Modulo graph embedding: mapping applications onto coarse-grained reconfigurable architectures
CASES '06 Proceedings of the 2006 international conference on Compilers, architecture and synthesis for embedded systems
Hierarchically organized layout for visualization of biochemical pathways
Artificial Intelligence in Medicine
On open problems in biological network visualization
GD'09 Proceedings of the 17th international conference on Graph Drawing
Semi-automatic drawing of metabolic networks
Information Visualization - Special issue on Best Papers of Visual Analytics Science and Technology (VAST) 2010
Model-driven reverse engineering of legacy graphical user interfaces
Automated Software Engineering
Hi-index | 3.85 |
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. Availability: All materials can be freely downloaded from http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/ Contact: kurata@bio.kyutech.ac.jp Supplementary information:http://kurata21.bio.kyutech.ac.jp/grid/grid_layout.htm; http://www.cadlive.jp/