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Hello Mike

On Mon, 21 Sep 2009 22:03:10 -0700
"Michael Hucka" <mhucka@caltech.edu> wrote:

> It seems like the most sensible approach here is that
> advocated by Oliver and Lucian (and maybe Stefan in his last
> msg?), wherein libSBML has two types of methods in certain
> situations where the need arises: (a) ones that produce SBML
> that has defaults filled in and (b) ones that don't. Type
> (a) methods would be simply conveniences added by libSBML.
>
> Lucian's additional idea of adding XML comments is rather
> clever:
>
> <unit kind="mole" exponent="1" scale="0" multiplier="1" />
> <!-- Note: values for elements 'exponent', 'scale', and
> 'multiplier' were provided by libSBML and not by the user. To
> prevent this message from appearing, these elements need to be set
> explicitly -->

Unfortunately nobody will see them unless you look into the SBML file.
This means using SBML to load the above file will not give the user the
required information.

I know my approach to this might sound a little bit drastic but I think
that libsbml should refuse to write the file. It is the users/tools
responsibility to provide valid information. This means for an element
all non optional attributes must be provided.

Everything else will get us back into the situation we are having now
with L2 though on a different level. The SBML file now contains the
complete information however we have no idea whether this is the
information the user had in mind or made up by libsbml.

Thanks,
Stefan


--
Stefan Hoops, Ph.D.
Senior Project Associate
Virginia Bioinformatics Institute - 0477
Virginia Tech
Bioinformatics Facility II
Blacksburg, Va 24061, USA

Phone: (540) 231-1799
Fax: (540) 231-2606
Email: shoops@vbi.vt.edu
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