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remove SI from README
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isaacsas committed Jan 9, 2025
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -72,10 +72,10 @@ be found in its corresponding research paper, [Catalyst: Fast and flexible model
- Model steady states can be [computed through homotopy continuation](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/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](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/nonlinear_solve/#steady_state_solving_simulation) using [SteadyStateDiffEq.jl](https://github.com/SciML/SteadyStateDiffEq.jl), or by [numerically solving steady-state nonlinear equations](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/nonlinear_solve/#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](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/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](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/dynamical_systems/#dynamical_systems_basins_of_attraction), [Lyapunov spectrums](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/dynamical_systems/#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](https://docs.sciml.ai/Catalyst/stable/inverse_problems/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](https://docs.sciml.ai/Catalyst/stable/inverse_problems/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.
<!-- - [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to [perform structural identifiability analysis](https://docs.sciml.ai/Catalyst/stable/inverse_problems/structural_identifiability/). -->

#### Features of packages built upon Catalyst
- Catalyst [`ReactionSystem`](@ref)s can be [imported from SBML files](https://docs.sciml.ai/Catalyst/stable/model_creation/model_file_loading_and_export/#Loading-SBML-files-using-SBMLImporter.jl-and-SBMLToolkit.jl) via [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl) and [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), and [from BioNetGen .net files](https://docs.sciml.ai/Catalyst/stable/model_creation/model_file_loading_and_export/#file_loading_rni_net) and various stoichiometric matrix network representations using [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl).
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2 changes: 1 addition & 1 deletion docs/src/index.md
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Expand Up @@ -41,10 +41,10 @@ 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 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.-->
- [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.
<!--- [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to perform structural identifiability analysis.-->

#### [Features of packages built upon Catalyst](@id doc_index_features_other_packages)
- Catalyst [`ReactionSystem`](@ref)s can be [imported from SBML files](@ref model_file_import_export_sbml) via [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl) and [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), and [from BioNetGen .net files](@ref model_file_import_export_sbml_rni_net) and various stoichiometric matrix network representations using [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl).
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