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The sbml spec, section 4.7.7 on compartments says

"If present, the value of outside for a given compartment must be the
id field of another compartment already defined in the model."

MathSBML interprets this literally with an emphasis on "already
defined" to mean that:

<listOfCompartments>
<compartment id="c2" ... >
<compartment id="c1" outside="c2" ... >
</listOfCompartments>

is allowed but

<listOfCompartments>
<compartment id="c1" outside="c2" ...>
<compartment id="c2" ... >
</listOfCompartments>

is not allowed, because in the second case it refers to "c2" before
"c2" is declared.

I am wondering if that is the intent of this statement in the spec,
or if MathSMBL is over-reacting and should not complain about the
forward reference in the second case.

Bruce

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Bruce E Shapiro, PhD
Co-Director, Biological Network Modeling Center
The Beckman Institute at Caltech
1200 East California Blvd
Mail Code 139-74, Pasadena CA 91125-7400 USA
Telephone +1.626.395.8161
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The 8th International Conference on Systems Biology
Long Beach, California, USA 1-6 October 2007
http://icsb-2007.org
All ICSB inquiries: icsb2007-info@caltech.edu
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