Re: [Miase-discuss] miaseOM

[Dagmar K. <dk...@in...>]

Hej Frank,
hej all,

> Thank you so much ... from the UML point of view things look nice, however
> it does not seem to correspond to what we had in the last version: 
>
> http://sys-bio.org/fbergman/MiaseBrainStorm_Biomodel8.xml
>   
I have taken that one as an example now.
> here we had a listOfModels as top level element, which in turn could consist
> of unchanged model instances or changed model instances with list of
> changes. In your UML diagram those still belong only to the tasks. 
>   
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 :)
> Also the listOfVariables was in the final version on the same level as
> ListOfFigures and ListOfColumns. And there was no listOfParameters anymore
>   
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?

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 :)


Does anybody want to suggest an SBase like class for MIASE? How do we 
name it and what attributes will it have?


[From Ions Mail]

 
- we describe 4 types of things: (i) what models, with or without changes, were simulated - in listOfModels, (ii) what were the simulation-specific settings - in listOfSimulations, (iii) what combination of the above two things were done in the actual simulation jobs - in listOfTasks, and (iv) what data was extracted, and how, from the one or more jobs described by the tasks, and how the data was represented graphically - in listOfOutputs


That's a good summary on what we agreed on. Raises the 
listOfModelChanges issue again!?

 
- the concrete details of an actual accomplishment of a "simulation experiment" described in a MIASE file would not be part of the MIASE specification, but would be included in SBML-style annotation elements (e.g. what simulator software was used, what version, on what platform, etc.)


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?

 
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!
 

Then, for the project developer issue: As Nicolas is the boss and he is 
on holiday... can we postpone the decision of to whome to give the 
sourceforge rights until FEB 17th? Until then, I can update the MIASE-OM 
versions for you if you want to!? Hope that is an exceptable compromise?!

Guys, thanks for all your input!
Have a nice weekend in case we don't speak again before (oh yes, I know 
we will).
Dagmar

-- 
Dagmar Koehn,GRK dIEM oSiRiS, http://www.diemosiris.de
Joachim-Jungius-Strasse 9, D-18059 Rostock, Germany
Tel: 0049-381-4987440, dk...@in...