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Fix GitHub readme links #982

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Jul 12, 2024
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Fix GitHub readme links #982

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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -69,9 +69,9 @@ be found in its corresponding research paper, [Catalyst: Fast and flexible model
- Support for [parallelization of all simulations](https://docs.sciml.ai/Catalyst/stable/model_simulation/ode_simulation_performance/#ode_simulation_performance_parallelisation), including parallelization of [ODE simulations on GPUs](https://docs.sciml.ai/Catalyst/stable/model_simulation/ode_simulation_performance/#ode_simulation_performance_parallelisation_GPU) using [DiffEqGPU.jl](https://github.com/SciML/DiffEqGPU.jl).
- [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to [generate LaTeX expressions](https://docs.sciml.ai/Catalyst/stable/model_creation/model_visualisation/#visualisation_latex) corresponding to generated mathematical models or the underlying set of reactions.
- [Graphviz](https://graphviz.org/) can be used to generate and [visualize reaction network graphs](https://docs.sciml.ai/Catalyst/stable/model_creation/model_visualisation/#visualisation_graphs) (reusing the Graphviz interface created in [Catlab.jl](https://algebraicjulia.github.io/Catlab.jl/stable/)).
- Model steady states can be computed through 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 using [SteadyStateDiffEq.jl](https://github.com/SciML/SteadyStateDiffEq.jl), or by numerically solving steady-state nonlinear equations using [NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl).
- 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](@ref dynamical_systems_basins_of_attraction), [Lyapunov spectrums](@ref dynamical_systems_lyapunov_exponents), and other dynamical system properties.
- [DynamicalSystems.jl](https://github.com/JuliaDynamics/DynamicalSystems.jl) can be used to compute model [basins of attraction]([@ref dynamical_systems_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.
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2 changes: 1 addition & 1 deletion docs/src/index.md
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Expand Up @@ -38,7 +38,7 @@ etc).
- Support for [parallelization of all simulations](@ref ode_simulation_performance_parallelisation), including parallelization of [ODE simulations on GPUs](@ref ode_simulation_performance_parallelisation_GPU) using [DiffEqGPU.jl](https://github.com/SciML/DiffEqGPU.jl).
- [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to [generate LaTeX expressions](@ref visualisation_latex) corresponding to generated mathematical models or the underlying set of reactions.
- [Graphviz](https://graphviz.org/) can be used to generate and [visualize reaction network graphs](@ref visualisation_graphs) (reusing the Graphviz interface created in [Catlab.jl](https://algebraicjulia.github.io/Catlab.jl/stable/)).
- 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).
- 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).
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