Visualization and Analysis of Dynamic Networks

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DynNetwork development was taken up initially by Sabina Sara Pfister back in GSoC 2012. She laid out a strong foundation for dynamic network visualization in Cytoscape and my job was to extend the plugin’s functionality to help users analyse time changing networks. The two of us were mentored by Jason Montojo. We had developed a decent tool over the course of two GSoC programs to aid dynamic network analysis and our efforts culminated in DynNetwork getting accepted for an oral presentation at the International Network for Social Network Analysis (INSNA), Sunbelt 2014 which was held in St. Petersburg, FL in February.

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Visualization and Analysis of Dynamic Networks

  1. 1. Sabina Sara Pfister Ph.D. Neuroinformatics ETH, Zurich Jimmy Morzaria B.E.(Hons) Computer Science M.Sc.(Hons) Mathematics BITS-Pilani, Goa Jason Montojo, MSc Software Engineer Cytoscape, GeneMANIA Research Officer The Donnelly Centre University of Toronto
  2. 2. • Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. • It supports of a rich collection of Apps for various kinds of problem domains, including bioinformatics, social network analysis and semantic web. • Cytoscape is developed in Java.
  3. 3. • DynNetwork is an application which adds to Cytoscape the functionality to visualize and analyse dynamic networks. • Allows users to not only import and visualize dynamic networks interactively but also provides them with features to view dynamic attributes, compute centrality parameters and plot charts for the same.
  4. 4. • Serve as a tool for researchers working in dynamic network analysis. • Serve as a platform for testing dynamic layout and clustering algorithms. • Provide an event-based implementation of dynamic network storage and visualization, for future extension toward fully event driven graphs. • Provide users with centrality parameters for dynamic network data, to aid analysis.
  5. 5. • Event based implementation of dynamic network storage and visualization. • Entities (nodes/ individuals, edges/interactions) are a set of events. • Every event has a real-valued time coordinate indicating when it occurs. • If the event is not instantaneous, it also has an ending coordinate to indicate its duration. • Events can describe attribute or position changes. [1] Skye Bender-deMoll, Dan McFarland(2006) The Art and Science of Dynamic Network Visualization. [1]
  6. 6. • DynNetwork allows you to visualize dynamic networks in Cytoscape. • It also allows you to apply dynamic layouts, for instance, Kamada-Kawai Layout, Prefuse Force directed Layout.
  7. 7. • DynNetwork lets you compute centrality parameters for the dynamic network and also plot a timeseries. • A user could compute the following centrality parameters for the dynamic network to aid dynamic network analysis: • Degree, Indegree, Outdegree • Closeness • Radiality • Eccentricity • Betweenness • Stress • Eigenvector • Centroid
  8. 8. • Implementation of dynamic layout algorithms, for instance, Yi-fan Hu's Multilevel Layout, Magnetic Force Layout, etc. • Real time streaming of Dynamic Graphs in Cytoscape. • Let users interactively construct dynamic networks in Cytoscape. For detailed documentation and source code visit: https://code.google.com/p/dynnetwork/ Post your queries/issues on: https://groups.google.com/forum/#!forum/cytoscape-discuss

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