Visual exploration of isotope labeling networks in 3D
Visual exploration of isotope labeling networks in 3D
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DOI：
10.1007/s00449-007-0177-1
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发表时间：
2008-04-01
影响因子：
3.8
通讯作者：
Wiechert, W.
中科院分区：
文献类型：
--
作者：
Droste, P.;Weitzel, M.;Wiechert, W.
同位素标记网络(ILN)是解释同位素标记分子在代谢网络中流动的图表。此外，它们是同位素示踪剂代谢通量分析(MFA)的结构支柱，已被确立为通量组学中的标准实验工具。为了配置MFA的同位素标记实验(ILE)，即使是从业者也必须在一定程度上了解相应的ILN的结构。图形算法有助于分析网络结构，但会产生相当抽象的结果。在这里，主要的障碍是这些网络的高维度和大量的网络组件，因此很难手动计算。在理论和实验的界面上，开发了三维交互式可视化工具CumoVis，以逐步探索网络结构。ILN内的导航和定向是通过利用基础代谢物网络的自然3D结构来支持的，在每个代谢物节点的顶部堆积有标记的颗粒。通过旋转、缩放、前进和后退路径跟踪以及最重要的网络组件减少来促进网络探索。CumoVis的所有功能都用一个教育例子和一个描述柠檬酸循环中碳流的现实网络来解释。
Isotope labeling networks (ILNs) are graphs explaining the flow of isotope labeled molecules in a metabolic network. Moreover, they are the structural backbone of metabolic flux analysis (MFA) by isotopic tracers which has been established as a standard experimental tool in fluxomics. To configure an isotope labeling experiment (ILE) for MFA, the structure of the corresponding ILN must be understood to a certain extent even by a practitioner. Graph algorithms help to analyze the network structure but produce rather abstract results. Here, the major obstruction is the high dimension of these networks and the large number of network components which, consequently, are hard to figure out manually. At the interface between theory and experiment, the three-dimensional interactive visualization tool CumoVis has been developed for exploring the network structure in a step by step manner. Navigation and orientation within ILNs are supported by exploiting the natural 3D structure of an underlying metabolite network with stacked labeled particles on top of each metabolite node. Network exploration is facilitated by rotating, zooming, forward and backward path tracing and, most important, network component reduction. All features of CumoVis are explained with an educational example and a realistic network describing carbon flow in the citric acid cycle.