Guitart-Pla Oriol, Kustagi Manjunath, Rügheimer Frank, Califano Andrea, Schwikowski Benno
Systems Biology Lab, Institut Pasteur, 75724 Paris Cedex 15, France and Department of Systems Biology, Columbia University, New York, NY 10032, USA.
Bioinformatics. 2015 May 1;31(9):1499-501. doi: 10.1093/bioinformatics/btu812. Epub 2014 Dec 18.
Research on methods for the inference of networks from biological data is making significant advances, but the adoption of network inference in biomedical research practice is lagging behind. Here, we present Cyni, an open-source 'fill-in-the-algorithm' framework that provides common network inference functionality and user interface elements. Cyni allows the rapid transformation of Java-based network inference prototypes into apps of the popular open-source Cytoscape network analysis and visualization ecosystem. Merely placing the resulting app in the Cytoscape App Store makes the method accessible to a worldwide community of biomedical researchers by mouse click. In a case study, we illustrate the transformation of an ARACNE implementation into a Cytoscape app.
Cyni, its apps, user guides, documentation and sample code are available from the Cytoscape App Store http://apps.cytoscape.org/apps/cynitoolbox
从生物数据推断网络的方法研究正在取得重大进展，但网络推断在生物医学研究实践中的应用却滞后了。在此，我们展示了Cyni，一个开源的“填充算法”框架，它提供了常见的网络推断功能和用户界面元素。Cyni允许将基于Java的网络推断原型快速转换为流行的开源Cytoscape网络分析和可视化生态系统的应用程序。只需将生成的应用程序放置在Cytoscape应用商店中，全世界的生物医学研究人员社区通过鼠标点击就能使用该方法。在一个案例研究中，我们展示了将ARACNE实现转换为Cytoscape应用程序的过程。
Cyni及其应用程序、用户指南、文档和示例代码可从Cytoscape应用商店http://apps.cytoscape.org/apps/cynitoolbox获取。
