title: Standardizing the next generation of bioinformatics software development with BioHDF (HDF5).
abstract: Next Generation Sequencing technologies are limited by the lack of standard bioinformatics infrastructures that can reduce data storage, increase data processing performance, and integrate diverse information. HDF technologies address these requirements and have a long history of use in data-intensive science communities. They include general data file formats, libraries, and tools for working with the data. Compared to emerging standards, such as the SAM/BAM formats, HDF5-based systems demonstrate significantly better scalability, can support multiple indexes, store multiple data types, and are self-describing. For these reasons, HDF5 and its BioHDF extension are well suited for implementing data models to support the next generation of bioinformatics applications.
authors.affiliation: Geospiza Inc, Seattle, WA 98119, USA.
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Mason
authors.forename: Paul
authors.initials: P
authors.lastname: Zumbo
authors.forename: Stephan
authors.initials: S
authors.lastname: Sanders
authors.forename: Mike
authors.initials: M
authors.lastname: Folk
authors.forename: Dana
authors.initials: D
authors.lastname: Robinson
authors.forename: Ruth
authors.initials: R
authors.lastname: Aydt
authors.forename: Martin
authors.initials: M
authors.lastname: Gollery
authors.forename: Mark
authors.initials: M
authors.lastname: Welsh
authors.forename: N Eric
authors.initials: NE
authors.lastname: Olson
authors.forename: Todd M
authors.initials: TM
authors.lastname: Smith
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D003628:Database Management Systems; D030541:Databases, Genetic; D016415:Sequence Alignment / Q000592:standards / Q000706:statistics & numerical data* / Q000639:trends; D017421:Sequence Analysis / Q000592:standards / Q000706:statistics & numerical data* / Q000639:trends; D012984:Software / Q000592:standards / Q000639:trends; D012985:Software Design; D014584:User-Computer Interface