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

[Dagmar K. <da...@eb...>]

Hello Richard,

welcome on miase-discuss and sorry for the late reply. It is nice to 
hear that people in Edinburgh are interested in SED-ML!
Concerning your questions about a libsedml: we met last year during the 
SBML Hackathon and started developing *some* ideas for the SED-ML 
import/export for simulation tools. On the tool developers side, Frank 
Bergman (roadrunner), Ion Moraru (VCell), Henning Schmidt (SBToolbox) 
and Sven Sahle (COPASI) worked with us on the format and started some 
test implementation work during the meeting, but I haven't got any 
recent update how far they got and/or if they are still working on it.

I would be very glad if you could help with a libsedml for Java, maybe 
the others could join you to support other languages as well (as I think 
I remember Frank does not use Java...).
Did you think about using JAXB http://jaxb-builder.sourceforge.net/ to 
convert SED-ML into Java classes? In that case, the current XML Schema 
for SED-ML can be found on sourceforge 
http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/documents/schema/ . 
Please note that it is still a draft - however, you're more than welcome 
to work with it, please report any bugs you might find :-)
Otherwise, the UML diagrams can be found on the projects' homepage 
http://www.ebi.ac.uk/compneur-srv/sed-ml/index.html

I'd suggest you become a member of the MIASE project on sourceforge and 
start your own sub-project for the library work. You might even want to 
use another mailing-list for implementation issues and bug reporting? 
Just let me know what you need and I'll help if I can.

By the way, we are having our next MIASE meeting in April during the 
combined CellML meeting, if you'd be interested to join: 
http://www.cellml.org/workshop/workshop2009/

Best regards,
Dagmar Koehn

Richard Adams wrote:
> Hello,
>   My name is Richard Adams and I just wanted to introduce myself to  
> the list. I work as a software developer for the Goryanin and Millar  
> labs in Edinburgh, where there's a fair amount of interest in SED-ML  
> amongst modellers and developers here for  exchanging simulation expt  
> information, as we currently don't have any structured way of doing  
> this, even internally. I was wondering if there were any plans to  
> produce a 'libsedml' along the lines of libsbml? Just looking through  
> this list it's not very clear to me what the current status is - would  
> there be any point in us  attempting  an initial Java implementation  
> based on the UML specs,  if there will be a reference implementation  
> in the near future? Or, if there is already an effort underway to  
> develop such a library, is it something we could perhaps contribute  
> to, if that could help? As we're effectively starting from scratch,  
> and would have to develop our own internal exchange format anyway,  
> we'd be keen to help out, if we can.
>
> Thanks,
>
>
> Richard Adams
>
>