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sbmlteam / sbml-test-suite

The SBML Test Suite is a conformance testing system. It allows developers and users to test the degree and correctness of the SBML support provided in a software package.
https://sbml.org/software/sbml-test-suite/
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Compartment assignment rules #8

Closed luciansmith closed 8 years ago

luciansmith commented 16 years ago

From Chris Myers:

I've discovered what appears to be another problem in examples 310 to

  1. In these examples, there is a rule:

compartment = p1 * S1

where S1 is a species with HasOnlySubstanceUnits equal to false.
Therefore, S1 in the equation above should be a concentration.
However, S1 is given a value of initialAmount of 1.5. Which means
that S1 above should be 1.5 divided by the size of the compartment
(initially 0.15), so 1.5 / 0.15 or 10 which times p1 (0.1) yields 1
for the initial compartment size. Then, S1 is not 10 but actually
1.5, which means the compartment size is 0.15. This process repeats,
and the compartment size cannot be set consistently.

These need to be changed :-)

Reported by: sarahkeating

luciansmith commented 15 years ago

Using a species that belongs to a compartment in an assignment rule for that compartment is an indeirect cyclic reference and therefore is not valid.

Original comment by: sarahkeating

luciansmith commented 15 years ago

These models have been changed to include a varying parameter which is used in the compartment assignment rule; thus causing the compartment to vary.

Original comment by: sarahkeating

luciansmith commented 14 years ago

Original comment by: sarahkeating