up

docs/src/index.md

@@ -37,8 +37,7 @@ etc).
 - [JumpProcesses.jl](https://github.com/SciML/JumpProcesses.jl) can be used to numerically sample generated Stochastic Chemical Kinetics Jump Process models.
 - 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).
+- The GraphMakie package has [Makie](https://docs.makie.org/stable/) recipes that can be used to generate and [visualize reaction network graphs](@ref visualisation_graphs) - 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.-->

docs/src/introduction_to_catalyst/introduction_to_catalyst.md

@@ -81,14 +81,17 @@ latexify(rn)
 ```@example tut1
 rn #hide
 ```
-Assuming [Graphviz](https://graphviz.org/) is installed and command line
-accessible, within a Jupyter notebook we can also graph the reaction network by
+Catalyst also has functionality for visualizing networks using the [Makie](https://docs.makie.org/stable/)
+plotting ecosystem. The relevant packages to load are Catalyst, GraphMakie, and a Makie backend
+such as GLMakie. Doing so and then using the `plot_network` function allows us to 
+visualize the network: 
 ```julia
+using Catalyst, GraphMakie, GLMakie
 g = Graph(rn)
 ```
 giving
 
-![Repressilator solution](../assets/repressilator.svg)
+![Repressilator solution](../assets/repressilator_graph_makie.png)
 
 The network graph shows a variety of information, representing each species as a
 blue node, and each reaction as an orange dot. Black arrows from species to

docs/src/model_creation/network_analysis.md

@@ -32,9 +32,10 @@ tutorial we showed how the above network could be visualized as a
 species-reaction graph. There, species are represented by the nodes of the graph
 and edges show the reactions in which a given species is a substrate or product.
 ```julia
-g = Graph(repressilator)
+using Catalyst, GraphMakie, GLMakie
+g = plot_network(repressilator)
 ```
-![Repressilator solution](../assets/repressilator.svg)
+![Repressilator solution](../assets/repressilator_graph_makie.png)
 
 We also showed in the [Introduction to Catalyst](@ref introduction_to_catalyst) tutorial that
 the reaction rate equation ODE model for the repressilator is