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The main reason to use GeoServer as platform  between data and visualization is to create WebServices from netCDF's, to style data and to enable the time variable so that the data in a netCDF can be animated in a Web interface. GeoServer can not handle netCDF files out of the box. You need to install an extension for GeoServer. These extensions can be found at the website of boundlessgeo (bear in mind that the extensions depend on the version of GeoServer that is used). 

The GeoServer netCDF plugin documentation has some notes on supported netCDF's. It is quite clear that only netCDF's are supported with the following dimensions:


where dimensions between () are optional. The variables should have at leas least dimension lat, lon. If time and z are dimensions, the order is time, z, lat, lon. 

The number of variables can vary from 1 to many as long as the dimensions are kept the same. This has implications in a lot of cases, especially where coordinates are not in lat/lon (WGS84) but in projections systems.