Visualization and Analysis of Dynamic Networks in Cytoscape

DEVELOPERS: SABINA SARA PFISTER, J IMMY MORZARIA, JASON MONTOJO

SUPPORTED BY: NATIONAL RESOURCE FOR NETWORK BIOLOGY(NRNB), GOOGLE SUMMER OF CODE 2012,2013

DATE: 20 T H FEBRUARY, 2014

Sabina Sara PfisterPh.D. NeuroinformaticsETH, Zurich

Jimmy MorzariaB.E.(Hons) Computer ScienceM.Sc.(Hons) MathematicsBITS-Pilani, Goa

Jason Montojo, MScSoftware EngineerCytoscape, GeneMANIAResearch OfficerThe Donnelly CentreUniversity of Toronto

Cytoscape Introduction• 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.

DynNetwork Introduction• 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.

DynNetwork Goals• 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.

Concept of Dynamic Networks in DynNetwork• 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]

Importing dynamic network data using Xtensible Graph Markup and Modeling Language(XGMML)

Visualizing the dynamic network in Cytoscape• 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.

Dynamic Network Attributes and Centrality Timeseries• 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

Dynamic Network Attributes and Centrality Timeseries Snapshot

Demo and Future Work• 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