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Update HISTORY.md
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TorkelE committed Jun 10, 2024
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Expand Up @@ -93,7 +93,7 @@ to assess (global) structural identifiability for all parameters and variables o
- Automatically handles conservation laws for structural identifiability problems (eliminates these internally to speed up computations).
- A more detailed of how this extension works can be found [here](https://docs.sciml.ai/Catalyst/stable/inverse_problems/structural_identifiability/).

#### Bifurcation identifiability extension
#### Bifurcation analysis extension
- Add a CatalystBifurcationKitExtension, permitting BifurcationKit's `BifurcationProblem`s to be created from Catalyst reaction networks. Example usage:
```julia
using Catalyst
Expand All @@ -110,15 +110,15 @@ bif_par = :k1
u_guess = [:X => 5.0, :Y => 2.0]
p_start = [:k1 => 4.0, :k2 => 1.0, :k3 => 1.0, :k4 => 1.5, :k5 => 1.25]
plot_var = :X
bprob = BifurcationProblem(wilhelm_2009_model, u_guess, p_start, bif_par; plot_var=plot_var)
bprob = BifurcationProblem(wilhelm_2009_model, u_guess, p_start, bif_par; plot_var = plot_var)

p_span = (2.0, 20.0)
opts_br = ContinuationPar(p_min = p_span[1], p_max = p_span[2], max_steps=1000)
opts_br = ContinuationPar(p_min = p_span[1], p_max = p_span[2], max_steps = 1000)

bif_dia = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside=true)
bif_dia = bifurcationdiagram(bprob, PALC(), 2, (args...) -> opts_br; bothside = true)

using Plots
plot(bif_dia; xguide="k1", yguide="X")
plot(bif_dia; xguide = "k1", guide = "X")
```
- Automatically handles elimination of conservation laws for computing bifurcation diagrams.
- Updated Bifurcation documentation with respect to this new feature.
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