Bioinformatics with Python Cookbook - Second Edition

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The preceding example was designed to exercise more than the REST interface to Cytoscape; we interfaced with the PSICQUIC server and used the NetworkX graph library, a functionality that can be useful without Cytoscape. To start with, there is plenty of documentation for NetworkX and Cytoscape available on their web pages (https://cytoscape.org/, https://networkx.github.io/). The Kyoto Encyclopedia of Genes and Genomes (KEGG) is one of the most useful resources that you can use with Cytoscape; as this is very well-documented, we opted for a less common example based on UniProt. A fantastic piece of documentation for interacting with Cytoscape via REST interfaces using IPython, including a KEGG example, is available at http://nbviewer.ipython.org/github/idekerlab/cy-rest-python/blob/develop/index.ipynb ...