Support external defined observable functions

[matthiaskoenig]

In many cases, I want to optimize derived quantities from my model simulations, such as the area under the curve (AUC) or the maximum concentration (Cmax). These metrics cannot always be defined using simple mathematical expressions, so it would be extremely useful to support externally defined observable functions.

One idea is to extend the observableFormula syntax to include a special indicator or keyword that marks such observables as externally defined. For example:

id	formula
auc	external(time, caffeine)
cmax	external(time, caffeine)

Here, the keyword external signals that the computation is handled outside the standard expression engine, and the arguments specify the model symbols that the external function depends on (e.g., time, caffeine).

This approach would allow users to define and integrate custom observable functions into their own workflows. While such functions wouldn’t be directly reproducible (since they depend on custom user-defined logic), this mechanism would enable flexible implementation of more complex metrics for tasks like model calibration or optimization.

There are, of course, many challenges around how to define, manage, and execute these external functions in a consistent way, but even a simple mechanism to declare them would be a helpful step forward.

[dweindl]

Hi, I'd find it very difficult to accommodate that in PEtab in that generality. For the specific examples, I think it should be possible to encode them in SBML, but there sure may be other cases where that doesn't work. If really necessary, I would rather see that as a potential extension, where it is then also clearly defined where those observables are defined and how they are supposed to be evaluated.