Research Article
A Force Directed Layout Algorithm for Biological Networks
|
International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
|
| Volume 120 - Issue 21 |
| Published: June 2015 |
| Authors: Pritish Dubey, Ashwini Shingare, Vrushali Inamdar |
10.5120/21355-4314
|
Pritish Dubey, Ashwini Shingare, Vrushali Inamdar . A Force Directed Layout Algorithm for Biological Networks. International Journal of Computer Applications. 120, 21 (June 2015), 42-47. DOI=10.5120/21355-4314
@article{ 10.5120/21355-4314,
author = { Pritish Dubey,Ashwini Shingare,Vrushali Inamdar },
title = { A Force Directed Layout Algorithm for Biological Networks },
journal = { International Journal of Computer Applications },
year = { 2015 },
volume = { 120 },
number = { 21 },
pages = { 42-47 },
doi = { 10.5120/21355-4314 },
publisher = { Foundation of Computer Science (FCS), NY, USA }
}
%0 Journal Article
%D 2015
%A Pritish Dubey
%A Ashwini Shingare
%A Vrushali Inamdar
%T A Force Directed Layout Algorithm for Biological Networks%T
%J International Journal of Computer Applications
%V 120
%N 21
%P 42-47
%R 10.5120/21355-4314
%I Foundation of Computer Science (FCS), NY, USA
Abstract
In this paper, we present a layout algorithm for clustered graphs which is a modified force directed algorithm. We have used Spring Embedder algorithm by Eades as base for our algorithm and modified it to suit the constraints of general biological graphs. Our main contribution is adopting spring embedder algorithm to maintain clustered structure of original graph with inherent depth of nesting and handling different node sizes. Results show that our layout algorithm draws graphs with acceptable quality with respect to aesthetic criteria for graph drawing. The algorithm has been integrated with systems biology visualization suit called "eSkin", which allows lay outing and analyze biological graphs.
References
- Eric Weisstein, "Graph Theory", May 13 2015 Available: http://mathworld. wolfram. com/Graph. html
- Coleman and Stott Parker, 12 Dec. 1996, "Aesthetics-Based Graph Layout for Human Consumption", Journal of Software Practice & Experience, Volume 26, p 1415-1438
- Helen C. Purchase, Beryl Plimmer, Baker, Pilcher, 2010, "Graph Drawing Aesthetics in User-Sketched Graph Layouts", AUIC '10 Proceedings of the Eleventh Australasian Conference on User Interface, Volume 106, p 80-88.
- John Morris, Allan Kuchinsky, 2014, "Analysis and Visualization of Biological Networks with Cytoscape".
- "Biological Pathways",National Human Genome Research Institute. April 5 2015,[Online] Available https://www. genome. gov/27530687 .
- Kathy Ryall, Joe Marks and Stuart Shieber, 1997, "An interactive constraint-based system for drawing graphs", Proceedings of the 10th annual ACM symposium on User interface software and technology, p 97-104.
- Peter Eades, 1984, "A heuristic for graph drawing". Congressus Numerantium, 42:149–160.
- P. Asokarathinam, Cohen – Sutherland Line Clipping Algorithm, November 27, 1996. [Online] http://www. cs. helsinki. fi/group/goa/viewing/leikkaus/lineClip. html
- Yi-Yi Lee, Chun-Cheng Lin, Hsu-Chun Yen, 2006 "Mental Map Preserving Graph Drawing Using Simulated Annealing" at Asia Pacific Symposium on Information Visualization (APVIS 2006).
- T. Fruchterman and E. Reingold, 1991, "Graph drawing by force-directed placement", Software Pract. Exp. , 21(11), p 1129–1164.
- H. C. Purchase, 2002, "Metrics for Graph Drawing Aesthetics", at Journal of Visual Languages and Computing.
- KEGG Pathway Database April 27, 2015. [Online] http://www. genome. jp/kegg/pathway. html
- Josep Díaz, Jordi Petit and Maria Serna, September 2002, "A survey of graph layout problems", Journal of ACM Computing Surveys (CSUR) Surveys Homepage archive Volume 34 Issue 3, Pages 313-356.
- Yifan Hu, 2005, "Efficient and high quality force-directed graph drawing". The Mathematica Journal, 10:37–71.
- J. B. Kruskal, 1964, "Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis", Psychometrika, 29:1–27.
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