[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 cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] simulation metadata editing
Are the models/metadata/simulation-results in any sort of Version Control System (Subversion comes to mind)? By including VCS tags in the text of the model/metadata/simulation- results, then whenever these files are read/printed, the version number and date can be also displayed. With a version control system, it would also be possible for a user to be inspecting/using one (slightly older) version while a newer version of the simulation is being created. Also, the 'history' of a document can be displayed from the vcs- metadata, along with a log of all changes to a document. Simulation results can be declared 'stale' at some time delay or count older than the current version and deleted if storage space is a scarce resource. Bob G On Dec 4, 2006, at 03:36, Matt wrote: (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 cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
Re: [cellml-discussion] simulation metadata editing
Bob Gustafson wrote: Are the models/metadata/simulation-results in any sort of Version Control System (Subversion comes to mind)? Models are assigned a 'version' and a 'variant', and the model curation workflow means that models are never changed or deleted, instead a copy of the model is made in the CellML repository. The URL of the model therefore identifies the model. The file http://www.cellml.org/wiki/cellmlrepositories.pdf/download describes the difference between a variant and a version (note the document is somewhat out of date. In particular, we are using the Zope Object Database to store models, not CVS). By including VCS tags in the text of the model/metadata/simulation- results, then whenever these files are read/printed, the version number and date can be also displayed. With a version control system, it would also be possible for a user to be inspecting/using one (slightly older) version while a newer version of the simulation is being created. This is dealt with in the CellML repository, because the URL of the new model doesn't become accessible through the site until the workflow for adding the model has been completed. The URL is also an easier identifier for existing RDF tools to work with, and allows RDF metadata to refer to an explicit model. Also, the 'history' of a document can be displayed from the vcs- metadata, along with a log of all changes to a document. The CellML metadata specification provides for the model to describe changes which have been made to it in a machine readable format. Please refer to http://www.cellml.org/specifications/metadata#sec_mod_history Simulation results can be declared 'stale' at some time delay or count older than the current version and deleted if storage space is a scarce resource. Simulation results are not stored in the metadata, only the information needed to compute that data (some important metadata still needs to be specified, the simulation metadata specification is still a draft and not complete yet. Eventually, the simulation metadata should contain enough information to reproduce exactly identical simulation results, given the model). The idea behind this is that a model and the simulation metadata allows people not only to see the data a paper author is talking about, but to confirm that it really is the output from the simulation, and make modifications to parameters to see what effect they have. Simulation metadata can refer to variables in the model, so it is possible that simulation metadata could refer to a variable which no longer exists (this would make the simulation metadata invalid). However, external simulation metadata would typically refer to a model by the complete URL, including the version and variant, and so would need to be explicitly updated to point to a new version and variant (at which time the author of the simulation metadata should fix any problems like this). Best regards, Andrew ___ cellml-discussion mailing list cellml-discussion@cellml.org http://www.cellml.org/mailman/listinfo/cellml-discussion
