A grid layout algorithm for automatic drawing of biochemical networks.
BACKGROUND
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.


BACKGROUND
All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/


BACKGROUND
http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/
Li
Weijiang
W
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan.
Kurata
Hiroyuki
H
D000465:Algorithms; D001185:Artificial Intelligence; D001671:Biochemistry / Q000379:methods; D002453:Cell Cycle / Q000502:physiology; D018797:Cell Cycle Proteins / Q000378:metabolism; D003196:Computer Graphics; D003198:Computer Simulation; D005786:Gene Expression Regulation / Q000502:physiology*; D008954:Models, Biological; D015398:Signal Transduction / Q000502:physiology*; D014584:User-Computer Interface; D015003:Yeasts / Q000166:cytology / Q000378:metabolism
D018797:Cell Cycle Proteins