A compound graph layout algorithm for biological pathways

Lecture Notes in Computer Science

Volumn 3383, Issue , 2004, Pages 442-447

  Dogrusoz, Ugur ^a,b   Giral, Erhan ^a   Cetintas, Ahmet ^a   Civril, Ali ^a   Demir, Emek ^a  

^a BILKENT UNIVERSITY   (Turkey)

^b Tom Sawyer Software   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SCIENCE; CONSTRAINT THEORY; DRAWING (GRAPHICS); GRAPH THEORY; ALGORITHMS; DIRECTED GRAPHS;

ARBITRARY NESTING; BIOLOGICAL PATHWAYS; COMPARTIMENTAL CONSTRAINTS; COMPOUND GRAPH LAYOUT ALGORITHMS;

ALGORITHMS; BIOINFORMATICS;

APPLICATION SPECIFIC; ARBITRARY NESTING; BIOLOGICAL PATHWAYS; COMPOUND GRAPH LAYOUT ALGORITHMS; FORCE-DIRECTED LAYOUT; MOLECULAR COMPLEXES; PATHWAY ANALYSIS;

EID: 24144477533     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (14)

1. M. Y. Becker and I. Rojas. A graph layout algorithm for drawing metabolic pathways. Bioinformatics, 17:461-467, 2001.
2. F. Bertault. Force-directed algorithm that preserves edge crossing properties. In J. Kratochvil, editor, GD '99, volume 1731 of Lecture Notes in Computer Science, pages 351-358. Springer-Verlag, 1999.
3. E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, and R. Cetin-Atalay. An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics, 20(3):349-356, 2002.
4. E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, and M. Ozturk. PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics, 18(7):996-1003, 2002.
5. G. Di Battista, P. Eades, R. Tamassia, and I. G. Tollis. Graph Drawing, Algorithms for the Visualization of Graphs. Prentice-Hall, 1999.
6. P. Eades, Q. Feng, and X. Lin. Straight-line drawing algorithms for hierarchical graphs and clustered graphs. In S. North, editor, GD '96, volume 1190 of Lecture Notes in Computer Science, pages 113-128. Springer-Verlag, 1997.
7. T. M. J. Fruchterman and E. M. Reingold. Graph drawing by force-directed placement. Software Practice and Experience, 21(11):1129-1164, 1991.
8. K. Fukuda and T. Takagi. Knowledge representation of signal transduction pathways. Bioinformatics, 17(9):829-837, 2001.
9. B. Gene and U. Dogrusoz. A constrained, force-directed layout algorithm for biological pathways. In G. Liotta, editor, GD '03, volume 2912 of LNCS, pages 349-356, 2003.
10. K. Sugiyama and K. Misue. A Generic Compound Graph Visualizer/ Manipulator: D-ABDUCTOR. In F. J. Brandenburg, editor, GD '95, volume 1027 of Lecture Notes in Computer Science, pages 500-503. Springer-Verlag, 1995.
11. P. D. Karp and S. Paley. Automated drawing of metabolic pathways. In Third International Conference on Bioinformatics and Genome Research, pages 225-238, Tallahassee, Florida, June 1994.
12. G. Sander. Layout of compound directed graphs. Technical Report A/03/96, University of Saarlandes, CS Dept., Saarbrücken, Germany, 1996.
13. F. Schreiber. High quality visualization of biochemical pathways in BioPath. In Silico Biology, 2(2):59-73, 2002.
14. K. Sugiyama and K. Misue. Visualization of structural information: Automatic drawing of compound digraphs. IEEE Transactions on Systems, Man and Cybernetics, 21(4):876-892, 1991.