Re: [Miase-discuss] ChangeMath

[Nicolas Le n. <le...@eb...>]

Frank Bergmann wrote:

>> ChangeMath COMPUTES a change. For instance, you can compute the new  
>> value for an attribute of model A based on the value of an attribute  
>> of model B and an external parameter. Therefore the listOfVariables  
>> use an XPath.
> 
> I remember a post about this from way back. I still don't quite  
> follow. An example here would really help. To me it seems like this is  
> an added complication we don't need. 

The complication was the reason why it was in white and not blue, and YES, 
I know everything is yellow in the last UML.

> At the time of writing, the tool  
> writing the ChangeMath will have to know about model B and the  
> external parameter, hence this could be written as  
> <changeAttribute ... sparing the reader the complications, of sorting  
> out the math, resolving the model it belongs to (which again might be  
> in a model format, the reader does not understand)

That removes one of the potential roles of SED-ML, which is the integration 
of different models, developed by different people. I understand what you 
say in the case of COPASI or RoadRunner exporting a SED-ML file. Now, 
imagine a large-scale project, similar in size to the metabolic network we 
published in August (33 authors, 2152 species, 1857 reactions), and some 
subgroups are in charge of the metabolism, some of the signalling. 
Phosphorylation in the signalling models depends on ATP, decided by the 
metabolic models. The consortium can write generic SED-ML files, that can 
be immune of changes in the initial concentration in ATP, set by the 
metabolic guys.

But I agree with you. If you can use ChangeAttribute or ChangeXML, use 
them. But in the future there will be need of computing. Let's keep it 
"white" until we need it (which may come with parameter scans)

-- 
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468, Skype:n.lenovere, AIM:nlenovere, MSN:nle...@ho...
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/