@@ -16,9 +16,9 @@ Generated models can be used with solvers throughout the broader
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for sensitivity analysis, parameter estimation, machine learning applications,
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etc).
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- ## Features
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+ ## [ Features] ( @ id doc_home_features)
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- #### Features of Catalyst
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+ #### [ Features of Catalyst] ( @ id doc_home_features_catalyst)
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- [ The Catalyst DSL] (@ref ref) provides a simple and readable format for manually specifying reaction
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network models using chemical reaction notation.
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- Catalyst ` ReactionSystem ` s provides a symbolic representation of reaction networks,
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deterministic and stochastic terms within resulting ODE, SDE or jump models.
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- [ Steady states] (@ref ref) (and their [ stabilities] (@ref ref)) can be computed for model ODE representations.
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- #### Features of Catalyst composing with other packages
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+ #### [ Features of Catalyst composing with other packages] ( @ id doc_home_features_composed)
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- [ OrdinaryDiffEq.jl] ( https://github.com/SciML/OrdinaryDiffEq.jl ) Can be used to [ perform model ODE
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simulations] (@ref ref).
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- [ StochasticDiffEq.jl] ( https://github.com/SciML/StochasticDiffEq.jl ) Can be used to [ perform model
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- [ GlobalSensitivity.jl] ( https://github.com/SciML/GlobalSensitivity.jl ) can be used to perform
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[ global sensitivity analysis] (@ref ref) of model behaviors.
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- #### Features of packages built upon Catalyst
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+ #### [ Features of packages built upon Catalyst] ( @ id doc_home_features_other_packages)
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- Catalyst [ ` ReactionSystem ` ] ( @ref ) s can be [ imported from SBML files] (@ref ref) via
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[ SBMLImporter.jl] ( https://github.com/SciML/SBMLImporter.jl ) and [ SBMLToolkit.jl] ( https://github.com/SciML/SBMLToolkit.jl ) ,
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and [ from BioNetGen .net files] (@ref ref) and various stoichiometric matrix network representations
@@ -149,9 +149,9 @@ is also needed.
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A more throughout guide for setting up Catalyst and installing Julia packages can be found [ here] (@ref catalyst_for_new_julia_users_packages).
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- ## Illustrative example
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+ ## [ Illustrative example] ( @ id doc_home_example)
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- #### Deterministic ODE simulation of Michaelis-Menten enzyme kinetics
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+ #### [ Deterministic ODE simulation of Michaelis-Menten enzyme kinetics] ( @ id doc_home_example_ode)
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Here we show a simple example where a model is created using the Catalyst DSL, and then simulated as
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an ordinary differential equation.
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@@ -177,7 +177,7 @@ sol = solve(ode)
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plot(sol; lw = 5)
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```
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- #### Stochastic jump simulations
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+ #### [ Stochastic jump simulations] ( @ id doc_home_example_jump)
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The same model can be used as input to other types of simulations. E.g. here we instead perform a
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jump simulation
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``` @example home_simple_example
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plot(jump_sol; lw = 2)
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```
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- ## Elaborate example
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+ ## [ Elaborate example] ( @ id doc_home_elaborate_example)
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In the above example, we used basic Catalyst-based workflows to simulate a simple model. Here we
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instead show how various Catalyst features can compose to create a much more advanced model. Our
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model describes how the volume of a cell ($V$) is affected by a growth factor ($G$). The growth
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