A Customized force-directed layout algorithm for biological graphs whose vertices have enzyme commission attributes

Danacı, Hasan Fehmi
Force directed layout algorithm is popularly used to draw biological graphs. However, it employs only graph structure. When we would like to embed domain-specific knowledge, such as biological or chemical attributes related to the vertices, force directed layout algorithm should be modified. It is then important to draw more readable layouts for biologists without the dispose of aesthetically pleasing way that comes from force-directed algorithm’s nature. This thesis aims to describe a modified and improved force-directed layout algorithm, EClerize, for biological graphs that represent pathways in which the vertices are identified with EC (Enzyme Commission) numbers. The vertices with the same EC class numbers are treated as members of the same cluster. Positions of vertices in clusters are affected by mainly two factors: biological similarity of each vertex in the same cluster and theoretical length between the vertices. EClerize is tested on a number of biological pathways and the improvement with respect to the original algorithm is presented.


A Customized force-directed layout algorithm with genetic algorithm techniques for biological graphs whose vertices have enzyme commission attributes
Aksoydan, Fırat; Atalay, Mehmet Volkan; Department of Computer Engineering (2019)
A pathway can be visualized as a graph whose layout is drawn by a force-directed algorithm. In our previous study, we have described EClerize which is a customized and improved Kamada Kawai force-directed algorithm in order to visualize pathways that contain nodes with attributes as EC numbers. EClerize creates clusters of vertices with enzymes that belong to the same EC class. Here, we make use of genetic algorithm (GA) to obtain a global optimum solution for EClerize and we integrate undirected graph layo...
A Layout algorithm for visualization of graph alignments
Akarsu, Andaç; Can, Tolga; Department of Computer Engineering (2017)
Graph layout algorithms are commonly used when visualizing. Usually these algorithms focus on a single graph. To be able to visualize multiple graphs at once, such as the results of graph alignment algorithms on biological networks, new layout algorithms need to be developed. A layout algorithm for visualizing graph alignments should display the aligned graphs separately, so that both the graphs and their alignment can be viewed individually. In addition, for better interpretation of the alignment results, ...
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Citation Formats
H. F. Danacı, “A Customized force-directed layout algorithm for biological graphs whose vertices have enzyme commission attributes,” M.S. - Master of Science, Middle East Technical University, 2015.