June 2015
Intermediate to advanced
306 pages
6h 50m
English
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Plotting protein interactions with Cytoscape the hard way
Cytoscape (http://cytoscape.org/) is a platform to visualize 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 stored in the UniProt database.
Getting ready
You will need to install the Cytoscape version 3.2.1 (or higher), which will require Java 7 or preferably 8. You will also need the cyREST application ...
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