Video Tip of the Week: yEd Graph Editor for visualizing pathways and networks

This week’s video tip of the week closes out a series that began last month. I started to explore one gene co-expression tool, which led me to another tool for visualization, and so on. This week’s tool is the final piece that you need to know about if you want to create the kind of interaction/network diagrams used in the modeling of a system that I covered last week.

The yEd Graph Editor is different than some of the tools. As a corporate product, it doesn’t have

yFiles layouts options in Cytoscape

yFiles layouts options in Cytoscape

the kind of scientific paper trail that some academic tools will. But if you search Google Scholar for “yED Graph Editor” you’ll see people from a wide range of disciplines have used it for their research projects. I first learned about yEd when I was using Cytoscape, and saw that some of the choices for layouts were based on the yEd features. This short overview video from the yWorks folks will explain what some of those layout styles are.

As you can see in this video, the use of yEd is not only for biological interactions–it can do a whole lot of graphing that is entirely unrelated to biology. But the features work for biological networks, and you can customize the graphics to represent your own topic of interest.

There are longer videos with more detail on the use cases for yEd. This one uses a sample flow chart to illustrate the basic editing features. It quickly covers many helpful aspects of establishing and editing a visualization.

You can also find videos from folks who use yEd for their projects on YouTube, some of which might be more specific for a given field of research. But these should give you the basics of why yEd can be used for the types of projects that you saw in the previous tips with Virtually Immune and BioLayoutExpress3D. And like I noted with Virtually Immune, you can get your hands on the files in the Pathway Models collection, and launch a yEd file to go into the features with a detailed example. The complexity you can generate with these models is astonishing.

There was no reference specifically for yEd that I was able to locate, but you can find that lots of people use yEd graph editor on a wide range of research topics in Google Scholar. So if you are looking to see if someone in your research area has used yEd, you may find some examples. If you are going to consider exploring the BioLayout and Virtually Immune tools, it will help to understand the framework. And also as I mentioned in Cytoscape–understanding yEd helped me to grasp the layout options there too. So try out yEd for pathway and network visualization if you have needs for those types of representations in your research and presentations. It’s free to download and use.

Quick links:

yED Graph Editor:

yEd Graph Editor Manual:


Wright D.W., Tim Angus, Anton J. Enright & Tom C. Freeman (2014). Visualisation of BioPAX Networks using BioLayout Express3D, F1000Research, DOI:

Smoot M.E., K. Ono, J. Ruscheinski, P.-L. Wang & T. Ideker (2010). Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics, 27 (3) 431-432. DOI: