Mike Folk
ABSTRACT
In this paper, we give an overview of the HDF5 technology suite and some of its applications. We discuss the HDF5 data model, the HDF5 software architecture and some of its performance enhancing capabilities.
- http://www.hdfgroup.org/HDF5/doc/index.htmlGoogle Scholar
- HDF5 User's Guide http://www.hdfgroup.org/HDF5/doc/UG/index.html.Google Scholar
- HDF5 Reference Manual http://www.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html.Google Scholar
- Koziol, Q. 2011. HDF5 Encyclopedia of Parallel Computing. To appear.Google Scholar
- Date, C. J. and Darwen, H. 1998. Foundation for Object/Relational Databases -- The Third Manifesto. Addison Wesley. Google ScholarDigital Library
- Thomsen, E. 2002. OLAP Solutions: Building Multidimensional Information Systems. Second Edition. Wiley. Google ScholarDigital Library
- Brown, P. 2001. Object-Relational Database Development. Informix Press. Google ScholarDigital Library
- HDF5 File Format Specification Version 2.0 http://www.hdfgroup.org/HDF5/doc/H5.format.htmlGoogle Scholar
- Performance Analysis and Issues http://www.hdfgroup.org/HDF5/doc/H5.user/Performance.htmlGoogle Scholar
- Universal File Interface (UFI) http://www.barrodale.com/bcs/universal-file-interface-ufiGoogle Scholar
- HDF5 Tools http://www.hdfgroup.org/HDF5/doc/RM/Tools.htmlGoogle Scholar
- HDFView http://www.hdfgroup.org/hdf-java-html/hdfview/Google Scholar
- MathWorks http://www.mathworks.com/Google Scholar
- Mathematica http://www.wolfram.com/Google Scholar
- VisIt https://wci.llnl.gov/codes/visit/Google Scholar
- EnSight http://www.ensight.com/Google Scholar
- HDF5 High-level APIs http://www.hdfgroup.org/HDF5/doc/HL/Google Scholar
- Gosink, L. et al. 2005. HDF5-FastQuery: Accelerating Complex Queries on HDF5 Datasets using Fast Bitmap Indices. http://crd.lbl.gov/~kewu/ps/LBNL-59602.pdfGoogle Scholar
- Mainzer, J. and Koziol, Q. 2010. RFC: High-Level HDF5 API routines for HPC Applications. http://www.hdfgroup.uiuc.edu/RFC/HDF5/HPC-High-Level-API/H5HPC_RFC-2010-09-28.pdfGoogle Scholar
- Folk, M. and Heber, G. and Koziol, Q. 2011. HDF5 Information Set. To appear.Google Scholar
- W3C. 2010. XQuery 3.0: An XML Query Language. http://www.w3.org/TR/xquery-30/Google Scholar
- Nam, B. and Sussman, A. 2003. Improving Access to Multidimensional Self-describing Scientific Datasets. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.78.2998&rep=rep1&type=pdf Google ScholarDigital Library
- Altet, F. and Vilata, I. 2007. OPSI: The indexing system of PyTables 2 Professional Edition. http://www.pytables.org/docs/OPSI-indexes.pdfGoogle Scholar
- Chan, C-Y. and Ioannidis, Y. E. 1998. Bitmap Index Design and Evaluation. SIGMOD. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.87.1270&rep=rep1&type=pdf Google ScholarDigital Library
- Lahdenmaeki, T. and Leach, M. 2004. Relational Database Index Design and the Optimizers. John Wiley & Sons, Inc. Google ScholarDigital Library
- Alekseyenko, A. V. and Lee, C. J. 2007. Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics Vol. 23, No 11, pp. 1386--1393. Google ScholarDigital Library
- BioHDF http://www.biohdf.org/Google Scholar
- HDF5 Image and Palette Specification. 2007. http://www.hdfgroup.org/HDF5/doc/HL/RM_H5IM.htmlGoogle Scholar
- HDF5 Table Specification. 2002. http://www.hdfgroup.org/HDF5/doc/HL/H5TB_Spec.htmlGoogle Scholar
- HDF5 Dimension Scale Specification and Design Notes. 2005. http://www.hdfgroup.org/HDF5/doc/HL/H5DS_Spec.pdfGoogle Scholar
- Howison, M. et al. 2010. Tuning HDF5 for Lustre File Systems. https://secure.nersc.gov/projects/presentations/HDF5_DonofrioNERSC.pdfGoogle Scholar
- Introduction to the HDF5 Packet Table API. 2005. http://www.hdfgroup.org/HDF5/doc/HL/H5PT_Intro.htmlGoogle Scholar
- Informix DataBlades. 2010. http://www-01.ibm.com/software/data/informix/blades/Google Scholar
- Data Cartridge -- Oracle Wiki. 2010. http://wiki.oracle.com/page/Data+CartridgeGoogle Scholar
- Message Passing Interface. 2010. http://www.mcs.anl.gov/research/projects/mpi/Google Scholar
- NASA's Earth Observing System. 2010. http://eospso.gsfc.nasa.gov/Google Scholar
- The ECS SDP Toolkit Home Page. 2010. http://newsroom.gsfc.nasa.gov/sdptoolkit/TKDocuments.htmlGoogle Scholar
- NESDIS Satellite Information. 2010. http://www.nesdis.noaa.gov/SatInformation.htmlGoogle Scholar
- NetCDF (network Common Data Form). 2010. http://www.unidata.ucar.edu/software/netcdf/Google Scholar
- SciDB. Overview of SciDB, Large Scale Array Storage, Processing and Analysis. SIGMOD' 10. http://www.scidb.org/download/sigmod691-brown.pdfGoogle Scholar
- Kuehn, J. A. 1996. Faster Libraries for Creating Network-Portable Self-Describing Datasets. Cray User GroupGoogle Scholar
- XML Linking Language (XLink) Version 1.1. 2010. http://www.w3.org/TR/xlink11/Google Scholar
- Standardizing the Next Generation of Bioinformatics Software Development with BioHDF. BioHDF BoF SC09. 2009.Google Scholar
- Halpin, T. 2001. Information Modeling and Relational Databases. Morgan Kaufmann Publishers. Google ScholarDigital Library
- The NetCDF-4 Data Model. 2010.Google Scholar
- The "Classic" NetCDF Data Model. 2010.Google Scholar
- Barrodale Computing Services. 2010. http://www.barrodale.com/Google Scholar
- Aura OMI NO2 Level 3 Global (0.25 deg Grids) Data Product-OMNO2e Version 003. http://disc.sci.gsfc.nasa.gov/Aura/data-holdings/OMI/omno2e_v003.shtmlGoogle Scholar
- NASA. OMI Data Products and Data Access. 2010. http://disc.sci.gsfc.nasa.gov/Aura/overview/data-holdings/OMI/index.shtmlGoogle Scholar
- NASA. Aura. 2010. http://disc.sci.gsfc.nasa.gov/AuraGoogle Scholar
- Ramapriyan, H. K and Moses, J. 2011. NASA's Earth Science Data Systems -- Lessons Learned and Future Directions. To appear.Google Scholar
- HDF OPeNDAP Project. 2010. http://www.hdfgroup.org/projects/opendap/Google Scholar
- OPeNDAP: Open-source Project for a Network Data Access Protocol. 2010. http://www.opendap.org/Google Scholar
- Yang, M. and Lee H. 2009. Using a Friendly OPeNDAP Client Library to access HDF5 data. The 89th AMS annual meeting.Google Scholar
- Gallagher, J. et al. 2007. The Data Access Protocol -- DAP 2.0. ESE-RFC-004.1.1Google Scholar
- Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S. and Karolchik, D. 2010. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics, 26, 2204--2207. Google ScholarDigital Library
- Li, H. 2011. Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics, 27, 718--719. Google ScholarDigital Library
- Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G. and Durbin, R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078--2079. Google ScholarDigital Library
- Mason, C. E., Zumbo, P., Sanders, S., Folk, M., Robinson, D., Aydt, R., Gollery, M., Welsh, M., Olson, N. E. and Smith, T. M. 2010. Standardizing the next generation of bioinformatics software development with BioHDF (HDF5). Adv Exp Med Biol, 680, 693--700.Google ScholarCross Ref
- Shendure, J. and Ji, H. (2008) Next-generation DNA sequencing. Nat Biotechnol, 26, 1135--1145.Google ScholarCross Ref
- Making Science Data Easier to Use with OPeNDAP. 2010. http://wiki.esipfed.org/index.php/Making_Science_Data_Easier_to_Use_with_OPeNDAP#EOS_HDF_Data_Readability_.28without_OPeNDAP.29Google Scholar
- Open Data Protocol (OData). 2010. http://www.odata.org/Google Scholar
- Kahn, S. D. 2011. On the future of genomic data, Science, 331, 728--729.Google ScholarCross Ref
Index Terms
- An overview of the HDF5 technology suite and its applications
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