The power of data visualization, according to Gary Bader

“When a researcher runs a genomics experiment, they're immediately faced with more data than they can handle,” says Gary Bader, University of Toronto professor and Donnelly Centre PI. “That's increasing over time. Experiments are generating more and more data at exponential rates.” 

Bader was early in his career when he realized the widespread need to visualize biological pathway data. As a PhD student focused on the creation of network analysis methods, he joined forces with Seattle-based researchers at the Institute for Systems Biology to help begin to fill the large gap of genomics visualization software. That project in 2002 shaped Bader’s career, paving the way for the creation of different open source software platforms. The collaboration grew into the 2003 public release of Cytoscape, a visualization software platform primarily developed to aid biological data interpretation. Later, a 2007 paper expanded the use of the software, showing users how to combine networks with genomics data, and how to use that network information to interpret that data. 

“Before visualization software, people had to manually draw the networks. They mostly didn't,” says Bader. “There's only a handful of such networks drawn that I've seen. Otherwise, [researchers] would look at big tables of information without getting the big picture view of it. They'd go through a table view and see A and B are related, C and D are related, but they wouldn't think about networks.” 

Cytoscape changed that status quo. The program displays molecular interaction networks with integrated annotations and gene expression profiles, creating a visual that helps biologists understand how genes are related to each other and how they function. 

“You can get information about the genes, which are the circles,” Bader explains, pointing to a generated image. “These lines that connect them are experimental information that might've been collected in this building.” 

It was a novel development: Bader recalls being a student, introducing the idea of network visualization to the field of biology and showing the software to Charlie Boone, another professor and PI at the Donnelly. At the time, Boone had a pile of budding yeast protein interaction data and was unsure how to interpret it. 

“I showed him the spreadsheet data as a network view, revealing the proteins that were involved in the budding process,” says Bader. “It made sense immediately: Charlie recognized new biological patterns in the data, which formed the basis of a paper that was later published in Science. These patterns weren’t obvious from the spreadsheets. That's the power of visualization." 

Cytoscape has gone through many updates over the nearly two decades it has been available, including the addition of hundreds of community-submitted applications (apps), covering further support in every area. 

Because of his work, Bader now holds the title of a Highly Cited Researcher, as determined by analytics company Clarivate. The Cytoscape software has been downloaded over 1 million times with millions of separate app installations. 

“Over time it's expanded, but it's still the standard for anyone who makes a network with an experiment,” Bader says. “There’s a good chance that a network picture you see in a publication is made with Cytoscape.”