A compound graph layout algorithm for biological pathways

Ugur Dogrusoz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir

Research output: Chapter in Book/Report/Conference proceedingConference contribution

24 Citations (Scopus)

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.

Original languageEnglish (US)
Title of host publicationLecture Notes in Computer Science
EditorsJ. Pach
Pages442-447
Number of pages6
Volume3383
StatePublished - 2004
Externally publishedYes
Event12th International Symposium on Graph Drawing, GD 2004 - New York, NY, United States
Duration: Sep 29 2004Oct 2 2004

Other

Other12th International Symposium on Graph Drawing, GD 2004
CountryUnited States
CityNew York, NY
Period9/29/0410/2/04

ASJC Scopus subject areas

  • Computer Science (miscellaneous)

Cite this

Dogrusoz, U., Giral, E., Cetintas, A., Civril, A., & Demir, E. (2004). A compound graph layout algorithm for biological pathways. In J. Pach (Ed.), Lecture Notes in Computer Science (Vol. 3383, pp. 442-447)

A compound graph layout algorithm for biological pathways. / Dogrusoz, Ugur; Giral, Erhan; Cetintas, Ahmet; Civril, Ali; Demir, Emek.

Lecture Notes in Computer Science. ed. / J. Pach. Vol. 3383 2004. p. 442-447.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Dogrusoz, U, Giral, E, Cetintas, A, Civril, A & Demir, E 2004, A compound graph layout algorithm for biological pathways. in J Pach (ed.), Lecture Notes in Computer Science. vol. 3383, pp. 442-447, 12th International Symposium on Graph Drawing, GD 2004, New York, NY, United States, 9/29/04.
Dogrusoz U, Giral E, Cetintas A, Civril A, Demir E. A compound graph layout algorithm for biological pathways. In Pach J, editor, Lecture Notes in Computer Science. Vol. 3383. 2004. p. 442-447
Dogrusoz, Ugur ; Giral, Erhan ; Cetintas, Ahmet ; Civril, Ali ; Demir, Emek. / A compound graph layout algorithm for biological pathways. Lecture Notes in Computer Science. editor / J. Pach. Vol. 3383 2004. pp. 442-447
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