An important component of scientific work is being able to take your data with you as you move from one position to another, and being able to work with the data files on the computer systems at your new institute. Similarly, it's vital to be able to exchange data files with colleagues or just read your own files in multiple different packages.
Therefore it is important to have standards-based data formats that are openly and well documented so that anyone can implement a reader and writer for the format. Please use this page to list:
- the data formats you use
- the Debian packages needed for working with the format
- software used with that format that's not in Debian
hdf5
[http://hdf.ncsa.uiuc.edu/["HDF5"]/ Hierarchical Data format] is an extremely flexible format, possibly too flexible for its own good
- Open Spec: YES
- Packages
[http://packages.debian.org/stable/science/hdf5-tools hdf5-tools] (and many other related packages)
FITS
[http://fits.gsfc.nasa.gov/ Flexible Image Transport System] was developed for astronomy, but could be used by many disciplines. One notable feature is good support for World Coordinates, i.e. translation between pixel coordinates and physical coordinates such as Longitude & Latitude, Frequency, Stokes parameters (polarisation). Arbitrary numbers of dimensions are supported as well, but not so flexibly as in hdf5.
- Open Spec: YES
- Packages
[http://packages.debian.org/stable/devel/libcfitsio2 libcfitsio2] (plus perl wrappers)
[http://packages.debian.org/stable/math/pdl pdl] display & analysis
[http://packages.debian.org/stable/science/saods9 saods9] image viewer
XML variants
[wiki:Self:VOTable http://www.ivoa.net/Documents/latest/VOT.html] Virtual Observatory Table format
- Open Spec: YES
- Packages
Links
Chemical MIME/file types
[http://www.ch.ic.ac.uk/chemime/ Chemical MIME types] can be introduced to the Linux desktop with [http://cvs.wgdd.de/cgi-bin/cvsweb/chemical-mime-data/ chemical-mime-data] ([http://sourceforge.net/projects/cdk old site]). You will find most information about these MIME types and the project in the source of the package.
All chemical applications (e.g. [http://packages.debian.org/xdrawchem xdrawchem] or [http://packages.debian.org/openbabel openbabel]), which can handle the freedesktop.org MIME specs benefit from this package. Older specs for e.g. GNOME <= 2.4 or KDE <= 3.x are a bit harder to support, because their magic databases are not expandable.
The MIME-types are not part of the official shared-mime-info package/projects, because these MIME-types have never been registered with IANA (see also [http://lists.freedesktop.org/archives/xdg/2005-May/006858.html]).
General
[http://www.microformats.org/ microformats] may be a useful avenue to explore
A [http://www.openraw.org/ raw] digital camera format is essential for scientific imaging work
- [http;//www.iptc.org/["IPTC4XMP"]/ IPTC metadata] looks interesting and has fairly open licence terms