November 2018
Intermediate to advanced
360 pages
9h 36m
English
Content preview from Bioinformatics with Python Cookbook - Second Edition
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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 Cytoscape to be running, so start Cytoscape with cyREST before running the following recipe.
You should also install py2cytoscape (via pip) and NetworkX. You can find this content in the Chapter10/Cytoscape.ipynb Notebook.
As this will require a massive download of software, the Chapter10/Cytoscape.ipynb Notebook will not work in our Docker implementation.