A grid layout algorithm for automatic drawing of biochemical networks
A grid layout algorithm for automatic drawing of biochemical networks
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DOI：
10.1093/bioinformatics/bti290
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发表时间：
2005-05-01
期刊：
影响因子：
5.8
通讯作者：
Kurata, H
中科院分区：
文献类型：
--
作者：
Li, WJ;Kurata, H
动机：可视化在复杂生化网络的研究中是不可或缺的。可用的图形布局算法不足以令人满意地绘制此类网络。需要新的方法来自动可视化拓扑结构并促进对网络功能的理解。结果：我们提出了一种新的布局算法来绘制复杂的生化网络。网络被建模为方格网格上交互节点的系统。根据拓扑关系和两个节点的几何位置，设计每个节点对之间的离散成本函数。布局是通过最小化总成本来产生的。我们设计了一种快速算法来最小化离散成本函数，通过该算法可以有效地生成候选布局。模拟退火程序用于选择更好的候选者。我们的算法证明了它能够在相对紧凑的布局区域中清晰地展示集群结构，而无需任何先验知识。我们开发了 Windows 软件来实现 CADLIVE 算法。
Motivation: Visualization is indispensable in the research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to visualize automatically the topological architectures and facilitate the understanding of the functions of the networks.Results: We propose a novel layout algorithm to draw complex biochemical networks. A network is modeled as a system of interacting nodes on squared grids. A discrete cost function between each node pair is designed based on the topological relation and the geometric positions of the two nodes. The layouts are produced by minimizing the total cost. We design a fast algorithm to minimize the discrete cost function, by which candidate layouts can be produced efficiently. A simulated annealing procedure is used to choose better candidates. Our algorithm demonstrates its ability to exhibit cluster structures clearly in relatively compact layout areas without any prior knowledge. We developed Windows software to implement the algorithm for CADLIVE.