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December 2003, Volume 2, Number 4, Pages 201-217
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| Original Article |
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| GeneVis: simulation and visualization of genetic networks |
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| Charles Baker1, Sheelagh Carpendale2, Przemyslaw Prusinkiewicz2 and Michael Surette3 |
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1Southern Alberta Mass Spectrometry Centre, Health Sciences Centre, University of Calgary, Calgary, Alberta, Canada
2Department of Computer Science, University of Calgary, Calgary, Alberta, Canada
3Department of Microbiology and Infectious Disease, University of Calgary, Calgary, Alberta, Canada
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Correspondence to: Sheelagh Carpendale, Department of Computer Science, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, Canada T2N 1N4. Tel: +(403) 220 6015; Fax: +(403) 284 4707; E-mail: sheelagh@cpsc.ucalgary.ca |
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| Abstract |
| GeneVis simulates genetic networks and visualizes the process of this simulation interactively, providing a visual environment for exploring the dynamics of genetic regulatory networks. The visualization environment supports several representational modes, which include: an individual protein representation, a protein concentration representation, and a network structure representation. The individual protein representation shows the activities of the individual proteins. The protein concentration representation illustrates the relative spread and concentrations of the different proteins in the simulation. The network structure representation depicts the genetic network dependencies that are present in the simulation. GeneVis includes several interactive viewing tools. These include animated transitions from the individual protein representation to the protein concentration representation and from the individual protein representation to the network structure representation. Three types of lenses are used to provide different views within a representation: fuzzy lenses, base pair lenses, and the network structure ring lens. With a fuzzy lens an alternate representation can be viewed in a selected region. The base pair lenses allow users to reposition genes for better viewing or to minimize interference during the simulation. The ring lens provides detail-in-context viewing of individual levels in the genetic network structure representation.
Information Visualization (2003) 2, 201-217. doi:10.1057/palgrave.ivs.9500055 |
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| Keywords |
| Bio-visualization; visual representation; integrated views; computational biology; dynamic visualization; simulation; genetic networks |
| Received 6 August 2003; revised 15 September 2003; accepted 17 September 2003 |
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