Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

Koji Kyoda,Shuichi Onami,Kenneth H L Ho,Yukako Tohsato

doi:10.1093/bioinformatics/btu767

Abstract

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats.Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis.Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/.Contact: sonami@riken.jpSupplementary Information: Supplementary data are available at Bioinformatics online.

Highlights

With the rapid progress in live-cell imaging and modeling techniques, quantitative spatiotemporal dynamics of biological objects such as molecules, cells and organisms can be obtained from experimental measurements and computer simulations (Keller, 2013; Mogilner et al, 2006; Oates et al, 2009)
A short summary of the quantitative biological dynamics data described in the Biological Dynamics Markup Language (BDML) file
Affiliation and e-mail address must be included with each BDML file

Summary

Introduction

With the rapid progress in live-cell imaging and modeling techniques, quantitative spatiotemporal dynamics of biological objects such as molecules, cells and organisms can be obtained from experimental measurements and computer simulations (Keller, 2013; Mogilner et al, 2006; Oates et al, 2009). Quantitative data can be obtained from computer simulations, e.g. single-molecule dynamics in Escherichia coli (Arjunan and Tomita, 2010) and microtubule-dependent nuclear dynamics in C.elegans embryos (Kimura and Onami, 2005). Most of these data are publicly available, it is often difficult to reuse them because of their intricate structure and the lack of detailed explanations of their formats

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