Free Software For Scientists – Cytoscape

A few years ago, a medical writer friend of mine showed me a paper on a new tool called Cytoscape.  He said, “see what you think of it, and let me know.”  At the time we were both working on a project called Genome5000, to knockout the 5000 most druggable genes in the human genome.  Any time you’re doing target validation studies, you want to get some idea of the pathways that may be effected in order to get a more mechanistic view of the phenotypes you’re observing.  And this was what sparked our interest in Cytoscape. 

Cytoscape is an open source project designed to help scientists visualize biomolecular networks.  It’s written in Java and thus runs on most operating systems.  Its main sponsors are UCSD’s Trey Ideker Lab, Memorial Sloan-Kettering, Institute for Systems Biology, and the Pasteur Institute.  Cytoscape has a rich set of plugins provided by a large number of contributors.  One of the more recent additions is a KEGG Pathway reader.

The latest release of Cytoscape (version 2.7.0) added support for BioPAX 3 networks and nested networks.  The latter allows you to simplify a complex diagram, by grouping sets of nodes into subnetworks and representing the subnetwork by a single node. 

Getting Started 

Getting started with Cytoscape is fairly simple:
  1. Go to the Cytoscape download page.  Fill out the short form, and submit it.  You will be taken to a page containing a list of download links.
  2. Select the link that’s appropriate for your operating system.  After your browser finishes downloading the installer program, start the installer, and follow the installation instructions.

Loading Pathways

One of the first things that you’ll want to do is load a pathway for your target of interest.  In my example, I want to see the pathways that contain VEGF.

  1. From the File menu, select Import Network from Web Services.  A dialog box will appear as shown below:
  2. My search for VEGF returned a number of different entries.  To refine the list, I click on VEGF/Rho/ROCK/Integrin Complex. This causes a pathway to appear in the network selection box on the right-hand side of the dialog.  I double-click the Signaling events mediated by VEGFR1 and VEGFR2 from the NCI Pathways database, and the network is then downloaded.  I click the close button to dismiss the dialog and I can now see a network.
  3. At first glance, the network is a real rats nest of nodes and edges.  However, if you select the Layout > yFiles > Organic layout you’ll soon see the nodes laid out in a more intuitive format.  The one comment here is that there doesn’t seem to be a way to layout the nodes based on their cellular localization.   I found an out-of-date plugin called Cerebral which was designed to do just this, but I couldn’t get it to create a new view based on the GO cellular localization data that I had.  I’m hoping to find out more at the Barcamp meeting next month.

Learning More

We’ve discussed the tip of the iceberg so far concerning Cytoscape.  There’s a lot more to this application than I can cover in a blog posting, including the ability to create networks based on gene expression data, an a web-based visualization tool called CytoscapeWeb.  The members of Cytoscape’s user community; however,  have created a number of online tutorials that you can access to help you learn more about it’s functionality.  In addition to the standard text/screenshot type tutorials, you’ll find some video tutorials posted on YouTube, thus making it easier to get started with Cytoscape. 


If you’d like to meet some of the developers of Cytoscape, they’ll be appearing at the Cytoscape Symposium and Retreat July 18-20 at the University of Michigan. And also at the San Diego Barcamp developers conference July 10-11th.

About Mark Fortner

I write software for scientists doing drug discovery and cancer research. I'm interested in Design Thinking, Agile Software Development, Web Components, Java, Javascript, Groovy, Grails, MongoDB, Firebase, microservices, the Semantic Web Drug Discovery and Cancer Biology.
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