[Non-urgent - Ready] Advanced introduction to Catalyst and its internal #890
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TorkelE
commented
May 30, 2024
| (k1*k2)/k2, X --> 0 | ||
| end | ||
| reactions(rn)[1].rate | ||
| ``` |
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Here I had more on symbolic simplifications performed, but looking at examples, it seems that these are never really done (even with structural_simplify).
TorkelE
commented
May 30, 2024
| !!! warn | ||
| When accessing species and parameters that are stored in a system using the above approach it is important to ensure that the model is *complete*. Model completeness is described [here](@ref ref). | ||
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| ## [Independent variables](@id advanced_intro_to_catalyst_independent_vars) |
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We should have a short section on independent variables somewhere (I hadn't really heard of this before MTK started using these), and somewhere here seemed natural. The main purpose of this one is that whenever we mention "independent variable" somewhere, we can link this section, and those who are unfamiliar with the term can read up on what it means.
TorkelE
commented
May 30, 2024
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| Symbolic variables-based representation is strictly superior to symbol-based representation. However, it is generally only used in combination with programmatic modelling (as during DSL-based modelling we never actually declare the symbolic variables, and thus cannot use them directly). To use symbolic variables-based representation in combination with the DSL, the [`@unpack` macro can be used](@ref ref). | ||
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| ### [System-based symbolic designation](@id advanced_intro_to_catalyst_designations_sys_symb) |
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The new section on how to access content of models got a more extensive description of this.
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Again not sure what to call this one.
This is basically a third introduction page. While the two previous ones are more or less parallel (i.e. have the same purpose, but for people who know/do not know Julia), this one is a continuation. It doesn't really go through any core stuff per see, but have two functions: