NRNB sponsors a variety of competitions for the communities around network biology tools. These competitions range from app development to bug bounties. Check out ongoing competitions and the results of past competitions below. Also feel free to suggest a competition.

February Bug Bounty 2013


  • Giovanni Dall'Olio - 47 points
  • Carol Scalice - 20 points
  • Anna Dieckmann - 10 points
  • Dirk - 10 points
  • Hideo Matsuda - 10 points
  • Navin Rauniyar - 10 points
  • Ramayya - 10 points
  • Savvas Genitsaris - 10 points
  • Michael Heuer - 8 points

Cytoscape 3.2 Launch Challenge November 2014


Best example of using Cytoscape for Biology

  • Thomas Kelder

    1st - Thomas Kelder: The Food - Genomics - Disease landscape: A network linking food ingredients with human disease through underlying molecular interactions.

  • Mark Grimes

    2nd - Mark Grimes: Co-cluster correlation network of phoshporylated proteins in neuroblastoma samples.

  • Ponnusamy Kalaiarasan

    3rd - Ponnusamy Kalaiarasan: Crosstalk among the modules and hubs in the apoptosis protein-protein interaction network.

Most novel use of Cytoscape

  • Christos Vaitsis

    1st - Christos Vaitsis: Mapping of learning outcomes and teaching methods of one course in an undergraduate medical program.

  • Leandro Lima

    2nd - Leandro Lima: Network of citations constructed using BioPython/PubMed API.

  • Steven Hallam

    3rd - Steven Hallam: The image combines network analysis with single-cell genomic sequencing to infer metabolic interactions between uncultivated microbes inhabiting salt stratified Sakinaw Lake.

  • Sherilyn Bell

    3rd - Sherilyn Bell: Using Cytoscape to visualize commercial personal DNA testing data such as chromosome start and end points, genetic distance, surnames etc.

Most aesthetically pleasing network visualization in Cytoscape

  • Roberto Mosca

    1st - Roberto Mosca: The binary protein-protein interaction landscape of Escherichia coli. Cytoscape used to generate the networks.

  • Daniel Himmelstein

    2nd - Daniel Himmelstein: Heterogeneous Network Visualization with Cytoscape: An Integrative Approach to the Genetics of Complex Human Disease.

  • Shazia Haider

    3rd - Shazia Haider: Protein-protein interaction network of apoptosis regulatory protein coding genes.

Most valuable feature to add to Cytoscape

  • 1st - Gordon Bean:

    Provide a “wizard” user interface for simple styles based on common data-driven visualizations to:

    • Teach the user about basic visual style techniques, such as mapping discrete colors to discrete node classes and using edge weights to denote edge score or strength.
    • Ask the user to select attributes that match these criteria (Cytoscape can scan data for each attribute to loosely determine what attributes might be appropriate - i.e. continuous, discrete, pass-through, etc).
    • Automatically bind these attributes to sensible style properties that match the rest of the style theme.

  • 2nd - Mark Fortner:

    Use Oracle JavaFX packager for Cytoscape installers, which package the required version of Java with the application, thus cutting down on the amount of headscratching by users.

  • 3rd - Srikanth Bezawada:

    • Provide case studies on social network data and visualizing transportation networks data.
    • Implement generic feature to allow an app to be run on a large set of networks and allow for efficient extraction of app results to compare networks on a large scale.

  • 3rd - Thomas Pfau:

    Implement edges with multiple sources and targets to allow for programmatic representation of more complex interactions. For example, they could be used to represent Gene-Protein-Reaction relationships without necessitating the introduction of Enzyme subunits.