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sbmlsecretary / test-sbml-specifications

Test repo for transferring issues.
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Inconsistency in example on p.114 #41

Closed sbmlsecretary closed 2 years ago

sbmlsecretary commented 17 years ago

SBML L2v3r1 p. 114 line 61:

The text says the values are in concentration, but the model SBML gives them as amount. Which should was intended? Either the text or the model are incorrect, depending on whether the intention is to have the initial values given in concentrations or amounts.

Reported by: mhucka

Original Ticket: "sbml/sbml-specifications//97":https://sourceforge.net/p/sbml/sbml-specifications//97

sbmlsecretary commented 17 years ago

Logged In: YES user_id=1045203 Originator: NO

This is not the case. The *species* are effectively in amount. What the text says is "The *species variables* X, Y1n, Y1c, and Y2 *in the following equations* are all in terms of concentrations". In the equation, the symbols represent concentrations because hasOnlySubstanceUnits is not true.

I think this is not an issue and propose to delete it.

Original comment by: lenov

sbmlsecretary commented 17 years ago

Original comment by: lenov

sbmlsecretary commented 17 years ago

Original comment by: mhucka

sbmlsecretary commented 17 years ago

Logged In: YES user_id=343670 Originator: YES

OK, I see that now, but I think the text too easily leads the reader to think otherwise. The reason this question came up at all is that someone emailed me about the passage with this same confusion.

I think it wouldn't hurt for us to consider a rewording. I've changed the title of this issue report to reflect that. Nicolas, are you ok with at least trying to change the wording to explicitly point out what you have said in your note above? (The one with timestamp 2007-08-31 02:56.)

Original comment by: mhucka

sbmlsecretary commented 17 years ago

Logged In: YES user_id=1045203 Originator: NO

How about replacing:

"The species variables X, Y1n, Y1c, and Y2 in the following equations are all in terms of concentrations,"

by

"In the following equations, the symbols of the species X, Y1n, Y1c, and Y2 represent concentrations (because while the initial values are given in amount, the spatial dimension of the respective compartements is higher than 0, and the attribute hasOnlySubstanceUnits is never set, and therefore defaults to false)."

Original comment by: lenov

sbmlsecretary commented 17 years ago

Original comment by: mhucka

sbmlsecretary commented 17 years ago

Logged In: YES user_id=343670 Originator: YES

I take back what I wrote in 2007-08-31 06:54 -- I remember now why I thought it was inconsistent, and I believe there is still a problem.

The statement online 61 is that the following variables are in concentrations. Then on line 63, Y2 = 1. This must be interpreted as a concentration if we believe the statement on line 61, correct? But then in the SBML of the model, the value of species Y2 is given as initialAmount="1" in a compartment whose volume is 5. According to the SBML, then, the initial concentration of that species is 1/5, not 1.

Am I correct, or do I need to go find stronger coffee?

Original comment by: mhucka

sbmlsecretary commented 17 years ago

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I agree with the two changes: The rewording, and the change of concentration to 1/5

Original comment by: lenov

sbmlsecretary commented 17 years ago

Original comment by: lenov

sbmlsecretary commented 17 years ago

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

Original comment by: lenov

sbmlsecretary commented 17 years ago

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

Original comment by: sarahkeating

sbmlsecretary commented 17 years ago

Original comment by: lenov

sbmlsecretary commented 17 years ago

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The concentration needs to be changed to 1/5.

Original comment by: shoops

sbmlsecretary commented 17 years ago

Logged In: YES user_id=862059 Originator: NO

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

Original comment by: shoops

sbmlsecretary commented 17 years ago

Original comment by: mhucka

sbmlsecretary commented 17 years ago

Logged In: YES user_id=343670 Originator: YES

Fixed for SBML L2v3r2.

Original comment by: mhucka