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Bioinformatics. 2015 Apr 1;31(7):1044-52. doi: 10.1093/bioinformatics/btu767. Epub 2014 Nov 19.

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

Author information

1
Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and.
2
Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and National Bioscience Database Center, Japan Science and Technology Agency, Tokyo 102-0081, Japan.

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/.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
25414366
PMCID:
PMC4382901
DOI:
10.1093/bioinformatics/btu767
[Indexed for MEDLINE]
Free PMC Article

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