>
> OK. I've said what I had to say as clearly as I know how. I think
> it's a
> vital issue that we ignore at our peril. But this is a community
> effort. A
> lot of you have not yet posted to this thread. What do you think?
> Should I
> just let this go?
As you ask for our opinion as part of the community, here is what we
do. For our visualizations we definitely wanted to display modifiers
for all SBML models that we get. as we
1) can not count on the list of modifiers to be available (or
complete) and
2) strongly disagree with the take that a missing modifier makes an
SBML model invalid to the point where some other software were to
refuse to read the model at all
we silently parse the kinetic laws and slip missing modifiers into the
ListOfModifiers. This solved the problem for us.
However we stop with the kinetic law. We do not go ahead and test
rules, whether they *might* contain additional modifiers. This might
very well lead to the problem that mike was thinking about that you
might end up with all species being included as modifiers. If that
were intended by a modeler the creating software should have put them
there in the first place.
| 
09 Aug '08 01:02
