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Bioinformatics Advance Access published online on January 27, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti290
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Bioinformatics © Oxford University Press 2005; all rights reserved.
Received November 11, 2004
Revised January 16, 2005
Accepted January 24, 2005

Article

A grid layout algorithm for automatic drawing of biochemical networks

Weijiang Li 1 and Hiroyuki Kurata 1*

1 Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502 Japan

* To whom correspondence should be addressed.
Hiroyuki Kurata, E-mail: kurata{at}bio.kyutech.ac.jp


  Abstract

Motivation: Visualization is indispensable to research of complex biochemical networks. Available graph layout algorithms are not adequate for satisfactorily drawing such networks. New methods are required to automatically visualize topological architectures and facilitate understanding 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 (Kurata et al., 2003).

Availability: All materials can be freely downloaded from http://kurata21.bse.kyutech.ac.jp/grid/grid_layout.htm (Log ID: kurata; Password: testpass).


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