We recently published our Cytoscape App to the Cytoscape App Store.
Cytoscape is a wonderful graph visualization tool that is open-source, available on Desktops, and quite handy for graph analysis and visualization.
Our plugin allows Cytoscape to connect to databases, servers, and Apache Spark/Hadoop using the VitalService API.
The plugin is available directly in Cytoscape, or here: http://apps.cytoscape.org/apps/vitalaigraphvisualization
Cytoscape is available here: http://cytoscape.org/
Prior to using the plugin, the Vital AI software must be installed and configured. The Vital AI software can be downloaded from here: http://vital.ai/#download
The Cytoscape plugin uses the VITAL_HOME environmental variable to find the Vital AI software and configuration files.
For those using Mac OSX, OSX needs some extra help for desktop applications like Cytoscape to use environmental variables.
Here is a good StackOverflow answer which helps Mac OSX use environmental variables: http://stackoverflow.com/a/32405815/2138426
The first tab in the Vital AI plugin enables selecting which VitalService endpoint to connect to. These come from the VitalService configuration file found at:
For Prime endpoints, an authorization key is used to connect. For convenience, you can put such keys into your vitalsigns configuration file, like so:
The naming convention is: “vitalservicename”-key
So, the corresponding VitalService configuration entry would be:
type = VitalPrime
appID = analytics
endpointURL = “http://127.0.0.1:9081/java”
Now back to the plugin…
Here is the Connection tab. Select the desired VitalService endpoint from the drop-down and hit “Connect”.
Now that we have connected, we can use the “Search” tab to search.
We can select which databases (“Segments”) to include, as well as what property to search. In this case the “Wordnet” database is selected and the “name” property.
Let’s put all the results into a network.
Now let’s select them all and find what is connected to them. This is called an “expansion” query and looks for everything connected to the starting node up to two hops (edges) away.
Starting the expansion…
Expanding all the selected nodes… The “Paths” tab is used to select whether the expansion will be for one hop (one edge) or two hops (two edges), the direction of the desired edges (forward, backward, or both), and which “Segments” to include in the expansion.
And now we have some results!
Let’s zoom in on part of the network. We can then further analyze the results, continue to explore and expand the network, or tune the visualization.
If we are connected to a Prime endpoint, we can use the Paths tab to select the node and edge types to filter with during an expansion query.
Also with a Prime endpoint, we can use the “DataScripts” tab to run datascripts on the server. Datascripts can be used to analyze data, trigger Spark or Hadoop jobs, use a prediction model, or anything you like.
Please send along any comments or questions, and hope you enjoy using Cytoscape and our plugin to visualize your data.