Barsky Aaron, Munzner Tamara, Gardy Jennifer, Kincaid Robert
Department of Computer Science, University of British Columbia.
IEEE Trans Vis Comput Graph. 2008 Nov-Dec;14(6):1253-60. doi: 10.1109/TVCG.2008.117.
Systems biologists use interaction graphs to model the behavior of biological systems at the molecular level. In an iterative process, such biologists observe the reactions of living cells under various experimental conditions, view the results in the context of the interaction graph, and then propose changes to the graph model. These graphs ser ve as a form of dynamic knowledge representation of the biological system being studied and evolve as new insight is gained from the experimental data. While numerous graph layout and drawing packages are available, these tools did not fully meet the needs of our immunologist collaborators. In this paper, we describe the data information display needs of these immunologists and translate them into design decisions. These decisions led us to create Cerebral, a system that uses a biologically guided graph layout and incorporates experimental data directly into the graph display. Small multiple views of different experimental conditions and a data-driven parallel coordinates view enable correlations between experimental conditions to be analyzed at the same time that the data is viewed in the graph context. This combination of coordinated views allows the biologist to view the data from many different perspectives simultaneously. To illustrate the typical analysis tasks performed, we analyze two datasets using Cerebral. Based on feedback from our collaborators we conclude that Cerebral is a valuable tool for analyzing experimental data in the context of an interaction graph model.
系统生物学家使用相互作用图来模拟生物系统在分子水平上的行为。在一个迭代过程中，这些生物学家观察活细胞在各种实验条件下的反应，在相互作用图的背景下查看结果，然后对图模型提出修改建议。这些图作为所研究生物系统的一种动态知识表示形式，并随着从实验数据中获得新的见解而不断演变。虽然有许多图布局和绘图软件包可用，但这些工具并不能完全满足我们免疫学家合作者的需求。在本文中，我们描述了这些免疫学家的数据信息显示需求，并将其转化为设计决策。这些决策促使我们创建了Cerebral系统，该系统使用生物引导的图布局，并将实验数据直接整合到图显示中。不同实验条件的小多重视图和数据驱动的平行坐标视图能够在图的背景下查看数据的同时分析实验条件之间的相关性。这种协调视图的组合使生物学家能够同时从许多不同的角度查看数据。为了说明所执行的典型分析任务，我们使用Cerebral分析了两个数据集。根据合作者的反馈，我们得出结论，Cerebral是在相互作用图模型的背景下分析实验数据的一个有价值的工具。
