On open problems in biological network visualization

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5849 LNCS, Issue , 2010, Pages 256-267

  Albrecht, Mario ^a   Kerren, Andreas ^b   Klein, Karsten ^c   Kohlbacher, Oliver ^d   Mutzel, Petra ^c   Paul, Wolfgang ^c   Schreiber, Falk ^e   Wybrow, Michael ^f  

^a MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^b LINNAEUS UNIVERSITY   (Sweden)

^c TU DORTMUND UNIVERSITY   (Germany)

^d UNIVERSITY OF TÜBINGEN   (Germany)

^e MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^f MONASH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; EFFICIENT ALGORITHM; GRAPH DRAWING; GRAPH-DRAWING PROBLEM; LIFE-SCIENCES; NETWORK ANALYSIS; NETWORK BIOLOGY; OPEN PROBLEMS; POSSIBLE SOLUTIONS; VISUALIZATION METHOD;

ALGORITHMS; BIOLOGY; ELECTRIC NETWORK ANALYSIS; VISUALIZATION;

DRAWING (GRAPHICS);

EID: 77951540298     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-11805-0_25     Document Type: Conference Paper

References (25)

1. BioCarta, http://biocarta.com/
2. Barsky, A., Gardy, J., Hancock, R., Munzner, T.: Cerebral: a cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation. Bioinformatics 23(8), 1040-1042 (2007) (Pubitemid 47050596)
3. Becker, M., Rojas, I.: A graph layout algorithm for drawing metabolic pathways. Bioinformatics 17(5), 461-467 (2001) (Pubitemid 32440307)
4. Brandes, U., Dwyer, T., Schreiber, F.: Visualizing related metabolic pathways in two and a half dimensions. In: Liotta, G. (ed.) GD 2003. LNCS, vol. 2912, pp. 111-122. Springer, Heidelberg (2004) (Pubitemid 39744177)
5. Cline, M., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., Hanspers, K., et al.: Integration of biological networks and gene expression data using Cytoscape. Nature Protocols 2(10), 2366-2382 (2007)
6. Demir, E., Babur, O., Dogrusöz, U., Gürsoy, A., Nisanci, G., Çetin Atalay, R., Ozturk, M.: PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 18(7), 996-1003 (2002) (Pubitemid 34846483)
7. Dogrusöz, U., Giral, E., Cetintas, A., Civril, A., Demir, E.: A compound graph layout algorithm for biological pathways. In: Pach, J. (ed.) GD 2004. LNCS, vol. 3383, pp. 442-447. Springer, Heidelberg (2005)
8. Funahashi, A., Morohashi, M., Kitano, H.: CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Biosilico 1(5), 159-162 (2003)
9. Görg, C., Pohl, M., Qeli, E., Xu, K.: Visual Representations. In: Kerren, A., Ebert, A., Meyer, J. (eds.) GI-Dagstuhl Research Seminar 2007. LNCS, vol. 4417, pp. 163-230. Springer, Heidelberg (2007)
10. Junker, B., Klukas, C., Schreiber, F.: VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7, 109 (2006)
11. Karp, P., Ouzounis, C., Moore-Kochlacs, C., Goldovsky, L., Kaipa, P., Ahren, D., Tsoka, S., Darzentas, N., Kunin, V., Lopez-Bigas, N.: Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Research 33, 6083-6089 (2005) (Pubitemid 41742547)
12. Karp, P., Paley, S.: Automated drawing of metabolic pathways. In: Proc. International Conference on Bioinformatics and Genome Research, pp. 225-238 (1994)
13. Karp, P., Paley, S., Romero, P.: The pathway tools software. Bioinformatics 18(S1), S225-S232 (2002)
14. Kohn, K., Aladjem, M.: Circuit diagrams for biological networks. Molecular Systems Biology 2, e2006.0002 (2006)
15. Li, W., Kurata, H.: A grid layout algorithm for automatic drawing of biochemical networks. Bioinformatics 21(9), 2036-2042 (2005) (Pubitemid 40668042)
16. Michal, G.: Biochemical Pathways, 4th edn. (Poster). Roche (2005)
17. Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: Genomic Object Net: a platform for modeling and simulating biopathways. Applied Bioinformatics 2, 181-184 (2004)
18. Nicholson, D.: Metabolic Pathways Map (Poster). Sigma Chemical Co. (1997)
19. Novère, N.L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M., Wimalaratne, S., Bergman, F.T., et al.: The Systems Biology Graphical Notation. Nature Biotechnology 27(8), 735-741 (2009)
20. Offenhuber, D., Donath, J.: Comment Flow: visualizing communication along network paths. Poster presented at IEEE InfoVis 2007 (2007)
21. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., Kanehisa, M.: KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 27, 29-34 (1999) (Pubitemid 29209394)
22. Schreiber, F.: High quality visualization of biochemical pathways in BioPath. Silico Biology 2(2), 59-73 (2002)
23. Sirava, M., Schäfer, T., Eiglsperger, M., Kaufmann, M., Kohlbacher, O., Bornberg-Bauer, E., Lenhof, H.: BioMiner - modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics 18(S2), 219-230 (2002) (Pubitemid 41073238)
24. Suderman, M., Hallett, M.: Tools for visually exploring biological networks. Bioinformatics 23(20), 2651-2659 (2007) (Pubitemid 350048327)
25. Yost, B., North, C.: Single complex glyphs versus multiple simple glyphs. In: CHI 2005 extended abstracts on human factors in computing systems, pp. 1889-1892. ACM, New York (2005)