CytoscapeRetreat2006/Plugins

Plugin & Usage Expo

Estimating 15 minute presentations

Part I

• Guy Warner (Unilever, UK)

  • Development and Application of a Network-Based Approach for the Analysis of Toxicological Data

• Scooter Morris (UCSF)

  • structureViz: Integrating Structure-based Visualization with Cytoscape

    • Network visualization and graph analysis of biological data has been demonstrated to provide researchers with significant insights into the relationships and processes of biological macromolecules. Futher analysis of these relationships and processes often involves viewing and comparing molecules at the structural level. structureViz provides an interface between Cytoscape and UCSF/Chimera, a widely-used molecular visualization package, providing a link between the network view and the structural view.

• Gary Bader (University of Toronto)

  • NetSearch: Querying a Graph for Motifs

    • Plugin written by Rosalba Giugno, Alfredo Ferro and their team, including Giuseppe Pigola, at University of Catania & New York University

  • Protein interaction plugin
  • Bingo code update - to create an API
• David Kane (SRA Int., NCI)
  • We would like to discuss how we might go about using Cytoscape as a Biopax-aware MIM editor

Part II

• Piet Molenaar (University of Amsterdam)

  • Cytoscape as a Repository: Visualization and Analysis of Human Genetics Data

    • As 'real life' human tumors are caused by multiple defects in many different pathways, obtaining an overview of the whole network involved is important. In our lab focus is therefore on high-throughput analysis and bioinformatics to detect potential relations between genes. To validate these interactions cell lines with inducible expression of transgenes and siRNA are analyzed in time-series and array data of large tumor series is used.
• Matthias Reimann (Technische Universitat Dresden, Germany)

  • EagleVista

    • We have developed a novel visualisation, which detects modules in networks and displays them in a way which reduces the number of edges significantly. As a result, complex networks can be displayed in a much more convenient way. The plugin includes a few algorithms to get the new visualisation from a ordinary graph in cytoscape.
• James Vlasblom (U of Toronto)

  • GenePro: A Cytoscape plug-in for visualization and analysis of interaction networks

    • GenePro allows visualization of interaction networks at multiple levels of resolution. At low resolution, GenePro displays clusters of proteins/genes as nodes, and relationships between them as edges. Each node can optionally be colored as a pie graph, which enables mapping of biological attributes on to members of the clusters. At high resolution, individual clusters can be examined in more detail. GenePro also offers options for mapping condition dependent mRNA expression levels onto the clusters.

• Giles Weaver (Unilever, UK)

  • Cytoscape for Metabolic Networks

• Ethan Cerami (MSKCC)

  • Quick Find (10-15 minutes)

• Allan Kuchinsky, Aditya Vailaya (Agilent Technologies)

  • Agilent Literature Search: Version 2.3

  • Heatstrip Visualization

  • INRIA InfoVis Toolkit plugins: Matrix Visualization and Excentric Labels