DIPSBC - data integration platform for systems biology collaborations
DIPSBC - data integration platform for systems biology collaborations
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DOI：
10.1186/1471-2105-13-85
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发表时间：
2012-05-08
影响因子：
3
通讯作者：
Herwig, Ralf
中科院分区：
文献类型：
--
作者：
Dreher, Felix;Kreitler, Thomas;Herwig, Ralf
背景：现代生物医学研究通常是由世界各地的实验室合作组织的。特别是在系统生物学中，分析复杂的分子系统，需要生成和解释异质数据以进行解释，例如从基因表达研究和质谱测量到用于检测分子相互作用和功能测定的实验技术。XML已经成为表示和交换这些数据的最重要的格式。然而，除了标准的发展仍然是一个根本缺乏的数据集成系统，能够利用这些交换格式，组织在一个综合的方式和数据的解释和analysis.Results的应用程序链接的数据：我们已经开发了DIPSBC，一个交互式的数据集成平台，支持合作研究项目，基于Foswiki，Solr/Lucene，和特定的助手应用程序。我们描述了实现的主要功能，并突出了系统的性能与几个用例。该系统的所有组件都是独立于平台的开源开发，因此可以很容易地被研究人员采用。该平台的示例性安装还提供了几个助手应用程序以及系统使用和设置的详细说明，可在http://dipsbc.molgen.mpg.de.Conclusions上获得：DIPSBC是一个用于中等规模协作项目的数据集成平台，已经在几个研究协作中进行了测试。由于其模块化设计和XML数据格式的合并，它非常灵活且易于使用。
Background: Modern biomedical research is often organized in collaborations involving labs worldwide. In particular in systems biology, complex molecular systems are analyzed that require the generation and interpretation of heterogeneous data for their explanation, for example ranging from gene expression studies and mass spectrometry measurements to experimental techniques for detecting molecular interactions and functional assays. XML has become the most prominent format for representing and exchanging these data. However, besides the development of standards there is still a fundamental lack of data integration systems that are able to utilize these exchange formats, organize the data in an integrative way and link it with applications for data interpretation and analysis.Results: We have developed DIPSBC, an interactive data integration platform supporting collaborative research projects, based on Foswiki, Solr/Lucene, and specific helper applications. We describe the main features of the implementation and highlight the performance of the system with several use cases. All components of the system are platform independent and open-source developments and thus can be easily adopted by researchers. An exemplary installation of the platform which also provides several helper applications and detailed instructions for system usage and setup is available at http://dipsbc.molgen.mpg.de.Conclusions: DIPSBC is a data integration platform for medium-scale collaboration projects that has been tested already within several research collaborations. Because of its modular design and the incorporation of XML data formats it is highly flexible and easy to use.