reference update

SciML · Nov 12, 2023 · f20d62a · f20d62a
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -12,6 +12,7 @@ NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationBBO = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b"
+OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OptimizationOptimisers = "42dfb2eb-d2b4-4451-abcd-913932933ac1"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 PEtab = "48d54b35-e43e-4a66-a5a1-dde6b987cf69"

diff --git a/docs/src/inverse_problems/behaviour_optimization.md b/docs/src/inverse_problems/behaviour_optimization.md
@@ -1,8 +1,8 @@
 # Optimization for non-data fitting purposes
-In previous tutorials we have described how to use [PEtab.jl](@ref petab_parameter_fitting) and [Optimization.jl](@ref optimization_parameter_fitting) for parameter fitting. This involves solving an optimisation problem (to find the parameter set yielding the best model-to-data fit). There are, however, other situations that require solving optimisation problems. Typically, these involve the creation of a custom cost function, which optimum can then be found using Optimization.jl. In this tutorial we will describe this process, demonstrating how parameter space can be searched to find values that achieve a desired system behaviour. A more throughout description on how to solve these problems are provided by [Optimization.jl's documentation](https://docs.sciml.ai/Optimization/stable/). 
+In previous tutorials we have described how to use [PEtab.jl](@ref petab_parameter_fitting) and [Optimization.jl](@ref optimization_parameter_fitting) for parameter fitting. This involves solving an optimisation problem (to find the parameter set yielding the best model-to-data fit). There are, however, other situations that require solving optimisation problems. Typically, these involve the creation of a custom cost function, which optimum can then be found using Optimization.jl. In this tutorial we will describe this process, demonstrating how parameter space can be searched to find values that achieve a desired system behaviour. A more throughout description on how to solve these problems are provided by [Optimization.jl's documentation](https://docs.sciml.ai/Optimization/stable/) and the literature [^1]. 
 
 ## Maximising the pulse amplitude of an incoherent feed forward loop.
-Incoherent feedforward loops (network motifs where a single component both activates and deactivates a downstream component) are able to generate pulses in response to step inputs [^1]. In this tutorial we will consider such an incoherent feedforward loop, attempting to generate a system with as prominent a response pulse as possible. Our model consists of 3 species: $X$ (the input node), $Y$ (an intermediary), and $Z$ (the output node). In it, $X$ activates the production of both $Y$ and $Z$, with $Y$ also deactivating $Z$. When $X$ is activated, there will be a brief time window where $Y$ is still inactive, and $Z$ is activated. However, as $Y$ becomes active, it will turn $Z$ off, creating a pulse.
+Incoherent feedforward loops (network motifs where a single component both activates and deactivates a downstream component) are able to generate pulses in response to step inputs [^2]. In this tutorial we will consider such an incoherent feedforward loop, attempting to generate a system with as prominent a response pulse as possible. Our model consists of 3 species: $X$ (the input node), $Y$ (an intermediary), and $Z$ (the output node). In it, $X$ activates the production of both $Y$ and $Z$, with $Y$ also deactivating $Z$. When $X$ is activated, there will be a brief time window where $Y$ is still inactive, and $Z$ is activated. However, as $Y$ becomes active, it will turn $Z$ off, creating a pulse.
 ```@example behaviour_optimization
 using Catalyst
 incoherent_feed_forward = @reaction_network begin
@@ -86,4 +86,5 @@ opt_sol = solve(opt_prob, OptimizationOptimJL.BFGS())
 
 ---
 ## References
-[^1]: [Goentoro, L et al. *The incoherent feedforward loop can provide fold-change detection in gene regulation*, Molecular Cell (2009).](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896310/)
+[^1]: [Mykel J. Kochenderfer, Tim A. Wheeler *Algorithms for Optimization*, The MIT Press (2019).](https://algorithmsbook.com/optimization/files/optimization.pdf)
+[^2]: [Lea Goentoro, Oren Shoval, Marc W Kirschner, Uri Alon *The incoherent feedforward loop can provide fold-change detection in gene regulation*, Molecular Cell (2009).](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896310/)