Re: [Miase-discuss] sed-ml library?

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

Hello Richard,

>
>   The project is at
>
>     http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/jlibsedml/
>
>   Any input on API design etc very welcome!

I'd be hoping for library in the style of libSBML, i.e. a C/C++ based  
library with wrappers for other languages. Though I do realize that  
generation from the schema won't quite work for that.

>
>   Dagmar suggested further implementation issues to be discussed on
> the sourceforge miase bugzilla.
>
>   Just working with this now there seem to be quite a lot of issues  
> to address
> in order to achieve an implementation. Here are some,
>
>   A Schema issues:
>   --------------

I ended up not using the Schema as such but rather the schema +  
example + the notes from our discussions. But your points are valid  
and should be adopted.

The biggest issue I had in my implementation was with XPath and the  
problem that SBML models have a default namespace, which is not  
supported by XPath.

http://shrinkster.com/13w7


>
>
>   B)    Coordination with model
>   ----------
>     PRevious posts have raised this issue, is there any progress on
> this? There is a lot of validation that can be done just with the
> sedml file, but if we want to check that a parameter or variable name
> exists, or the xpath is correct,
>   then we need access to the model. It seems to me that there are
> different scenarios:
>
>        1) A model is referenced to a validated public repository e.g.,
> BioModels
>           In this case the library can download the model. This seems
> the  easiest solution, as revisions of Biomodels are versioned (btw,
> would a version attribute  for the model element be useful?) and so a
> tool can make decisions on whether the model is correct or not.
>

While 1) is possible personally, I prefer a more local solution :),  
IMHO we don't need a version attribute, the model that is pointed to  
is the one the software should read, not another version.

>
>         2) A model is not yet in the public domain, but for example
> the client wants to share  simulation info with a collaborator. In
> this case probably the model and  the sedml file would have to sent
> together in a zip file to preserve
>   relative file paths, but this leaves quite an onus on the user or
> tool to keep the two files coordinated.
>

as pointed out in my previous mail, I don't think there will be any  
hassle whatsoever with this solution. as soon as we think of it not as  
a zip file, but as a miase-file that only software handles that will  
be resolved.

>         3) Could a model file be optionally  embedded in a sedml file?
>   This gets round the need to keep sedml independent of sbml, also a
> single file gets round the file coordination issue,  but it raises new
> problems of keeping in synch possibly multiple copies of a model. But
> for non-curated models that must be an issue anyway?
>

personally I don't like this option too much. If an embedding solution  
is wanted, I prefer it to work the other way around, have MIASE  
embedded in i.e. SBML. That is the solution  that was favored by some  
people in the discussions as well.

> C Validation requirements
> --------------------------

the offered validations certainly make sense. The only thing i like to  
add, is that i like my id's to be unique in general.

Cheers
Frank