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2015 ; 31
(7
): 1044-52
Nephropedia Template TP
gab.com Text
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English Wikipedia
Biological Dynamics Markup Language (BDML): an open format for representing
quantitative biological dynamics data
#MMPMID25414366
Kyoda K
; Tohsato Y
; Ho KH
; Onami S
Bioinformatics
2015[Apr]; 31
(7
): 1044-52
PMID25414366
show ga
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.