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Nicolas,


MH>> c) Tools reading SBML should behave as follows:

>> 2) If a tool understands only sboTerms and not the math
>> formulas, it is like other tools today that do not
>> understand SBML maths. Users should be made aware of
>> how the tool is interpreting the SBML, and it might be
>> perfectly acceptable to the tool's users. As with
>> other tools that do not interpret the math, the tool
>> would not pass all parts of the SBML validation suite
>> and would not be considered fully SBML compliant.

NLN>That goes in favor of possible kineticLaws with only sboTerms IMHO.

I disagree for the following reasons:-

If you have connectivity to the sboTerm and, (as some suggest) it has to
have a mathematical translation attached to it so that the symbols are in
a standard order, then there is no excuse for not writing the mathML.
If you don't have the connectivity, a <notes> <B>kineticlaw is mass
action</B></notes> avoids problems of spelling errors that we have
sometimes seen when using some of the named equations. It is at least as
informative as the kineticLaws with only sboTerms.


Hugh Spence
GSK Scientific Computing and Mathematical Modelling
Medicines Research Centre
Gunnels Wood Road
Stevenage
UK
SG1 2NY