Re: [Miase-discuss] miaseOM

[Frank B. <fbergman@u.washington.edu>]

Heja, 

I guess I keep this short: 


> I have taken that one as an example now.



> I have changed that in the new version (on sourceforge). I was just
> wondering: What was the reason that we did not put the listOfChanges
> inside the changedModels? I guess it was because we wanted to apply one
> change to more than one model. Still, the way you described the
> listOfModels above, it would make more sense to put the changes
> directly on the changedModels... Just so that we are sure that the way we
do
> things is correct :)

Correct, you might want to apply changes to for example a series of models,
all coming from the same WildType. We thought it could look like this: 

<ListOfChanges>
	<SBMLParameterChange id="PChange1"
someAttributesTellingWhatParameterToChangeHow/>
	<SBMLAssignmentRuleChange id = "AChange1"
someMoreSpecificAttributesAndElementscontainingarule/>
</ListOfChanges>
<ListOfModels>
	<UnchangedModel id="M1" source="BIOMODEL86.xml" type="SBML / CellML
/ BioPAX"/>
	<ChangedModel id="M2" name="Model86 with changes"
modelReference="M1">
		<ListOfChangeReferences>
			<ChangeReference reference="PChange1"/>
		</ListOfChangeReferences>
	</ChangedModel>
</ListOfModels>


> You are right. I did not put those changes in the UML so far, because I
> actually couldn't remember the reason(s) to do that.
> Can anyone explain again?

Sorry ... explain what?

> 
> Concerning your remark on my data types: I think I didn't put any so
> far actually (all being strings). Thought to fix that later on. But
> suggestions are welcome :)

Hm ... I am sure I saw a "positiveInteger" on those types :) 

> 
> Does anybody want to suggest an SBase like class for MIASE? How do we
> name it and what attributes will it have?
Actually, you could just take it as is from the SBML spec, strip the SBO
term and call it SBase / MBase

> Do we give the annotation element any specific structure or do we just
> say: "Put the extra information in the annotation" and provide an
> example of how to do it?

I would say for right now we do not have to clarify that point :) ... ymmv

> 
> Basically, we are describing that in order to produce a certain
> "simualtion result" (e.g. a figure in a paper), one would have to take
> one, or more, models (SBML or otherwise), apply none, or some, changes
> to them (different parameters, or initial conditions, etc.), then run
> one, or more, simulations, using some specific simulator settings, than
> take the variable values obtained from those simulations and combine
> them using one or more arbitrary mathematical expressions
> (postprocessing), and then use the resulting collection of numerical
> data sets ("columns") and put them together in one or more graphs, as
> specified.  Whew!
> 

There you go ... that's quite a mouthful ...  I would have preferred
something simpler myself, but in order to keep it extensible I guess this is
the way it has to be. 

> Have a nice weekend in case we don't speak again before (oh yes, I know
> we will).

And a great weekend from here :) 
Cheers
Frank