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Hello Stefan, All,

On Tue, Sep 22, 2009 at 4:40 PM, shoops <shoops@vbi.vt.edu> wrote:
> I understand that problem and I am very sympathetic. But this problem is
> not new. You have the same problem with mandatory attributes in L2. The
> difference is that there are just a few more mandatory fields in L3. A
> software using libsbml will just have to fill them, so that valid SBML
> can be created.

Another example: you open a file supposed to be SBML, but with a few
errors that make it invalid. You fix some of them, but in one place,
you can't fix it until you ask the author first. How do you save your
changes?

Maybe it is not a new problem, but apparently an unsolved one, and
one that is going to become more severe.

Usually, you would expect that if you can create it in memory, you
can create it on disk. You would be quite annoyed if your SDK would
not allow you to save unfinished code in your favourite programming
language until you removed all compile errors, or if your e-mail agent
would not allow you to save an unfinished message until you added a
subject and a valid recipient address, or your text processor would
not allow you to save anything that did not pass the spell-checker. If
libSBML does not provide me with a way to save unfinished work, then
who would?

If there is concern that some one may save an invalid model and then
share it, we could provide the option of saving a clearly marked
unvalidated file, maybe one where the "sbml" tag is replaced by
"sbml-unvalidated".

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
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