Plotting protein interactions with Cytoscape the hard way

In this recipe, we will use Cytoscape (http://cytoscape.org/), which is a platform that's used for visualizing molecular interaction networks. Here, we will interact with Cytoscape using a REST interface. There are easier ways to perform this recipe, but we will take this opportunity to continue interacting with the PSICQUIC service. Also, we will exercise the NetworkX graph processing library (https://networkx.github.io/), which will be useful on its own.

Taking a page from Chapter 7, Using the Protein Data Bank, we will plot p53 interactions that are stored in the UniProt database.

Getting ready

You will need to install Cytoscape version 3.6.1 (or higher), which will require Java 8 (currently, it does not work with 9). You will also need the cyREST application in Cytoscape (see the Apps main menu in Cytoscape for this). The code will use a REST interface to communicate with Cytoscape, so it will run outside it, but it will require...