Cytoscape Integration

The MASS library uses Cytoscape as a GUI tool for interactive graph construction, editing, and visualization. The two main reasons are: Cytoscape’s popularity among scientific users and its well-defined plug-ins. Integrating MASS with Cytoscape requires two key interactions between the two systems through Cytoscape plug-ins:

• Import-network plug-in: pulling an in-memory graph from MASS and re-building it inside of Cytoscape into a native CyNetwork with a combination of CyNode and CyEdge entities.
• Export-network plug-in: serializing the currently selected Cytoscape CyNetwork into the MASS Graph- Places for sending to MASS.

To facilitate communication between Cytoscape and MASS, a user must run CytoscapeListener in her/his MASS main program as shown in the listing below on line 6. Then, Cytoscape plug-ins establish a TCP socket to communicate with MASS. Since a user interacts with Cytoscape on her/his graph visualization, Cytoscape invokes both import- and export-network plug-ins. They respectively send the following commands to MASS, followed by a transfer of a lightweight graph representation with only essential information such as the vertex IDs and their neighbors:

• getGraph: initiates retrieving the in-memory graph from MASS that sends the serialized message to Cytoscape.
• setGraph: sends the current CyNetwork to MASS that rebuilds the corresponding GraphPlaces object inside of it.

These two commands are interpreted by CytoscapeListener automatically and are applied to a given graph in parallel of the main program. With its command interpretation in background, a user can repeatedly observe the progress of graph computation (line 7 below).

import MASS.*;
  

public class GraphVisualization {
  public void main(String[] args) {
    MASS.init( );
    GraphPlaces graph = new GraphPlaces(1, "EmptyGraph");
    
    MASSListener listener = new CytoscapeListener(graph);
    ...; // Graph computation
    
    listener.finish();
    MASS.finish();
  } 
}

As shown below, in a snapshot of Cytoscape’s GUI, by selecting the Import Network menu option, Cytoscape’s import-network plug-in kicks off the ImportNetworkTask module that sends a getGraph request to MASS CytoscapeListener to retrieve its in-memory graph. The plug-in then de-serializes the MASS response into a Cytoscape representation of the graph: a CyNetwork. To achieve a simple and consistent visualization of a graph, a few minor styles were applied to the Cytoscape nodes created (vertices with neighbors in blue rectangles, those with no neighbors in red circles, and a userclicked vertex in a yellow rectangle).

Cytoscale Graph Creation