A layout algorithm for signaling pathways

Date
2006-01-20
Advisor
Instructor
Source Title
Information Sciences
Print ISSN
0020-0255
Electronic ISSN
1872-6291
Publisher
Elsevier
Volume
176
Issue
2
Pages
135 - 149
Language
English
Type
Article
Journal Title
Journal ISSN
Volume Title
Abstract

Visualization is crucial to the effective analysis of biological pathways. A poorly laid out pathway confuses the user, while a well laid out one improves the user's comprehension of the underlying biological phenomenon. We present a new, elegant algorithm for layout of biological signaling pathways. Our algorithm uses a force-directed layout scheme, taking into account directional and rectangular regional constraints enforced by different molecular interaction types and subcellular locations in a cell. The algorithm has been successfully implemented as part of a pathway visualization and analysis toolkit named Patika, and results with respect to computational complexity and quality of the layout have been found satisfactory. The algorithm may be easily adapted to be used in other applications with similar conventions and constraints as well. Patika version 1.0 beta is available upon request at http://www.patika.org. © 2004 Elsevier Inc. All rights reserved.

Course
Other identifiers
Book Title
Keywords
Bioinformatics, Signaling pathways, Cellular pathway analysis, Information visualization, Pathway visualization, Graph layout
Citation
Published Version (Please cite this version)