Michael Ellison

University of Alberta

If DNA and nucleic acids are the building blocks of life, there is a virtual construction zone at work at the University of Alberta.

The creation of virtual cells – ones that can be manipulated and studied in cyberspace – is close to reality at the university’s

Institute for Biomolecular Design.

“We’ve managed to speed up the process by about 10,000 times,” says Ellison, executive director of Project CyberCell

and a biochemistry professor at the university. “We expect to create a complete compulational model of a simple living cell in two years.”

Project CyberCell has been in operation since 2002. Its goal is to create an accurate, dynamic and virtual model of a simple living organism. Since its inception, the $15.6 million project has filed two patents.

Their work is attracting attention from around the globe.

“We’re really the only group in Canada tackling this problem,” Ellison says.

CyberCell uses the uni-cellular Escherichia coli (E.Coli) bacterium as its model. Even though it is one of the simplest micro-organisms the team could have chosen, E.Coli still contains more than 4,600 different proteins that must be explored.

So far, the group has begun to define the minimal set of genes required for an E.Coli cell to survive within optimal conditions.

A major focus for the group has been the development and refinement of a virtual cell membrane, says Ellison.

“(The membrane) is really what defines a cell from its environment,” he says.“It controls how the cell responds to its environment and interacts with its environment.”

Using their virtual version of E.Coli, the group is attempting to create a computer mimic of the membrane’s processes, function and design.

“We are in the process of getting the membrane to grow and divide,” says Ellison.

In the background, Project CyberCell is using WestGrid resources to conduct benchmarking studies. The simulations they use require large amounts of computational power, Ellison says.

WestGrid’s high performance computing facilities enable the group to perform and perfect the simulations needed to create their virtual components of a living cell.

Eventually, Ellison says, the team will be at a point where it can accurately model the machinery within a cell that creates DNA and builds proteins.

The simulations are a benchmark for biology’s evolving relationship with computers, he adds. For many years the field has lacked the ability to simulate its experiments, Ellison says. This Achilles’ heel became more pronounced as other more physical fields, such as engineering, continued to advance their simulation capabilities.

A project like CyberCell using WestGrid technology helps close that gap. CyberCell’s experiments with E.Coli cells have opened new doors to the possibilities of studying in a virtual environment.

And ultimately, these simulation capabilities bring CyberCell another step closer to creating a virtual micro-organism. This could be used not only to cut health care costs, but also speed up the development of new drugs and test new treatments.