Lucian Smith

Ah, good to know. I assume that there's code somewhere that matches up those capabilities to the kisao terms in the SED-ML files? I assume that's the place we'd want...

OK, so that means that we need to add this information to the KiSAO ontology directly, though not using the parent/child hierarchy, but some other relationship. I'm not very familiar...

OK, it looks to me like that that get_substitutable_algorithms_for_policy doesn't deal with steady state algorithms at all, which would explain why I ran into my problem--I assume that without some...

The same problem exists for https://sed-ml.org/examples/L1V3/L1V3_repeated-steady-scan-oscli.omex which likewise believes that nothing can simulate the steady state simulations (in fact, at least tellurium and copasi can do both). Also: I updated...

This looks fixed? Closing, but feel free to re-open if there are any lingering issues.

The mathematical meaning of a SpeciesReference is its stoichiometry, so it's the 'stoichiometry' attribute. It's analogous to the 'size' attribute of a compartment, or the 'value' attribute of a Parameter....

I think I see your confusion! You wrote: > So the stoichiometry of X in reaction J0 is 1, but overridden with Xref. This isn't true! The stoichiometry of X...

Here's another way to explain it. In once place in the model, we define a parameter Z with a value of 0: ``` ``` And in another part of the...

Great! I'll watch for ways to put this in the docs; perhaps in the .m files in the test suite itself. I'm not sure what you mean by 'does these...

@paulflang : OK, I can imagine such a converter, that would convert any initial assignments to a double and just assign that to the 'stoichiometry' attribute, and (as you note)...