an open format for representing quantitative data of biological dynamics
Rapid advances in live-cell imaging and modeling techniques enable many research groups to obtain a huge amount of quantitative biological dynamics data on spatiotemporal dynamics of biological objects such as molecules, cells, and organisms. However, their data cannot often be compared and analyzed by the same software tools because of different data formats. BDML (Biological Dynamics Markup Language) aims to facilitate data exchange and development of software tools for data visualization and analysis.
BDML is an open format for representing quantitative biological dynamics data. It is based on Extensible Markup Language (XML). By using BDML, a wide variety of quantitative biological dynamics data from molecules to cells to organisms can be described. To describe a large size of quantitative biological dynamics data, we developed BD5 data format, which supports HDF5-based storage of quantitative biological dynamics data as the extension of BDML data format.
BDML schema and specification: http://ssbd.qbic.riken.jp/bdml/
BD5 specification: will be available soon.
Koji Kyoda, Yukako Tohsato, Kenneth H.L. Ho, Shuichi Onami (2015) Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. Bioinformatics 31, 1044-1052.