From: Andrew Miller <[EMAIL PROTECTED]> Subject: Re: [cellml-discussion] automated connection creation Date: Wed, 08 Aug 2007 09:39:10 +1200 Message-ID: <[EMAIL PROTECTED]>
ak.miller> James Lawson wrote: ak.miller> > It would be really easy to create some kind of script / automation ak.miller> > process that automatically connects up variables of the same name if ak.miller> > they have matching interfaces. ak.miller> > ak.miller> > Say you have a component A with variables a and b. a is defined in A and ak.miller> > has pub interface out, while b is imported from B, where it is defined. ak.miller> > So you also have component B with variables a and b, a having pub ak.miller> > interface in and b having pub interface out. ak.miller> > ak.miller> > Surely it would be very simple to just have some button to click in ak.miller> > PCEnv or COR that links up these variables? I'm not saying this is done ak.miller> > by default - you'd have to select the option once you'd defined all your ak.miller> > variable interfaces. It wouldn't be able to handle connecting variables ak.miller> > with different names, but it would at least be a start. There would also ak.miller> > be problems with variables with the same name that aren't supposed to be ak.miller> > all connected together, but this, IMO, is just bad CellML practice. ak.miller> > Imports might be an issue too. I find creating connections the most ak.miller> > tedious aspect of coding up a CellML model, and I think the benefits ak.miller> > would vastly outweigh the problems, and of course, people wouldn't have ak.miller> > to use it... ak.miller> > ak.miller> > I also thought, surely someone has already thought of this and thrown ak.miller> > the idea out. But if this could be implemented it would be extremely ak.miller> > useful. ak.miller> > ak.miller> I don't think that it is as simple as using names - I don't think it is ak.miller> always bad practice to use the same names for two different things - ak.miller> this is in fact the norm for when you import the same thing twice. You ak.miller> would also not always get the topology of the model correct if you tried ak.miller> to compose models this way. ak.miller> ak.miller> Noma's group at Kyoto University uses their Cell Model Ontology metadata ak.miller> to allow the tool to "edit the composition of a model with intelligent ak.miller> assistance" (refer to Takao' Shimayoshi's slides from the CellML Workshop, ak.miller> http://www.cellml.org/workshop2007/presentations/070403cellmlworkshopshimayoshi-handout.pdf/download ak.miller> page 3 in the PDF). If we were going to implement something like this, I ak.miller> think we would want to base it on metadata about the interpretation of ak.miller> variables and not on variable names, and it would have to be a ak.miller> semi-supervised process not a completely automated one, to get the ak.miller> topology right. Thanks for referring our research. I also think the full-automatic connection using only names has some issues. In mixing several models, a model A, for example, uses a name 'V' for the membrane potential, and another model B uses the same name 'V' for the cell volume. So, our strategy is first identifying components and variables using intelligent estimations and user corrections, then automatically connecting variables. The estimation currently uses lexical keyword matching of names, matching of units, and structural analysis of the original CellML file. To get the detail algorithm, please refer to our paper, doi:10.2197/ipsjdc.2.726. Best wishes, SHIMAYOSHI Takao. _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
