Authors: Chi Nam Ignatius Pang and Tara Bartolec

This Cytoscape workshop include step-by-step instructions on how to visualize a small protein-protein interaction network of around 300 proteins and 230 edges that was generated from cross-linking mass spectrometry (XL-MS) experiments (Bartolec et al. 2020 Anal. Chem. 92(2):1874–1882 https://doi.org/10.1021/acs.analchem.9b03975).

Cytoscape can be downloaded from this website (https://cytoscape.org/download.html). It requires Java 11 (https://adoptopenjdk.net/). This tutorial was developed based on version 3.8.0 of Cytoscape but in theory should work with later releases as well.

These tutorial materials were created for the 1st Australasian Data Visualisation and Bioinformatics Symposium (ADVBS), pre-Lorne proteomics conference workshop. The workshop was held 4 - 5th February 2020 in Melbourne University.

The PDF of the tutorial notes is attached and the original document is available in Google Doc via this hyperlink: https://docs.google.com/document/d/1Z1ClYtVAUuxVbTGlORAGb5McaOoHwgXcFBusgEZmGhs/edit?usp=sharing