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Re: [Miase-discuss] miase-discuss
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From: Moraru,Ion <Mo...@NE...> - 2008-02-10 21:52:33
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Hi Dagmar, I subscribed to the maillist, and I'm posting this message there, too, but I am keeping the email recipients until everybody subscribes - I can't see who subscribed already, since the list of subscribers is hidden... Also, I've added Mike to the recipients list - Mike, please check out the sourceforge page for latest OM diagram and a little digest of our previous email exchanges that Dagmar has put on the maillist. OK, now getting to the subject: 1. developer list / who has rights to upload - sure, it is fine to wait for Nicolas to get back until acting on that 2. current version of OM diagram (I looked at version 1.5) is now much improved, close to the final example and proposal from Okinawa 3. I have an updated .dia file that includes some of the additions/changes that I am describing below, should I just email it to you for now? 4. I like the alternative of subclassing from MBase, instead of SBase (but where MBase provides /almost/ the same stuff as SBase), it is cleaner that way, especially since we agreed that MIASE should support more formats than just SBML 5. Modification class - should have one subclass for now, SBMLModelModification, specific on how to describe changes to a Model that is in SBML format 6. ChangedModel and UnchangedModel classes should be ChangedSBMLModel and UnchangedSBMLModel, reflecting the current support for SBML format; their "type" attribute (inherited from model) should be "SBML"; additional similar subclasses are to be expected in the future, e.g. for CellML, BioPAX3, VCML models etc. 7. Open question regarding #6 above: should the language version and level be specified in the "type" attribute? i.e. should we have a finer granularity, like type=SBML_L2_R3? 8. ChangedModel should have 1 required attribute, modelReference, referencing one UnchangedModel; it should also have 1 or more elements referencing 1 or more Modification to be applied to the unchanged model 9. Expression class needs some more significant changes. Basically, it will have a listOfDeclaredParameters (declared locally, that is), which you already have OK; then it needs a listOfSymbols (see 10 below); and it needs a Math element, which again is OK the way you have it (the syntax in the example which you are referring to is indeed specific to the MathML language) 10. Symbol class - this defines the symbols that are being used in addition to the declared parameters in the Math of an Expression in order to compute the actual values for the data column; a Symbol can be of 2 types: (i) a predefined symbol, like ___TIME___ (the only one that we discussed in Okinawa, for simulation time), or (ii) a locally defined symbol, which could be (most often) a variable from a model (e.g. a Species in an SBML model), but also a parameter from within that model; such locally defined symbol needs 2 attribute, a taskReference (from which it can uniquely access the model and simulation results), and an identifierReference (e.g. a SpeciesReference or a ParameterReference), pointing to the approipriate id in the Model referenced by the Task Sorry if #10 sounds complicated, it really isn't, maybe I'm just not explaining it very clearly... (for example an Expression class might want to describe something like (v1+v2)/2 where it would define symbols v1 and v2 as some species references from some task(s) and "2" as a locally declared parameter) Cheers, Ion ________________________________ From: Dagmar Koehn [mailto:dk...@in...] Sent: Fri 2/8/2008 2:53 AM To: Moraru,Ion Cc: Frank Bergmann; Henning Schmidt; Boss; Sven Sahle; Akira Funahashi Subject: miase-discuss Hej Ion, hej all, ignoring all the comments in all the other mails for the moment, I just wanted to ask you to subscribe to miase-discuss on sourceforge - that might be a much more convenient way of communicating... and now that the mailing list is (finally) working - why not use it :) mia...@li... Dagmar -- Dagmar Koehn,GRK dIEM oSiRiS, http://www.diemosiris.de <http://www.diemosiris.de/> Joachim-Jungius-Strasse 9, D-18059 Rostock, Germany Tel: 0049-381-4987440, dk...@in... |
