Hi Matt, To repond to your points:
1) I think the current state in the simulation metadata specification is that it is recommended best practice to specify a rdf ID for every simulation, mainly driven by the example of being able to define graphs for that simulation. Do you think we need to make it stronger and state that rdf ID's are required in the simulation metadata specification? 2) I think this is already the case, and I for one am certainly defining simulation metadata externally to model XML files (in some cases). 3) Currently the graph metadata refers to a given variable by specifying both a simulation and a model. But potentially a change in either the simulation metadata and/or the model will result in different results from the graph metadata (or invalidate the metadata completely in the worst case). 4) I agree, and think this belongs to a similar discussion on how CellML 1.1 model hierarchies function within the model repository. As a side note, I am currently using HDF5 to store my simulation results. Each simulation data set is annotated with most (if not all, I loose track of what I include) of the information defined by the simulation metadata and the URI of the particular model being used. As such, when I process a given piece of graph metadata I can check the simulation metadata in the result data set against the simulation metadata referenced from the graph metadata and force a particular simulation or group of simulations to be re-run if required. While this type of approach can help in terms of model development and the local use of models and metadata, I think once a model and/or metadata is included in the repository we need to be very careful about any changes that are allowed and that permitted changes are always made within the model curation workflow. Andre. -- David Nickerson, PhD Research Fellow Division of Bioengineering Faculty of Engineering National University of Singapore Email: [EMAIL PROTECTED] -----Original Message----- From: [EMAIL PROTECTED] on behalf of Matt Sent: Mon 04-Dec-06 5:36 PM To: For those interested in contributing to the development of CellML. Subject: [cellml-discussion] simulation metadata editing > > (peter wrote) > > > > 2. Need ability to edit metadata on website models -e.g. for sensible > > defaults on time integration parameters and graphical We need to be very careful to preserve a relationship between a simulation and the data obtained from it. I see a problem occurring where we have metadata describing a simulation which is bound to a model, and a graphical output (or set of data points) that are supposed to represent the output of this simulation, which is also bound to the model. There is only an implicit relation between the two such that updating the simulation metadata now produces an inconsistency with the graphs (or associated data points) of results. I think we need to think about in the simulation metadata: 1) uniquely identifying simulations (an rdf ID within the model). 2) referencing the model uri this simulation is referring to (there shouldn't be anything stopping the simulation metadata being picked up and processed in isolation of the model) 3) binding graphs of results to the simulation and not the model. 4) changing the metadata of a simulation needs to force a version change (or variant) in a similar way to models so that a mismatch between graphs or result sets can be detected. This part of the discussion thread seems to belong on CellML discussion now. cheers Matt _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
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