GeneVis: Visualization tools for genetic regulatory network dynamics

Proceedings of the IEEE Visualization Conference

Volumn , Issue , 2002, Pages 243-250

  Baker, C A H ^a   Carpendale, M Sheelagh T ^a   Prusinkiewicz, P ^a   Surette, M G ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

Biological visualization; Focus and context; Genetic networks; Lenses; Multi representation; Visualization

Indexed keywords

COMPUTER SIMULATION; GENES; LENSES; PROTEINS; VISUALIZATION;

GENETIC REGULATORY NETWORKS;

GENETIC ENGINEERING;

EID: 0036452975     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. C.A.H. Baker, M.S.T. Carpendale, and M.G. Surette. Simulation and visualization of genetic regulatory networks. Technical Report 2001-690-13, Department of Computer Science, University of Calgary, 2001.
2. E.A. Bier, M.C. Stone, K. Fishkin, W. Buxton, and T. Baudel. A taxonomy of see-through tools. In CHI'94 Proceedings, pages 358-364, New York, 1994. ACM Press.
3. M.S.T. Carpendale and C. Jirasek. A framework for unifying presentation space. In Proceedings of 14th Annual ACM Symposium on User Interface Software and Technology, pages 82-92, 2001.
4. H. de Jong, M. Page, C. Hernandez, and J. Geiselmann. Qualitative simulation of genetic regulatory networks: Method and application. In Proceedings of the 17th International Joint Conference on Artificial Intelligence, pages 4-10. Morgan Kaufmann, 2001.
5. A.J. Griffiths. An Introduction to genetic analysis. W.H. Freeman, 1996.
6. K.R. Heidtke and S. Schulze-Kremer. BioSim: A new qualitative simulation environment for molecular biology. In the Proceedings of the 6th Intl. Conf. on Intelligent Systems for Molecular Biology, pages 85-94. AAAI Press, 1998.
7. S. Kalir, J. McClure, K. Pabbaraju, C. Southward, M. Ronen, S. Leibler, M.G. Surette, and U. Alon. Ordering genes in a flagella pathway by analysis of expression kinetics from living bacteria. Science, 292:2080-2083, June 2001.
8. F.A. Kolpakov, E.A. Ananko, G.B. Kolesov, and N.A. Kolchanov. Genenet: a gene network database and its automated visualization. Bioinformatics, 14(6):529-537, 1998.
9. Y.K. Leung and M.D. Apperley. A review and taxonomy of distortion-oriented presentation technique. ACM Transactions on Computer-Human Interaction, 1(2): 126-160, June 1994.
10. B. Lwein. Genes VII. Oxford University Press, 2001.
11. D. Marr. Vision: A computational investigation into the human representation and processing of visual information. W.H. Freeman and Company, 1982.
12. H.H. McAdams and L. Shapiro. Circuit simulation of genetic networks. Science, 269:650-656, August 1995.
13. GeneNet Modeller. http://www.mgs.bionet.nsc.ru/mgs/systems/genenet/.
14. N. Le Novre and T.S. Shimizu. Stochsim: modelling of stochastic biomolecular processes. Bioinformatics, 17:575-576, 2001.
15. H.C. Purchase, R.F. Cohen, and M. James. Validating graph drawing aesthetics. In Proceedings of the Symposium on Graph Drawing, GD'95, volume 1027 of Lecture Notes in Computer Science, pages 435-446. Springer, 1995.
16. M. Samsonova, V. Serov, and A. Trushkina. Tools for visualization of genetic network structure and dynamics. In 1st Russian Electronic Conference On Bioinformatics, page 118. Fontanka Press, 2000.
17. M.G. Samsonova and V.N. Serov. Network: An interactive interface to the tools for analysis of genetic networks structure and dynamics. In the Proceedings of Pacific Symposium on Biocomputing, pages 102-111, 1999.
18. A. Wuensche. Genomic regulation modeled as a network with basins of attraction, http://www.santafe.org/wuensche/ddlab.html.
19. M. Yoshida, H. Shimano, Y. Shibagaki, H. Fukagawa, and T. Mizuno. Webgen-net: a workbench system for support of genetic network construction. In Poster presented at of Pacific Symposium on Biocomputing, 2001.