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An alternative would be to store each individual profile/trajectory/time series in a separate netCDF file. Collections would consist of a set of netCDF files stored in a zip or jar file. The zip file could also contain some sort of (XML?) manifest file that could contain metadata about the collection as a whole. Any metadata associated with an individual profile would be stored as a global attribute in the appropriate netCDF file. Editing a profile would be as simple as extracting the netCDF file from the archive, rewriting it, and then storing it back in the jar file.
I'd be hesitant about requiring splitting up such data into one file for each time step as from an archive point of view it would lead to the possibility of loosing some files and make the number of files to keep track of excessively large. A colleague of mine routinely outputs wind profiler data as netCDF using time and altitude as the dimensions, storing data for an entire day's worth of profile in the same file. Saying that he has also informed me that for some of the lower level products he does zip groups of netCDF files up to cut down on the size of data being moved around per block of data. I.e. rather than saying data should be split up into separate files time wise it would be better to take an open minded view based on the requirements of the data provider and end user. Graham