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The title of each list item is a link to the company or project website.
- Applied Biosystems
- Pacific Biosciences
- Oxford Nanopore
- Genomedata
- SDCubes
- mz5
- Unifying Biological Image Formats with HDF5
- Quantitative data: learning to share
The primary image data from Applied Biosystem's next generation DNA sequencers are stored in HDF5.
The primary image data from Pacific Biosciences' next generation DNA sequencers are stored in HDF5.
Oxford Nanopore uses HDF5 to store their primary instrument data. Their file format is open source and is available at its Sourceforge project page.
Genomedata is a file format for storing multiple tracks of genome-anchored numerical data (similar to BigWig and related formats).
Hoffman MM, Buske OJ, Noble WS. The Genomedata format for storing large-scale functional genomics data. Bioinformatics. 2010 26(11):1458-1459 LINK
Semantically Typed Data Cubes (SDCubes) combine XML and HDF5 to leverage the strengths of each for storing numerical data and metadata.
Millard BL, Niepel M, Menden MP, Muhlich JL, Sorger PK. Adaptive informatics for multifactorial and high-content biological data. Nature Meth. 2011 8:487-492. LINK
mz5 is a way to store mass spectrometry data in HDF5. It is a part of the proteoWizard project.
Wilhelm M, Kirchner M, Steen JA, Steen H. mz5: space- and time-efficient storage of mass spectrometry data sets. Mol Cell Proteomics. 2012 11(1):O111.011379. LINK
This article describes the advantages of HDF5 as an image format and how it could be used to unify the many disparate biological image formats.
Dougherty MT, Folk MJ, Zadok E, Bernstein HJ, Bernstein FC, Eliceiri KW, Benger W, Best C. Unifying Biological Image Formats with HDF5. Commun ACM. 2009 1;52(10):42-47. LINK
This article describes the use of HDF5 and several other technologies when dealing with large, heterogeneous datasets which need to be shared among researchers.
Baker M. Quantitative data: learning to share. Nature Meth. 2012 9:39-41. LINK
If you use HDF5 in a bioinformatics context and would like your project listed here, please email derobins at hdfgroup dot org.
- - Last modified: 13 February 2014