A compound graph layout algorithm for biological pathways

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A_compound_graph_layout_algorithm_for_biological_pathways.pdf (583.39 KB)

Date

2004-09-10

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Source Title

GD'04: Proceedings of the 12th international conference on Graph Drawing

Print ISSN

0302-9743

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Publisher

Springer, Berlin, Heidelberg

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Pages

442 - 447

Language

English

Type

Conference Paper

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Abstract

We present a new compound graph layout algorithm based on traditional force-directed layout scheme with extensions for nesting and other application-specific constraints. The algorithm has been successfully implemented within PATIKA, a pathway analysis tool for drawing complicated biological pathways with compartimental constraints and arbitrary nesting relations to represent molecular complexes and pathway abstractions. Experimental results show that execution times and quality of the produced drawings with respect to commonly accepted layout criteria and pathway drawing conventions are quite satisfactory. © Springer-Verlag Berlin Heidelberg 2004.

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Keywords

Computer science, Constraint theory, Drawing (graphics), Graph theory, Arbitrary nesting, Biological pathways, Compartimental constraints, Compound graph layout algorithms, Algorithms

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http://hdl.handle.net/11693/27422

Published Version (Please cite this version)

https://doi.org/10.1007/978-3-540-31843-9_45
 https://doi.org/10.1007/b105810

Collections

Scholarly Publications - Computer Engineering
Scholarly Publications - BCBI