title: Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.
abstract: BACKGROUND
  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.
  
  
  METHODS
  A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and.
authors.forename: Koji
authors.initials: K
authors.lastname: Kyoda
authors.affiliation: Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and.
authors.forename: Yukako
authors.initials: Y
authors.lastname: Tohsato
authors.affiliation: Laboratory for Developmental Dynamics, RIKEN Quantitative Biology Center, Kobe 650-0047, Japan and.
authors.forename: Kenneth H L
authors.initials: KH
authors.lastname: Ho
authors.affiliation: 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.
authors.forename: Shuichi
authors.initials: S
authors.lastname: Onami
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003198:Computer Simulation; D016208:Databases, Factual; D006801:Humans; D008954:Models, Biological; D011381:Programming Languages; D015398:Signal Transduction; D012984:Software; D014584:User-Computer Interface