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README.md

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## Breaking changes and new features
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**NOTE:** Version 14 is a breaking release, prompted by the release of ModelingToolkit.jl version 9. This caused several breaking changes in how Catalyst models are represented and interfaced with.
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**NOTE:** Version 14 is a breaking release, prompted by the release of ModelingToolkit.jl version 9.
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This caused several breaking changes in how Catalyst models are represented and interfaced with.
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Breaking changes and new functionality are summarized in the [HISTORY.md](HISTORY.md) file. This also includes a special migration guide for version 14.
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Breaking changes and new functionality are summarized in the [HISTORY.md](HISTORY.md) file.
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This also includes a special migration guide for version 14.
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## Tutorials and documentation
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documentation](https://docs.sciml.ai/Catalyst/dev/) describes unreleased features in
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the current master branch.
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An overview of the package, its features, and comparative benchmarking (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).
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An overview of the package, its features, and comparative benchmarking (as of version 13) can also
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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).
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## Features
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[DifferentialEquations.jl](https://docs.sciml.ai/DiffEqDocs/stable/)
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[ODE/SDE/jump solver](@ref ref), and can be used within `EnsembleProblem`s for carrying
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out [parallelized parameter sweeps and statistical sampling](@ref ref). Plot recipes
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are available for [visualizing of all solutions](@ref ref).
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are available for [visualization of all solutions](@ref ref).
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- Non-integer (e.g. `Float64`) stoichiometric coefficients [are supported](@ref ref) for generating
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ODE models, and symbolic expressions for stoichiometric coefficients [are supported](@ref ref) for
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all system types.
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- A [network analysis suite](@ref ref) permits the computation of linkage classes, deficiencies, and
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reversibilities.
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- [Conservation laws can be detected and utilised](@ref ref) to reduce system sizes, and to generate
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- [Conservation laws can be detected and utilized](@ref ref) to reduce system sizes, and to generate
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non-singular Jacobians (e.g. during conversion to ODEs, SDEs, and steady state equations).
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- Catalyst reaction network models can be [coupled with differential and algebraic equations](@ref ref)
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(which are then incorporated during conversion to ODEs, SDEs, and steady state equations).
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SDE simulations](@ref ref).
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- [JumpProcesses.jl](https://github.com/SciML/JumpProcesses.jl) Can be used to [model jump
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simulations](@ref ref).
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- Support for [parallelisation of all simulations]((@ref ref)), including parallelisation of
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- Support for [parallelization of all simulations](@ref ref), including parallelization of
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[ODE simulations on GPUs](@ref ref) using
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[DiffEqGPU.jl](https://github.com/SciML/DiffEqGPU.jl).
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- [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to [generate LaTeX
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expressions](@ref ref) corresponding to generated mathematical models or the
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underlying set of reactions.
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- [Graphviz](https://graphviz.org/) can be used to generate and [visualize reaction network graphs](@ref ref)
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(reusing the Graphviz interface created in [Catlab.jl](https://algebraicjulia.github.io/Catlab.jl/stable/).)
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- Models steady states can be computed through homotopy continuation using [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl)
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- Model steady states can be computed through homotopy continuation using [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl)
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(which can find *all* steady states of systems with multiple ones), by forward ODE simulations using
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[SteadyStateDiffEq.jl)](https://github.com/SciML/SteadyStateDiffEq.jl), or by nonlinear systems
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solving using [NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl).
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- [Optimization.jl](https://github.com/SciML/Optimization.jl), [DiffEqParamEstim.jl](https://github.com/SciML/DiffEqParamEstim.jl),
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and [PEtab.jl](https://github.com/sebapersson/PEtab.jl) can all be used to [fit model parameters to data](@ref ref).
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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 behaviours.
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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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- Catalyst [`ReactionSystem`](@ref)s can be [imported from SBML files](@ref ref) via
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## Elaborate example
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In the above example, we used basic Catalyst-based workflows to simulate a simple model. Here we instead show how various Catalyst features can compose to create a much more advanced model. Our model describes how the volume of a cell ($V$) is affected by a growth factor ($G$). The growth factor only promotes growth while in its phosphorylated form ($Gᴾ$). The phosphorylation of $G$ ($G \to Gᴾ$) is promoted by sunlight (modelled as the cyclic sinusoid $kₐ*(sin(t)+1)$) phosphorylates the growth factor (producing $Gᴾ$). When the cell reaches a critical volume ($V$) it goes through cell division. First, we declare our model:
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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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factor only promotes growth while in its phosphorylated form ($Gᴾ$). The phosphorylation of $G$
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($G \to Gᴾ$) is promoted by sunlight (modelld as the cyclic sinusoid $kₐ*(sin(t)+1)$), which
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phosphorylates the growth factor (producing $Gᴾ$). When the cell reaches a critical volume ($V$)
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it undergoes through cell division. First, we declare our model:
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```julia
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using Catalyst
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cell_model = @reaction_network begin
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kᵢ/V, Gᴾ --> G
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end
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```
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Next, we can use [Latexify.jl](https://korsbo.github.io/Latexify.jl/stable/) to show the ordinary differential equations associated with this model:
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Next, we can use [Latexify.jl](https://korsbo.github.io/Latexify.jl/stable/) to show the ordinary
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differential equations associated with this model:
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```julia
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using Latexify
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latexify(cell_model; form = :ode)
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![Elaborate SDE simulation](docs/src/assets/readme_elaborate_sde_plot.svg)
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Some features we used here:
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- The SDE was [simulated using StochasticDiffEq.jl], where we [scaled the SDE noise terms](@ref ref).
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- The cell volume was [modelled as a differential equation, which was coupled to the reaction network model](@ref ref).
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- The SDE was [simulated using StochasticDiffEq.jl]. We also [scaled the SDE noise terms](@ref ref).
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- The cell volume was [modeled as a differential equation, which was coupled to the reaction network model](@ref ref).
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- The cell divisions were created by [incorporating events into the model](@ref ref).
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- The model equations were [displayed using Latexify.jl](@ref ref), and the simulation [plotted using Plots.jl](@ref ref).
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