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. 2023 Oct 18;19(10):e1011530. doi: 10.1371/journal.pcbi.1011530

Fig 4. The simulation pipeline of a Catalyst model, with internal intermediates displayed.

Fig 4

Code as written by the user (yellow background), and as generated internally by Catalyst and ModelingToolkit (blue and grey backgrounds respectively) are shown, in addition to the generated structures and their fields (blue background, some of the internal fields are omitted in all displayed structures). (a) A symbolic ReactionSystem for a reversible dimerisation reaction is created using either the DSL, or programmatically using the Symbolics computer algebraic system. (b) The ReactionSystem can be converted into a ModelingToolkit ODESystem structure, corresponding to a symbolic RRE ODE model. (c) By providing initial conditions, parameter values, and a time span, the ODESystem can be simulated, generating an output solution. The generated (internal) Julia code for evaluating the derivatives defining the ODEs, which gets compiled and is input to the ODE solver, is displayed in grey. At each step, the user has the ability to investigate and manipulate the generated structures.