[Miase-discuss] MIME type - OM discrepancies - XPATH again

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

Hello again, attached the result of simulating the sample files. The next
step for me would be to actually export miase.

--- MIME type ---
I was also again considering the source problem. I really find it
problematic, that we have the separation of the description file and various
source files (the models, measurement data and such). Having multiple files
will ultimately result in one of those files not being present. I know that
Dagmar and Nicolas where definitely against embedding a miase description in
an SBML file. So how about this:

- we place the miase description file (e.g: miaseBioModels21.xml) along with
all source files that are on the local machine (i.e: having a URI beginning
with a file:// prefix) (and all other files you might want to include later
on) into an archive with the same name as the miase description file, but an
extension we can all agree upon ... like ..uhm '.miase' ... 
- next we register a MIME sub-type like application/miase+xml with the
network working group by  submitting a rfc. 

And voila, applications receiving a file with that mime type, just unzip it,
read the miase description, and find all sources along with it, no hassle,
no more missing files, and no dependence on a particular model description
language. Also, thanks to the whole thing just being a single file, suddenly
export of miase files will be so much easier and adoption by tool authors
should go along easier. This is an issue to be addressed before version 1
leaves the door. 

--- minor issues with the OM and sample running apart ---

- The OM describes the datagenerator as having a 'mathExpression' while the
example uses 'math' ... my prototype right now uses math as well, but this
might be changed. 
-  The OM defines a 'Column' element without attributes and a 1:1
relationship with a DataGenerator, right now I see no need for that one,
listOfColumns should contain a list of DataGenerators. 
- ChangeMath and ChangeXML are really one and the same, if you just modify
the XPATH target. Also for a tool, it is just as difficult to implement
change attribute, as is changeXML, so this really can be in the current
version I think. 
- Measurement data should not be next to output in the OM, as you will need
it somewhere close to a datagenerator and/or task. But we already said to do
that in later versions. 
- plot3D, will probably not work like it is drawn in the OM, this would
result in a plot3d, with a list of curve and a dangling list of surfaces
that only have a z axis. This should be revised. IMHO plot3d should extend
'output' directly and define logx,logy,logz and a list of surfaces.
-AnySimulationType is specified as blue, aka version 1, but is not specified
at all, it really should be used later :) 

--- still the gripe about XPATH and default namespaces ---
In my last mail I pointed out the trouble with XPATH and default namespaces,
but heard no feedback about it. What do you think?

Cheers
Frank