Dear all, I'm considering HDF5 for my storage needs in simulating a CellML model under multiple parameter scenarios. HDF5 is designed for efficient storage, retrieval, navigation and subsetting of huge data sets [1], with annotation [2]. I plan on storing both raw and post-processed data, so that if I detect problems at a higher level, I can go back and look at details and possibly re- run those simulations. David Nickerson described a similar approach in an earlier post [3].
However, setting up the data structure with annotations for physical units and such is quite time-consuming. On the other hand, the CellML representation holds all the required information. It would be very helpful to auto-generate an HDF5 data structure to hold output from simulations of CellML models. Such a tool should be fairly easy to write for someone familiar with both HDF5 and CellML, and would apply to all possible CellML models. I guess it would be overly restrictive to make an output format part of the CellML metadata specification. However, offering a standard output format would save duplication of effort and make it easier to share simulation results for further visualization and analysis. I'd like the opinions of the CellML regulars, in particular whether anything similar has been discussed previously. Best regards, Jon Olav Vik [1] http://www.hdfgroup.org/about/hdf_technologies.html [2] http://www.hdfgroup.org/training/HDFtraining/UsersGuide/MF_Annot.fm1.html [3] http://article.gmane.org/gmane.text.xml.cellml.general/234/match=hdf5 _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
