Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.
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DOI：
10.1093/bioinformatics/btu767
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发表时间：
2015-04-01
期刊：
影响因子：
--
通讯作者：
Onami S
中科院分区：
文献类型：
--
作者：
Kyoda K;Tohsato Y;Ho KH;Onami S
动机：活细胞成像和建模技术的最新进展导致产生了大量关于生物对象(如分子、细胞和生物体)的时空动力学的定量数据(来自实验测量和计算机模拟)。尽管许多研究小组独立致力于开发可视化和分析这些数据的软件工具，但由于数据格式不同，这些工具往往相互不兼容。结果：我们开发了一个开放的统一格式，生物动力学标记语言(BDML；当前版本：0.2)，它为从分子到细胞再到生物体的对象提供了一个表示定量生物动力学数据的基本框架。BDML基于可扩展标记语言(XML)。它的优点是机器和人类的可读性和可扩展性。BDML将提高数据可视化和分析软件工具的开发和评价效率。可用性和实现：BDML的规范和模式文件可在http://ssbd.qbic.riken.jp/bdml/.免费在线获得联系方式：sonami@riken.jp补充信息：生物信息学在线提供补充数据。
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.jp Supplementary Information: Supplementary data are available at Bioinformatics online.
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影响因子：
3
作者：
Boyle, Thomas J.;Bao, Zhirong;Murray, John I.;Araya, Carlos L.;Waterston, Robert H.
通讯作者：
Waterston, Robert H.
影响因子：
5.8
作者：
Hucka, M;Finney, A;Wang, J
通讯作者：
Wang, J
DOI：
10.1007/s11693-009-9047-2
发表时间：
2010-03-01
期刊：
Systems and synthetic biology
影响因子：
--
作者：
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通讯作者：
Tomita, Masaru
影响因子：
64.8
作者：
Grill, SW;Gönczy, P;Hyman, AA
通讯作者：
Hyman, AA
影响因子：
64.5
作者：
Kozlowski, Cleopatra;Srayko, Martin;Nedelec, Francois
通讯作者：
Nedelec, Francois