Should species amounts & compartment sizes be >= 0?

[sbmlsecretary]

SBML L2v2r1, no particular page or line number.

Nowhere does the SBML specification say that quantities of species (concentration or amounts) and compartment sizes must be non-negative. Should it?

Or to ask it another way, is there any type of model (perhaps not biochemical, but more generally anything in systems biology someone might want to model) where these initial values might legitimately be negative?

[Problem originally noted by Darren Wilkinson in private email to me on Sep. 22.]

MH

Reported by: mhucka

Original Ticket: "sbml/sbml-specifications//53":https://sourceforge.net/p/sbml/sbml-specifications//53

[sbmlsecretary]

Logged In: YES user_id=862059 Originator: NO

I agree that the change should not be taken.

Original comment by: shoops

[sbmlsecretary]

Logged In: YES user_id=862059 Originator: NO

I would not explicitly state that the species amounts or compartment size must be >= 0. On the one hand one might even consider 0 to be problematic for the compartment size. Whereas on the other hand is might be conceivable that in an initial assignment for a delay function either of the quantities has to be negative. I do not want to restrict the freedom of any modeler, even if means allowing unphysical models in SBML.

Original comment by: shoops

[sbmlsecretary]

Logged In: YES user_id=641982 Originator: NO

I agree with Stefan - who knows what is going on in the mind of a modeller - it is up to software to say "Hang on!! Are you sure about that"

Original comment by: sarahkeating

[sbmlsecretary]

Logged In: YES user_id=641982 Originator: NO

I agree that the change should not be taken.

Original comment by: sarahkeating

[sbmlsecretary]

Logged In: YES user_id=1045203 Originator: NO

I agree with Stefan and Sarah and therefore mark the issue as closed.

Original comment by: lenov

[sbmlsecretary]

Logged In: YES user_id=1045203 Originator: NO

I agree that the change should not be taken.

Original comment by: lenov

[sbmlsecretary]

• status: open --> closed

Original comment by: lenov

[sbmlsecretary]

• Group: Reported-Proposed --> Rejected-No_action

Original comment by: luciansmith

[sbmlsecretary]

Fixing the Milestone tags of old closed issues.

Original comment by: luciansmith

[sbmlsecretary]

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Original comment by: shoops