search

SED-ML / sed-ml

Simulation Experiment Description Markup Language (SED-ML)
http://sed-ml.org
5 stars 2 forks source link

Support richer inline descriptions of hybrid simulation algorithms #215

Open jonrkarr opened 2 years ago

jonrkarr commented 2 years ago

Presently, algorithms must be captured as a single KiSAO term. This creates the need to create additional terms for each hybrid combination. A more flexible approach would be to allow inline descriptions of combinations such as "X and Y" or "anyOf(X, Y, Z, ...)". This is motivated by tools such as Morpheus and E-Cell.

luciansmith commented 2 years ago

I believe there's no need to create unique terms for each hybrid combination. Instead, you just use KiSAO term 352 ('hybrid method') and then that term's algorithm parameters are the particular individual methods used. We actually have exactly this example on page 42 of the L1v4 spec.

I could see new KiSAO terms for 'anyOf' or 'and' as perhaps children of 352? But in general I agree that doing this in a generic way is the way to go.

jonrkarr commented 2 years ago

Yes, that's another option. We have used that route to capture nested algorithmic choices.

Still, I think this is worth discussion as part of broader revision for L2 about whether this is the best option or another scheme might be easier to understand.