref steady_state_solving_nonlinear) using [NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl). - [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) can be used to [compute bifurcation diagrams](@ref bifurcation_diagrams) of model steady states (including finding periodic orbits). - [DynamicalSystems.jl](https://github.com/JuliaDynamics/DynamicalSystems.jl) can be used to compute model [basins of attraction](@ref dynamical_systems_basins_of_attraction), [Lyapunov spectrums](@ref dynamical_systems_lyapunov_exponents), and other dynamical system properties. - + - [Optimization.jl](https://github.com/SciML/Optimization.jl), [DiffEqParamEstim.jl](https://github.com/SciML/DiffEqParamEstim.jl), and [PEtab.jl](https://github.com/sebapersson/PEtab.jl) can all be used to [fit model parameters to data](https://sebapersson.github.io/PEtab.jl/stable/Define_in_julia/). - [GlobalSensitivity.jl](https://github.com/SciML/GlobalSensitivity.jl) can be used to perform [global sensitivity analysis](@ref global_sensitivity_analysis) of model behaviors. - [SciMLSensitivity.jl](https://github.com/SciML/SciMLSensitivity.jl) can be used to compute local sensitivities of functions containing forward model simulations.