Notes from the Cytoscape Workshop

Recently, the Sanford Burnham Consortium hosted a workshop on Cytoscape.  Cytoscape is a tool for representing networks.  It’s primary users are biologists wanting to understand different types of biological networks, but it can also be used for computer networks, or social networks. The project is a multi-institutional collaboration between UCSD, the Institute for Systems Biology, Memorial Sloan Kettering, and the Pasteur Institute among others.  And this bit of workshop pre-reading gave a pretty good overview of how biologists could use Cytoscape in the wild.

The workshop started with a number of introductory talks that provided an overview of the project, showed some examples of how Cytoscape has been used in the past, and showed an example of recent work in analyzing prostate cancer genes.  At that point the meeting broke into separate sessions for beginners and advanced users, and since a colleague and I were attending we each took different sessions.

The advanced session, which I attended, gave a good overview of some of the features from the upcoming 3.10 release of Cytoscape. You can download the current beta version of it here.  The release includes features like:

  • The ability to export networks and style information as JSON.  This feature is particularly important if you want to be able to create a network in the Cytoscape desktop application, and share that data with colleagues via a simple web page.  The Cytoscape.js library can be used to render the JSON data.
  • An improved welcome screen that helps you get started with Cytoscape.  The previous version opened onto a blank screen and left you wondering “now what do I do”.
  • A command-line and REST interface.
  • Improved Vizmapper — this is the tool that lets you assign styles to different types of nodes and edges in the network.
  • Faster network filtering.
  • Improved support for PSICQUIC

You can see the workshop materials here.

Human interactome - round2 - Cytoscape

Human interactome – round2 – Cytoscape (Photo credit: andytrop79)

The usual results that I end up with when playing with Cytoscape are less than stellar and share more than a passing resemblance to a hairball.  So I was determined to learn some tips and tricks for visualizing lots of information more clearly.

In upcoming posts, I’ll talk more about these features and some of the ideas that the workshop generated, and some of the results from my own project.


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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