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SED-ML / sed-ml

Simulation Experiment Description Markup Language (SED-ML)
http://sed-ml.org
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Add `amount` and `concentration` as symbols #124

Closed matthiaskoenig closed 3 years ago

matthiaskoenig commented 3 years ago

To be able to set initial concentrations or initial amounts via SED-ML and to access the respective quantities in the data generators the additional symbols amount and concentration must be added. This works then in combination with the xpath selecting the object (species).

fbergmann commented 3 years ago

lets also add particlenumber.

nickerso commented 3 years ago

Is this specifically for SBML models (i.e., species) or should these concepts be applicable across modelling formats?

luciansmith commented 3 years ago

@nickerso : I believe this should indeed be applicable across modeling formats, but I'm not sure if it's quite as immediately useful to CellML (certainly it would work for BNGL, whose underlying object model is the same as SBML's).

This is what I have in the spec at the moment:

"symbol The optional symbol attribute of data type URN may be used in addition to the target when the particular value associated with the target may be described in multiple ways. In particular, a species whose value could be expressed either as a concentration or an amount may have its concentration set by using the symbol "urn:sedml:symbol:concentration", or its amount set by using the symbol "urn:sedml:symbol:amount"."

If we want to change these to KiSAO terms, that's fine with me; I'm happy to change the text once the terms exist.

(Also, I could add 'particleNumber' as an example in the spec or not, depending. It absolutely should be legal, but I don't know if it needs to be called out in the spec or if that would just be confusing.)

luciansmith commented 3 years ago

With https://github.com/SED-ML/sed-ml/commit/8361aa5e84912410db0eeee5310cfe462a540f9a I changed the above text to reference the new KiSAO terms instead of the sedml URNs. Other than that, everything is updated.