Welker David, Demchak Barry
University of California, San Diego, La Jolla, CA 92093, USA.
F1000Res. 2014 Jul 1;3:150. doi: 10.12688/f1000research.4546.1. eCollection 2014.
Much of the biologically significant functionality in Cytoscape is contained within third-party add-ons, called plugins in Cytoscape 2 and apps in Cytoscape 3. In the transition from Cytoscape 2 to Cystoscape 3, some of the underlying assumptions upon which plugins relied changed, requiring a significant porting effort for plugins to work as Cytoscape 3 apps. PanGIA is a Cytoscape add-on (http://apps.cytoscape.org/apps/pangia) designed to analyze and visualize genetic interaction data in light of physical interaction data. In order to convert the PanGIA plugin to an app, various challenges, including those related to a transformed data model, concurrency, and randomization had to be overcome. In the process, the ability to control randomization was added to the GUI, a feature which was not only integral to the porting process, but which also ensures more easily reproducible scientific analysis for PanGIA users. Most authors of Cytoscape 2 plugins will face similar challenges porting their software to work with Cytoscape 3, and this paper gives details of how the PanGIA port addressed them.
Cytoscape中许多具有生物学意义的功能都包含在第三方插件中，在Cytoscape 2中称为插件，在Cytoscape 3中称为应用程序。从Cytoscape 2过渡到Cytoscape 3时，插件所依赖的一些基本假设发生了变化，这要求对插件进行大量的移植工作才能使其作为Cytoscape 3应用程序运行。PanGIA是一个Cytoscape插件（http://apps.cytoscape.org/apps/pangia），旨在根据物理相互作用数据来分析和可视化遗传相互作用数据。为了将PanGIA插件转换为应用程序，必须克服各种挑战，包括与转换后的数据模型、并发和随机化相关的挑战。在此过程中，在图形用户界面（GUI）中添加了控制随机化的功能，该功能不仅是移植过程所必需的，而且还确保PanGIA用户能够更轻松地进行可重复的科学分析。大多数Cytoscape 2插件的作者在将其软件移植到与Cytoscape 3兼容时都会面临类似的挑战，本文详细介绍了PanGIA移植是如何解决这些问题的。
