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Sorry for the delay, but with everybody on vacation, this has been
lying around for some time.
In case anybody is wondering. This is the next version of a proposal
for a layout extension to SBML2.

This version includes some important new features like the possibility
to group several layout objects and the possibility to specify edges to
denote relations.
We also incorporated the suggestions we got from the discussion. E.g.
the syntax is now more SBML like as references attributes are called
after the thing that is being referenced. So the reference attribute to
the SBML compartment id in the compartmentGlyph is now called
compartment. We also got rid of all the ...GR(s), they are now called
...Glyph(s).
There are some smaller changes (See "List of Changes" in the document).

We tried to come up with layout problems that can not be solved with
this proposal and so far we have not been able to come up with any. So
if you know of some layout that can not be specified in terms of this
proposal, please let us know.

There has been a new proposal for a layout extension by Jonathan Webb a
few days ago. We would have preferred for Jonathan to give us some
feedback as to what he didn't like about the proposal that was already
there and so help to speed things up, because this is what a discussion
list is for and this is the reason why we made the proposal to the
discussion list in the first place.
Looking at his proposal we think that it is missing some things
that our proposal already has and that we think are important.

1) Jonathan himself stated in his document that it was not a full 3D
specification, but rather 2.5D. But with the inclusion of geometry
information on compartments in upcoming versions of SBML, we think that
the proposal should include the possibility to render objects in 3D.

2) Jonathan's proposal takes color specifications from HTML and limits
colors to RGB instead of RGBA. Partly transparent objects might really
be useful when working with 2.5D or 3D layouts, so colors should really
have an alpha channel.

3) As has been noted in earlier discussions on this list, there was an
agreement that metaids should not be used to reference objects. Jonathan
does this in his edge.

4) In the edge object of his proposal, Jonathan references the species
reference of the model for the edge, but since a species can be
represented by several graphical objects in a layout, there is no easy
way to
find out which of possibly several species glyphs should
be connected to a given reaction. He tries to circumvent this problem
by identifying the species glyphs by coordinates which will fail if to
species glyphs share the same coordinates.


We are aware of the fact that so far our proposal only includes layout
information since we wanted to separate the layout information from the
render information. So in order to get an agreement on the layout part,
we did not do much work on the render part yet. As we took from the
discussion, there was some agreement as to that it was a good idea to
separate render and layout information. As stated above, we tried to
find layout examples that could not be implemented with this proposal
and so far we found none. If someone finds such an example we would be
glad to hear of it so we could make the necessary changes. We also
would very much like more feedback on what else people are missing from
the proposal since this is the only way we can reach an agreement.
Mails that only state that something is missing without ever
elaborating on this are therefore not very helpful and won't help in
reaching an agreement.
We feel that this proposal has come a long way and we thank all the
people that participated in the discussion. We don't know, if this new
proposal has everything that people expect of it, but as far as we are
concerned, we would be ready to move on to getting the specification
for the render information written down. Now if the majority of people
on this list feel that they would rather go with Jonathan's proposal
and work from there, we would appreciate it if you let us know as soon
as possible.

Ralph

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