Cytoscape Users Meeting, Seattle April 25th

Download and unzip:

  1. The Basics Part I (Iliana, ~15mins)
    • What is Cytoscape
    • Installing Cytoscape & running it (go to download page, do not actually download!)

    • Quick tour of Cytoscape (start Cytoscape, quick review of the Cytoscape Desktop)
    • Network loading, network file formats (SIF, GML, major differences)
    • Node naming in Cytoscape (as explained in Cytoscape manual)
    • Network layout (quickly show it, do a layout)
    • Navigation: selection of nodes and edges, zooming operations, network overview window, cyto-panels, etc.
  2. The Basics Part II (Allan,~15mins)
    • Node attributes loading, node attributes file format, same for edge attributes
    • Attributes browser
    • Visual Sytles (explain, simple edit of an existing one, expression data section of tutorial will show students how to create a continuous calculator)
    • Cytoscape Properties Dialog
  3. Filters and Editor (Allan, ~15mins)
  4. Expression Data (Aditya,~20mins)
    • File format
    • How to load the file, view it in attributes browser
    • Visual style setting of node colors
    • PValues
    • If time, mention available plugins for expression data, perhaps show DynamicExpression

  5. Gene Ontology (Mike,~15mins)
    • Gene Ontology server wizard
    • How to annotate genes in the network
    • How to load your own annotations file for your species
  6. Plugin Overview (group,~25mins)
    • Mike: How to load plugins
    • Mike: Show plugins page on and mention variety
    • Mike: BINGO, GraphMerge

    • Aditya: LitSearch

    • Iliana: BioNetBuilder, NetworkAnalyzer

For this section we will divide into 3 groups of ~13 students. Each group will have two moderators, one of which should take notes. The moderators are: Allan, Aditya, Annette, Mike, Iliana, and an ISB volunteer for taking notes, Susi.


The first 30 mins should be spent playing the evolution game that Ethan Cerami invented. The game goes like this:

After the evolution game, the following list of discussion items can be shown/distributed to start a discussion for the next hour.

Following are topics of interest that we would like to cover in the user discussions. They can be used to prompt discussion if needed. Idea is to quickly show a list of topics at the beginning of the discussion session, then let the audience drive.

1. Installation experience.

2. Running Cytoscape

3. User interface and usability. Are the GUI features intuitive?

4. Visual Styles

5. Performance & responsiveness: Operations on large networks too slow?

6. Features: which are useful? useless?

7. Plugins: Are they easy to use?


IlianaAvila April 26th, 2006

I think that the meeting went well. We had a chaotic start because students were having issues with connecting to the wireless network. Additionally, students were running OS X and Windows. The students that were running Windows had no problems to launch Cytoscape (just double click on the .bat script). But OS X students could not double click on to run Cytoscape. Some of them double clicked on cytoscape.jar, but the plugins did not get loaded. The instructors had to personally help them by opening a terminal and typing ./

First lesson: we need to have an OS independent way of starting Cytoscape that loads plugins

Student's previous experience with Cytoscape varied from none to as much as 6 or more months of using it. Therefore, some of them thought the tutorial's pace was too fast, and others felt it was too slow. Additionally, the tutorial needs to be more seamless, and, more focused. Suggestions to improve the tutorial are:

The ISB user's presentations of their research using Cytoscape were very well received. These talks helped students to tie together concepts we had taught during the tutorial, and showed them how to use them in practice. Also, the fact that the research projects were published gave users high confidence in the usefulness of Cytoscape. The speakers did a very good job of clearly stating how Cytoscape facilitated the process of creating biological hypothesis that would be hard to come by without using Cytoscape.

During lunch, I shared a table with 3 students, and learned more about them. Important things I remember about our conversation were:

The discussion in my group was very productive. We played the evolution game, and there were two winning ideas:

People seemed to be happy after we adjourned. It seems to me that Cytoscape has a great opportunity to grow and reach more people right now. I think we need to take advantage of this opportunity now by focusing some of our resources on this kind of outreach projects and trying to base our releases on some of the issues that are brought up by end-users.

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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