init

TorkelE · TorkelE · commit 9d774bd48e29 · 2024-01-24T17:14:14.000-05:00
diff --git a/README.md b/README.md
@@ -48,6 +48,8 @@ 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):
+- 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
   Catalyst and its more advanced features as of version 12.1. [Workshop
   video](https://youtu.be/tVfxT09AtWQ), [Workshop Pluto.jl
@@ -60,6 +62,8 @@ Catalyst.jl](https://www.youtube.com/watch?v=5p1PJE5A5Jw).
   Modelling of Biochemical Reaction
   Networks](https://www.youtube.com/watch?v=s1e72k5XD6s)
 
+Finally, an overview of the package and its features (as of version 13) can also be found in its corresponding research paper, [Catalyst: Fast and flexible modeling of reaction networks](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011530).
+
 ## Features
 
 - A DSL provides a simple and readable format for manually specifying chemical
diff --git a/docs/src/catalyst_applications/bifurcation_diagrams.md b/docs/src/catalyst_applications/bifurcation_diagrams.md
@@ -1,6 +1,6 @@
 # [Bifurcation Diagrams](@id bifurcation_diagrams)
 
-Bifurcation diagrams describe how, for a dynamical system, the quantity and type of its steady states change as a parameter is varied[^1]. When using Catalyst-generated models, these can be computed with the [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) package. Catalyst provides a simple interface for creating BifurcationKit compatible `BifurcationProblem`s from `ReactionSystem`s. If you use this feature in your research, please [cite the BifurcationKit.jl](@ref bifurcation_kit_citation) and [Catalyst.jl](@ref catalyst_citation) publications.
+Bifurcation diagrams describe how, for a dynamical system, the quantity and type of its steady states change as a parameter is varied[^1]. When using Catalyst-generated models, these can be computed with the [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) package. Catalyst provides a simple interface for creating BifurcationKit compatible `BifurcationProblem`s from `ReactionSystem`s.
 
 This tutorial briefly introduces how to use Catalyst with BifurcationKit through basic examples, with BifurcationKit.jl providing [a more extensive documentation](https://bifurcationkit.github.io/BifurcationKitDocs.jl/stable/). Especially for more complicated systems, where careful tuning of algorithm options might be required, reading the BifurcationKit documentation is recommended. Finally, BifurcationKit provides many additional features not described here, including [computation of periodic orbits](https://bifurcationkit.github.io/BifurcationKitDocs.jl/stable/periodicOrbit/), [tracking of bifurcation points along secondary parameters](https://bifurcationkit.github.io/BifurcationKitDocs.jl/dev/branchswitching/), and [bifurcation computations for PDEs](https://bifurcationkit.github.io/BifurcationKitDocs.jl/dev/tutorials/tutorials/#PDEs:-bifurcations-of-equilibria).
 
diff --git a/docs/src/catalyst_applications/homotopy_continuation.md b/docs/src/catalyst_applications/homotopy_continuation.md
@@ -9,7 +9,7 @@ integer Hill exponents). The roots of these can reliably be found through a
 *homotopy continuation* algorithm. This is implemented in Julia through the
 [HomotopyContinuation.jl](https://www.juliahomotopycontinuation.org/) package.
 
-Catalyst contains a special homotopy continuation extension that is loaded whenever HomotopyContinuation.jl is. This exports a single function, `hc_steady_states`, that can be used to find the steady states of any `ReactionSystem` structure. If you use this in your research, please [cite the HomotopyContinuation.jl](@ref homotopy_continuation_citation) and [Catalyst.jl](@ref catalyst_citation) publications.
+Catalyst contains a special homotopy continuation extension that is loaded whenever HomotopyContinuation.jl is. This exports a single function, `hc_steady_states`, that can be used to find the steady states of any `ReactionSystem` structure.
 
 ## Basic example
 For this tutorial, we will use a model from Wilhelm (2009)[^1] (which
diff --git a/docs/src/catalyst_applications/nonlinear_solve.md b/docs/src/catalyst_applications/nonlinear_solve.md
@@ -6,7 +6,7 @@ We have previously described how `ReactionSystem` steady states can be found thr
 
 However, if all (or multiple) steady states are sought, using homotopy continuation is better.
 
-This tutorial describes how to create `NonlinearProblem`s from Catalyst's `ReactionSystemn`s, and how to solve them using NonlinearSolve. More extensive descriptions of available solvers and options can be found in [NonlinearSolve's documentation](https://docs.sciml.ai/NonlinearSolve/stable/). If you use this in your research, please [cite the NonlinearSolve.jl](@ref nonlinear_solve_citation) and [Catalyst.jl](@ref catalyst_citation) publications.
+This tutorial describes how to create `NonlinearProblem`s from Catalyst's `ReactionSystemn`s, and how to solve them using NonlinearSolve. More extensive descriptions of available solvers and options can be found in [NonlinearSolve's documentation](https://docs.sciml.ai/NonlinearSolve/stable/).
 
 ## Basic example
 Let us consider a simple dimerisation network, where a protein ($P$) can exist in a monomer and a dimer form. The protein is produced at a constant rate from its mRNA, which is also produced at a constant rate.
diff --git a/docs/src/introduction_to_catalyst/catalyst_for_new_julia_users.md b/docs/src/introduction_to_catalyst/catalyst_for_new_julia_users.md
diff --git a/docs/src/inverse_problems/petab_ode_param_fitting.md b/docs/src/inverse_problems/petab_ode_param_fitting.md
