How to interpret constant species in variable-sized compart.

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The specification documents for SBML.

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How to interpret constant species in variable-sized compart. #216

Closed sbmlsecretary closed 2 years ago

sbmlsecretary commented 12 years ago

Raised by Lucian during the SBML Editors' meeting during HARMONY 2012:

Consider a model with a species with no rules about how the species itself changes (no reactions, no rules), with the attribute 'hasOnlySubstanceUnits=false', and which is in a compartment whose size changes. Its amount does not change, but its concentration does. Is it valid to give this species the attribute 'constant=true', or must it be flagged 'constant=false'?

This is never explicitly stated in the spec.

Reported by: mhucka

Original Ticket: sbml/sbml-specifications//215

sbmlsecretary commented 12 years ago

The conclusion was that, even though the concentration will change, you can still flag this as 'constant=true' so that an algebraic rule can tell whether or not it may or may not determine this value.

Original comment by: luciansmith

sbmlsecretary commented 12 years ago

I agree with the proposed change and that it should be done.

Original comment by: luciansmith

sbmlsecretary commented 12 years ago

I am accepting this issue as valid.

Original comment by: ccmyers

sbmlsecretary commented 12 years ago

I am accepting this issue as valid.

Original comment by: lenov

sbmlsecretary commented 12 years ago

Considering we decided not to change the validation rule for this, but only add a clarification, this can be an L2v4 spec edit, not a l2v5-only change.

Original comment by: luciansmith

sbmlsecretary commented 12 years ago

I see no point in a L2V4 spec edit since we are releasing L2V5.

Original comment by: lenov

sbmlsecretary commented 12 years ago

There is a misunderstanding about the categories of bug reports. A report like this, about the L2v4 specification, is something to be fixed by issuing either a release 2, or an L2v5. The report, however, is still *about* L2v4. That is why it belongs here. We then use the reports as the basis for constructing the changes to be put in L2v5 (or if the change is small enough, L2v4r2).

Original comment by: mhucka

sbmlsecretary commented 10 years ago

labels: Level 2 Version 4 --> Level 2 Version 4, Level 3 Version 1 Core

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

status: open --> accepted
Group: Reported-Proposed --> Accept-conformance-implications

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

We actually discussed and came to a conclusion on this issue at an editor's meeting several years ago. The upshot was that the 'constant' flag on a Species a) references its amount, not (directly) the concentration, and b) is needed for algebraic rules.

See https://sourceforge.net/p/sbml/sbml-specifications/211/ for another aspect of this same issue.

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

I accept this issue as valid, and agree with the proposed solution.

Original comment by: mhucka

sbmlsecretary commented 10 years ago

I accept this issue as valid, and agree with the proposed solution.

Original comment by: dagwa

sbmlsecretary commented 10 years ago

status: accepted --> closed

Original comment by: luciansmith

sbmlsecretary commented 10 years ago

Fixed in SVN for both L2v5 and L3v2, and will be part of the forthcoming release of those specifications.

Original comment by: luciansmith