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Guiding the interactive exploration of metabolic pathway interconnections

机译：指导代谢途径互连的互动探索

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摘要

Approaches to investigate biological processes have been of strong interest in the past few years and are the focus of several research areas, especially Systems Biology. Biochemical networks as representations of processes are very important for a comprehensive understanding of living beings. Drawings of these networks are often visually overloaded and do not scale. A common solution to deal with this complexity is to divide the complete network, for example, the metabolism, into a large set of single pathways that are hierarchically structured. If those pathways are visualized, this strategy generates additional navigation and exploration problems as the user loses the context within the complete network.In this article, we present a general solution to this problem of visualizing interconnected pathways and discuss it in context of biochemical networks. Our new visualization approach supports the analyst in obtaining an overview to related pathways if they are working within a particular pathway of interest. By using glyphs, brushing, and topological information of the related pathways, our interactive visualization is able to intuitively guide the exploration and navigation process, and thus the analysis processes too. To deal with real data and current networks, our tool has been implemented as a plugin for the VANTED system.
机译：在过去的几年中，研究生物过程的方法引起了人们的极大兴趣，并且是若干研究领域（尤其是系统生物学）的重点。生化网络作为过程的表示形式，对于全面理解生物非常重要。这些网络的图形通常在视觉上很重，无法缩放。解决这种复杂性的常见解决方案是将整个网络（例如新陈代谢）划分为层次结构化的大量单个途径。如果将这些路径可视化，则当用户失去整个网络中的上下文时，此策略还会产生其他导航和探索问题。在本文中，我们为解决互连路径的可视化问题提供了一种通用解决方案，并在生化网络的上下文中进行了讨论。我们的新可视化方法可以帮助分析人员在相关途径内研究感兴趣的途径时获得概述。通过使用相关路径的标志符号，画笔和拓扑信息，我们的交互式可视化功能可以直观地指导探索和导航过程，从而也可以指导分析过程。为了处理真实数据和当前网络，我们的工具已作为VANTED系统的插件实现。

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  • 来源
    《Information visualization》 |2012年第2期|p.136-150|共15页
  • 作者

    Ilir Jusufi; Christian Klukas; Andreas Kerren; Falk Schreiber;

  • 作者单位

    School of Computer Science, Physics and Mathematics (DFM),Linnaeus University, Vaexjoe, Sweden;

    Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany;

    School of Computer Science, Physics and Mathematics (DFM), Computer Science Department, Linnaeus University, Vejdes Plats 7, Room B3019, SE-351 95 Vaexjoe, Sweden;

    Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany,Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany;

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  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

    network visualization; biochemical networks; navigation; glyphs;

    机译：网络可视化;生化网络;导航;字形;

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