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

Koji Kyoda; Kenneth H L Ho; Yukako Tohsato; Hiroya Itoga; Shuichi Onami

doi:10.1371/journal.pone.0237468

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

PLoS One. 2020 Aug 12;15(8):e0237468. doi: 10.1371/journal.pone.0237468. eCollection 2020.

Authors

Koji Kyoda^{1

2}, Kenneth H L Ho^{1

2}, Yukako Tohsato^{1

2

3}, Hiroya Itoga¹, Shuichi Onami^{1

2}

Affiliations

¹ Laboratory for Developmental Dynamics, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
² Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe, Japan.
³ Department of Information Science and Engineering, Ritsumeikan University, Shiga, Japan.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology
Databases, Factual
Programming Languages*
Software
Software Design

Grants and funding

This work was supported in part by the National Bioscience Database Center (NBDC) of the Japan Science and Technology Agency (JST) (to S.O.); Core Research for Evolutionary Science and Technology (CREST) Grant Number JPMJCR1511, JST (to S.O.); JSPS KAKENHI Grant Number JP18H05412 (to S.O.); the Strategic Programs for R&D (President’s Discretionary Fund) of RIKEN, Japan (to S.O.); and Open Life Science Platform, RIKEN, Japan (to S.O.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.