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docs/src/model_creation/dsl_advanced.md

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@@ -85,7 +85,7 @@ Generally, there are four main reasons for specifying species/parameters using t
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3. To designate metadata for species/parameters (described [here](@ref dsl_advanced_options_species_and_parameters_metadata)).
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4. To designate a species or parameters that do not occur in reactions, but are still part of the model (e.g a [parametric initial condition](@ref dsl_advanced_options_parametric_initial_conditions))
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!!! warning
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Catalyst's DSL automatically infer species and parameters from the input. However, it only does so for *quantities that appear in reactions*. Until now this has not been relevant. However, this tutorial will demonstrate cases where species/parameters that are not part of reactions are used. These *must* be designated using either the `@species` or `@parameters` options (or the `@variables` option, which is described [later](@ref constraint_equations)).
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### [Setting default values for species and parameters](@id dsl_advanced_options_default_vals)
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plot(sol)
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```
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!!! warning
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Just like when using `@parameters` and `@species`, `@unpack` will overwrite any variables in the current scope which share name with the imported quantities.
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### [Interpolating variables into the DSL](@id dsl_advanced_options_symbolics_and_DSL_interpolation)

docs/src/model_creation/programmatic_CRN_construction.md

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Alternatively, one can use the `name = :repressilator` keyword argument to the
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`ReactionSystem` constructor.
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!!! warning
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All `ReactionSystem`s created via the symbolic interface (i.e. by calling `ReactionSystem` with some input, rather than using `@reaction_network`) are not marked as complete. To simulate them, they must first be marked as *complete*, indicating to Catalyst and ModelingToolkit that they represent finalized models. This can be done using the `complete` function, i.e. by calling `repressilator = complete(repressilator)`. An expanded description on *completeness* can be found [here](@ref completeness_note).
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We can check that this is the same model as the one we defined via the DSL as

docs/src/model_simulation/simulation_structure_interfacing.md

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```
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Generally, when updating problems, it is often better to use the [`remake` function](@ref simulation_structure_interfacing_problems_remake) (especially when several values are updated).
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Indexing *should not* be used not modify `JumpProblem`s. Here, [remake](@ref simulation_structure_interfacing_problems_remake) should be used exclusively.
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A problem's time span can be accessed through the `tspan` field:
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```
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This can be used to form symbolic expressions using model quantities when a model has been created using the DSL (as an alternative to @unpack). Alternatively, [creating an observable](@ref dsl_advanced_options_observables), and then interface using its `Symbol` representation, is also possible.
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With interfacing with a simulating structure using symbolic variables stored in a `ReactionSystem` model, ensure that the model is complete.

docs/src/steady_state_functionality/steady_state_stability_computation.md

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# [Steady state stability computation](@id steady_state_stability)
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After system steady states have been found using [HomotopyContinuation.jl](@ref homotopy_continuation), [NonlinearSolve.jl](@ref steady_state_solving), or other means, their stability can be computed using Catalyst's `steady_state_stability` function. Systems with conservation laws will automatically have these removed, permitting stability computation on systems with singular Jacobian.
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Catalyst currently computes steady state stabilities using the naive approach of checking whether a system's largest eigenvalue real part is negative. While more advanced stability computation methods exist (and would be a welcome addition to Catalyst), there is no direct plans to implement these. Furthermore, Catalyst uses a tolerance `tol = 10*sqrt(eps())` to determine whether a computed eigenvalue is far away enough from 0 to be reliably used. This threshold can be changed through the `tol` keyword argument.
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## [Basic examples](@id steady_state_stability_basics)
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nothing # hide
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```
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For systems with [conservation laws](@ref homotopy_continuation_conservation_laws), `steady_state_jac` must be supplied a `u0` vector (indicating species concentrations for conservation law computation). This is required to eliminate the conserved quantities, preventing a singular Jacobian. These are supplied using the `u0` optional argument.

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