Forums

Hello Oliver,


On Tue, 22 Sep 2009 15:21:54 -0400
Oliver Ruebenacker <curoli@gmail.com> wrote:

> Hello Stefan, All,
>
> On Tue, Sep 22, 2009 at 9:37 AM, Stefan Hoops <shoops@vbi.vt.edu>
> wrote:
> > On Mon, 21 Sep 2009 22:03:10 -0700
> > "Michael Hucka" <mhucka@caltech.edu> wrote:
> >> 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.
>
> You are in the middle of editing a model, when your
> spouse/child/colleague/boss urgently needs to talk to you/use the
> computer. LibSBML does not let you safe, because you did not yet add
> all the required information. How do you save the model?

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.

Thanks,
Oliver


--
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
____________________________________________________________
To manage your libsbml-development list subscription, visit
https://utils.its.caltech.edu/mailman/listinfo/libsbml-development

For a web interface to the libsbml-development mailing list, visit
http://sbml.org/Forums/

For questions or feedback about the libsbml-development list,
contact sbml-team@caltech.edu