[cellml-discussion] Specifying the variable(s) of integration / independent variable(s) in MIASE

[Andrew Miller]

Dear all,

Based off the UML diagram at 
http://miase.cvs.sourceforge.net/*checkout*/miase/miaseOM/miaseOM/miaseOM.pdf?revision=1.5 
, I notice that the UniformTimeCourse UML class makes the assumption 
that the model is being evaluated across a time variable (in other 
words, that time is special in some sense).

I understand that one of the goals of MIASE is for it to be format 
independent. However, I believe that the assumption that time is special 
harms the applicability to languages such as CellML (which aim to 
represent models in a domain-independent form, which means that concepts 
like time are not built into the standard, but rather, are defined as 
part of the model).

As has been pointed out on an earlier thread on the MIAME mailing list, 
https://sourceforge.net/mailarchive/forum.php?thread_name=18374.18884.225456.303727%40mellow.local&forum_name=miase-discuss 
, I have previously defined a short draft specification designed to 
represent similar information (although I agree entirely with the idea 
of replacing this with a better specification common to multiple 
modelling languages).

The CellML Simulation Metadata focuses on the equivalent of the 
UniformTimeCourse simulation. However, these simulations are composed of 
one or more objects, which each associate with a variable in the CellML 
model and the range of the variable over the simulation (in the common 
case where time is the independent variable, there is one such object, 
which references time, and the initialStartTime and initialEndTime 
attributes on UniformTimeCourse simulation correspond to similar slots 
on the object in CSM).

It looks like a structure similar to that used in CellML Simulation 
metadata would make sense in MIASE too. This structure would have the 
additional benefit of providing some of the simulation information 
necessary for PDE simulations.

Best regards,
Andrew