GeneVis: Simulation and Visualization of Genetic Networks

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.

[1]  JAX-WS WebService,et al.  Creating a , 2003 .

[2]  U. Alon,et al.  Ordering Genes in a Flagella Pathway by Analysis of Expression Kinetics from Living Bacteria , 2001, Science.

[3]  A. Griffiths.  Introduction to Genetic Analysis , 1976 .

[4]  Steffen Schulze-Kremer,et al.  BioSim: A New Qualitative Simulation Environment for Molecular Biology , 1998, ISMB.

[5]  David Marr,et al.  VISION A Computational Investigation into the Human Representation and Processing of Visual Information , 2009 .

[6]  Maria Samsonova,et al.  NetWork: An Interactive Interface to the Tools for Analysis of Genetic Network Structure and Dynamics , 1999, Pacific Symposium on Biocomputing.

[7]  Sun Yong Kim,et al.  A Visualization Tool for Gene Network Discovery-G.NET , 2002 .

[8]  David Small,et al.  Case study: A virtual environment for genomic data visualization , 2002, IEEE Visualization, 2002. VIS 2002..

[9]  H. McAdams,et al.  Circuit simulation of genetic networks. , 1995, Science.

[10]  Alistair G. Rust,et al.  Ensembl 2002: accommodating comparative genomics , 2003, Nucleic Acids Res..

[11]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A Wuensche,et al.  Genomic regulation modeled as a network with basins of attraction. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[13]  Leland H. Hartwell,et al.  Genetics: From Genes to Genomes , 1999 .

[14]  H. Barlow.  Vision: A computational investigation into the human representation and processing of visual information: David Marr. San Francisco: W. H. Freeman, 1982. pp. xvi + 397 , 1983 .

[15]  M. Sheelagh T. Carpendale,et al.  GeneVis: visualization tools for genetic regulatory network dynamics , 2002, IEEE Visualization, 2002. VIS 2002..

[16]  M. Elowitz,et al.  Protein Mobility in the Cytoplasm ofEscherichia coli , 1999, Journal of bacteriology.

[17]  M. Sheelagh T. Carpendale,et al.  A framework for unifying presentation space , 2001, UIST '01.

[18]  Nicolas Le Novère,et al.  STOCHSIM: modelling of stochastic biomolecular processes , 2001, Bioinform..

[19]  John Riedl,et al.  Visualization of biological sequence similarity search results , 1995, Proceedings Visualization '95.

[20]  Robert F. Cohen,et al.  Validating Graph Drawing Aesthetics , 1995, GD.

[21]  William Buxton,et al.  A taxonomy of see-through tools , 1994, CHI '94.

[22]  Nikolay A. Kolchanov,et al.  GeneNet: a gene network database and its automated visualization , 1998, Bioinform..

[23]  L. Stein.  Creating a bioinformatics nation , 2002, Nature.

[24]  Hidde de Jong,et al.  Qualitative Simulation of Genetic Regulatory Networks: Method and Application , 2001, IJCAI.

[25]  Michitaka Hirose,et al.  Visualization for genome function analysis using immersive projection technology , 2002, Proceedings IEEE Virtual Reality 2002.