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Author: TorkelE

README.md

@@ -43,8 +43,7 @@ documentation](https://docs.sciml.ai/Catalyst/stable/). The [in-development
 documentation](https://docs.sciml.ai/Catalyst/dev/) describes unreleased features in
 the current master branch.
 
-Several Youtube video tutorials and overviews are also available, but note these use older 
-Catalyst versions with slightly different notation (for example, in building reaction networks):
+Several Youtube video tutorials and overviews are also available (however, these use older versions of Catalyst, and some notation may be out-of-date):
 - From JuliaCon 2023: A short 15 minute overview of Catalyst as of version 13 is
 available in the talk [Catalyst.jl, Modeling Chemical Reaction Networks](https://www.youtube.com/watch?v=yreW94n98eM&ab_channel=TheJuliaProgrammingLanguage).
 - From JuliaCon 2022: A three hour tutorial workshop overviewing how to use
@@ -63,6 +62,8 @@ Finally, an overview of the package and its features (as of version 13) can also
 
 ## Features
 
+#### Features of Catalyst
+
 - A DSL provides a simple and readable format for manually specifying chemical
   reactions.
 - Catalyst `ReactionSystem`s provide a symbolic representation of reaction networks,
@@ -71,17 +72,19 @@ Finally, an overview of the package and its features (as of version 13) can also
 - Non-integer (e.g. `Float64`) stoichiometric coefficients are supported for generating
   ODE models, and symbolic expressions for stoichiometric coefficients are supported for
   all system types.
-- The [Catalyst.jl API](http://docs.sciml.ai/Catalyst/stable/api/catalyst_api) provides functionality for extending networks,
-  building networks programmatically, network analysis, and for composing multiple
-  networks together.
+- The [Catalyst.jl API](http://docs.sciml.ai/Catalyst/stable/api/catalyst_api) provides functionality 
+  for extending networks, building networks programmatically, network analysis, and for composing 
+  multiple networks together.
+- A network analysis suite permitting the computation of linkage classes, deficiencies, reversibilities.
+- Conservation laws can be detected and applied to reduce system sizes, and generate
+  non-singular Jacobians, during conversion to ODEs, SDEs, and steady state equations.
 - `ReactionSystem`s generated by the DSL can be converted to a variety of
   `ModelingToolkit.AbstractSystem`s, including symbolic ODE, SDE and jump process
   representations.
 - Coupled differential and algebraic constraint equations can be included in
-  Catalyst models, and are incorporated during conversion to ODEs or steady
-  state equations.
-- Conservation laws can be detected and applied to reduce system sizes, and generate
-  non-singular Jacobians, during conversion to ODEs, SDEs, and steady state equations.
+  Catalyst models (and are incorporated during conversion to ODEs, SDEs, and steady
+  state equations).
+- Modelling of simulation events.
 - By leveraging ModelingToolkit, users have a variety of options for generating
   optimized system representations to use in solvers. These include construction
   of dense or sparse Jacobians, multithreading or parallelization of generated
@@ -97,17 +100,38 @@ Finally, an overview of the package and its features (as of version 13) can also
   expressions and Julia `Expr`s can be obtained for all rate laws and functions
   determining the deterministic and stochastic terms within resulting ODE, SDE
   or jump models.
+- Determination of steady state stabilities.
+
+
+#### Features of Catalyst composing with other packages
+- [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) Can be used to perform ODE simulation of CRN models.
+- [StochasticDiffEq.jl](https://github.com/SciML/StochasticDiffEq.jl) Can be used to perform SDE simulation of CRN models.
+- [JumpProcesses.jl](https://github.com/SciML/JumpProcesses.jl) Can be used to perform jump simulations of CRN models.
+- Support for automatic parallelisation of all simulations, including parallelisation of ODE simulations using
+  [DiffEqGPU.jl](https://github.com/SciML/DiffEqGPU.jl).
 - [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to generate
   LaTeX expressions 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. (Reusing the Graphviz interface created in
   [Catlab.jl](https://algebraicjulia.github.io/Catlab.jl/stable/).)
-
-## Packages supporting Catalyst
+- [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl) can be used to computer *all* steady states for CRN models with 
+  multiple steady states.
+- [NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl) can be used to find single steady states of CRN models (offering higher
+  performance than the homotopy continuation approach).
+- [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) can be used to compute bifurcation diagrams of CRN models' steady state
+  (including finding periodic orbits).
+- [DynamicalSystems.jl](https://github.com/JuliaDynamics/DynamicalSystems.jl) can be used to computer basins of attraction and Lyaponov spectrum for CRN models.
+- [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to perform structural identifiability analysis of
+  CRN models.
+- [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 CRN model
+  parameters to data.
+- [GlobalSensitivity.jl](https://github.com/SciML/GlobalSensitivity.jl) can be used to perform global sensitivity analysis of model behaviours.
+ 
+#### Features of packages built upon Catalyst
 - Catalyst [`ReactionSystem`](@ref)s can be imported from SBML files via
-  [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), and from BioNetGen .net
-  files and various stoichiometric matrix network representations using
+  [SBMLImporter.jl](https://github.com/SciML/SBMLImporter.jl) and [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), 
+  and from BioNetGen .net files and various stoichiometric matrix network representations using
   [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl).
 - [MomentClosure.jl](https://github.com/augustinas1/MomentClosure.jl) allows
   generation of symbolic ModelingToolkit `ODESystem`s, representing moment
@@ -121,10 +145,11 @@ Finally, an overview of the package and its features (as of version 13) can also
   resulting stochastic chemical kinetics with delays models.
 - [BondGraphs.jl](https://github.com/jedforrest/BondGraphs.jl) a package for
   constructing and analyzing bond graphs models, which can take Catalyst models as input.
-- [PEtab.jl](https://github.com/sebapersson/PEtab.jl) a package that implements the PEtab format for fitting reaction network ODEs to data. Input can be provided either as SBML files or as Catalyst `ReactionSystem`s.
+- [PEtab.jl](https://github.com/sebapersson/PEtab.jl) a package that implements the PEtab format for 
+fitting reaction network ODEs to data. Input can be provided either as SBML files or as Catalyst `ReactionSystem`s.
 
 
-## Illustrative examples
+## Simple example
 #### Gillespie simulations of Michaelis-Menten enzyme kinetics
 
 ```julia
@@ -164,6 +189,8 @@ ssol  = solve(sprob, LambaEM(), reltol=1e-3)
 plot(ssol; lw = 2, title = "Adaptive SDE: Birth-Death Process")
 ```
 
+## Elaborate example
+
 ![](https://user-images.githubusercontent.com/1814174/87864113-3bf9dd00-c932-11ea-8275-f903eef90b91.png)
 
 ## Getting help