Re: Draft proposal for a Systems Biology Results Markup Language
19 Aug '08 07:22
Pedro -- Thanks for getting this discussion started! As you know, I have
been arguing for years that models have a lot more to them than just the
current SBML contents. And that these things cannot just be added to SBML
for various pragmatic reasons.
I've got two comments. (All without even looking at your actual proposal
1) I think we need to recognize, if we are going to start on this, that
there are several data types that need attention. And of course, each such
type's files need a name, as defined by their suffix. Let's think about
some consistent naming convention NOW. I recommend that ALL of these file
formats have the naming convention Foo.sbmlX where X is a letter (2
letters?) that distinguishes the type, and hopefully has some sort of
mnemonic value. In your case it could be ".sbmlr" for "SBML - Results" or
perhaps ".sbmlsr" for "SBML - Simulation Results".
2) Again, there are lots of things that we need. I should dig up one of my
old emails about this... Anyway, from the point of view of my group, the
two most pressing things would be:
i) Parameter/Initial Conditions files. I've always said that putting this
information into the .sbml file is a horrible mistake, because a person
might want to change the parameter/ICs without changing the "model". Or
vice versa, for that matter!
ii) Experimental results description (as opposed to the simulation output
description). In other words, a definition of the phenomena that the model
is meant to match (and which, with suitable effort, the simulation output
can be measured against).
There are other things that we need, but they are more specialized or
less pressing for various reasons. I'd rank simulation output as third
on the list after these two in terms of importance.
Cliff Shaffer, Professor Phone: (540) 231-4354
Department of Computer Science Email: email@example.com
Virginia Tech, Blacksburg, VA 24061-0106 WWW: www.cs.vt.edu/~shaffer
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