BD5: An open HDF5-based data format to represent quantitative biological dynamics data

BD5 is a new binary data format based on HDF5 (hierarchical data format version 5). It can be used for representing quantitative biological dynamics data obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) is an XML (Extensible...

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Bibliographic Details
Published in:PloS one 2020-08, Vol.15 (8), p.e0237468-e0237468
Main Authors: Kyoda, Koji, Ho, Kenneth H.L, Tohsato, Yukako, Itoga, Hiroya, Onami, Shuichi
Format: Article
Language:English
Subjects:
Binary data
Biological research
Biology
Biology and Life Sciences
Cell division
Computational biology
Computer and Information Sciences
Computer applications
Computer simulation
Datasets
Document markup languages
Dynamics
Engineering and Technology
Extensible Markup Language
Format
Informatics
Laboratories
Language
Methods
Open data
Physical Sciences
Research and Analysis Methods
Social Sciences
Software
Technology application
XML (Extensible markup language)
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Description
Summary:BD5 is a new binary data format based on HDF5 (hierarchical data format version 5). It can be used for representing quantitative biological dynamics data obtained from bioimage informatics techniques and mechanobiological simulations. Biological Dynamics Markup Language (BDML) is an XML (Extensible Markup Language)-based open format that is also used to represent such data; however, it becomes difficult to access quantitative data in BDML files when the file size is large because parsing XML-based files requires large computational resources to first read the whole file sequentially into computer memory. BD5 enables fast random (i.e., direct) access to quantitative data on disk without parsing the entire file. Therefore, it allows practical reuse of data for understanding biological mechanisms underlying the dynamics.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0237468