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.
Highlights
Recent advances in bioimage informatics and mechanobiological simulation techniques have led to the production of a large amount of quantitative data of spatiotemporal dynamics of biological objects ranging from molecules to organisms [1]
File size can be a critical benchmark for a data format because the transfer of large files often fails
We found that the BD5 format reduces the file size by ~80% in comparison with the Biological Dynamics Markup Language (BDML) format when the data is large
Summary
Recent advances in bioimage informatics and mechanobiological simulation techniques have led to the production of a large amount of quantitative data of spatiotemporal dynamics of biological objects ranging from molecules to organisms [1]. The XML-based BDML format has the advantages of machine/human readability and extensibility. It is often problematic for accessing and retrieving data when the size of the BDML file becomes too large (e.g., our programs cannot load a BDML file over 20 GB on a standard workstation). This problem arises because parsing an XML-based file often requires large computational resources to first read the whole file sequentially into computer memory.
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