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HISTORY.md

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field has been changed (only when created through the `@reaction_network`
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macro). Previously they were ordered according to the order with which they
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appeared in the macro. Now they are ordered according the to order with which
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they appeard after the `end` part. E.g. in
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they appeared after the `end` part. E.g. in
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```julia
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rn = @reaction_network begin
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(p,d), 0 <--> X
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![rn_complexes](https://user-images.githubusercontent.com/9385167/130252763-4418ba5a-164f-47f7-b512-a768e4f73834.png)
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*2.* Support for units via ModelingToolkit and
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[Uniftul.jl](https://github.com/PainterQubits/Unitful.jl) in directly constructed
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[Unitful.jl](https://github.com/PainterQubits/Unitful.jl) in directly constructed
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`ReactionSystem`s:
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```julia
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# ]add Unitful

docs/old_files/advanced.md

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```
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occurs at the rate ``d[X]/dt = -k[X]``, it is possible to ignore this by using
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any of the following non-filled arrows when declaring the reaction: `<=`, ``, ``,
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``, ``, `=>`, ``, `` (`<=>` currently not possible due to Julia langauge technical reasons). This means that the reaction
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``, ``, `=>`, ``, `` (`<=>` currently not possible due to Julia language technical reasons). This means that the reaction
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```julia
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rn = @reaction_network begin

docs/src/api.md

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* `ModelingToolkit.unknowns(rn)` returns all species *and variables* across the
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system, *all sub-systems*, and all constraint systems. Species are ordered
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before non-species variables in `unknowns(rn)`, with the first `numspecies(rn)`
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entires in `unknowns(rn)` being the same as `species(rn)`.
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entries in `unknowns(rn)` being the same as `species(rn)`.
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* [`species(rn)`](@ref) is a vector collecting all the chemical species within
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the system and any sub-systems that are also `ReactionSystems`.
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* `ModelingToolkit.parameters(rn)` returns all parameters across the

docs/src/model_creation/model_file_loading_and_export.md

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# [Loading Chemical Reaction Network Models from Files](@id model_file_import_export)
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Catalyst stores chemical reaction network (CRN) models in `ReactionSystem` structures. This tutorial describes how to load such `ReactionSystem`s from, and save them to, files. This can be used to save models between Julia sessions, or transfer them from one session to another. Furthermore, to facilitate the computation modelling of CRNs, several standardised file formats have been created to represent CRN models (e.g. [SBML](https://sbml.org/)). This enables CRN models to be shared between different softwares and programming languages. While Catalyst itself does not have the functionality for loading such files, we will here (briefly) introduce a few packages that can load different file types to Catalyst `ReactionSystem`s.
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Catalyst stores chemical reaction network (CRN) models in `ReactionSystem` structures. This tutorial describes how to load such `ReactionSystem`s from, and save them to, files. This can be used to save models between Julia sessions, or transfer them from one session to another. Furthermore, to facilitate the computation modelling of CRNs, several standardised file formats have been created to represent CRN models (e.g. [SBML](https://sbml.org/)). This enables CRN models to be shared between different software and programming languages. While Catalyst itself does not have the functionality for loading such files, we will here (briefly) introduce a few packages that can load different file types to Catalyst `ReactionSystem`s.
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## [Saving Catalyst models to, and loading them from, Julia files](@id model_file_import_export_crn_serialization)
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Catalyst provides a `save_reactionsystem` function, enabling the user to save a `ReactionSystem` to a file. Here we demonstrate this by first creating a [simple cross-coupling model](@ref basic_CRN_library_cc):

docs/src/model_creation/network_analysis.md

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It is evident from the preceding graph that the network is not reversible.
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However, it satisfies a weaker property in that there is a path from each
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reaction complex back to itself within its associated subgraph. This is known as
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*weak reversiblity*. One can test a network for weak reversibility by using
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*weak reversibility*. One can test a network for weak reversibility by using
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the [`isweaklyreversible`](@ref) function:
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```@example s1
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# need subnetworks from the reaction network first

docs/src/v14_migration_guide.md

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```
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## Lost support for most units
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As part of its v9 update, ModelingToolkit changed how units were handled. This includes using the package [DynamicQuantities.jl](https://github.com/SymbolicML/DynamicQuantities.jl) to manage units (instead of [Uniful.jl](https://github.com/PainterQubits/Unitful.jl), like previously).
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As part of its v9 update, ModelingToolkit changed how units were handled. This includes using the package [DynamicQuantities.jl](https://github.com/SymbolicML/DynamicQuantities.jl) to manage units (instead of [Unitful.jl](https://github.com/PainterQubits/Unitful.jl), like previously).
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While this should lead to long-term improvements, unfortunately, as part of the process support for most units was removed. Currently, only the main SI units are supported (`s`, `m`, `kg`, `A`, `K`, `mol`, and `cd`). Composite units (e.g. `N = kg/(m^2)`) are no longer supported. Furthermore, prefix units (e.g. `mm = m/1000`) are not supported either. This means that most units relevant to Catalyst (such as `µM`) cannot be used directly. While composite units can still be written out in full and used (e.g. `kg/(m^2)`) this is hardly user-friendly.
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