Cytoscape – Visualizations demystified


Cytoscape is open source tool for complex network analysis and visualizing networks. Cytoscape’s initial goal was to

  1. visualize molecular interaction networks and biological pathways
  2. integrate these networks with annotations, gene expression profiles and other state data

But, users brought lot of innovation to use of cytoscape and started using it for visualizing and analyzing different networks like social networks, traffic networks etc. Soon, Cytoscape became general tool for all network analysis and visualization.

Cytoscape core product gives a basic set of features for integrating the data, analyzing the data, and visualizing the network data. If you are looking for additional features related to specific analysis, apps or plugins are present in their apps market which are tailered towards network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.   These apps are generally produced by users of Cytoscape in Java. Most of the Apps are free and are available at Cytoscape App Store.


Here is how analysis window looks –


Pros –

  1. Open source tool available for free. Most of the analytics plugins are also free.
  2. Takes care of big data analytics problem and has no limits on how much data can be inserted into the tool for visualization
  3. Integrates easily with Python and Java.
  4. Easy to use GUI. No need for programming for basic visualization and analysis.

Cons –

  1. For complex research like network simulation, centrality measures calculation etc; there are no apps for now in apps market place of cytoscape.
  2. No apps for ETL of the data. So, you have to perform all the data transformation and cleaning in Python then load the cleaned data into cytoscape for further visualization.
  3. As initial app was developed only for molecular activity visualization and protein-protein interaction, generalization to other network analysis is bit tough and needs certain innovation from programming perspective.

Summary –

If you are looking for an app to visualize your network data and come up with basic analysis before investing way too much in terms of tool, cytoscape is perfect for you. Also, this is one of the best and most sophisticated apps for biological network analysis and research.