UCSD Researchers Taking First Steps Toward Creating the 3D Virtual Cell

Currently, three-dimensional models of cells are drawn by hand, while two-dimensional molecular graphics are processed by computers.

“We’re trying to move towards the ability to simulate computationally the actions of a living cell, all the metabolic processes, regulations, replications, these types of biological processes,” Philip Bourne, professor of pharmacology at UCSD’s Skaggs School of Pharmacy and Pharmaceutical Sciences, said.

The idea stemmed from Bourne’s work with changing the general scientific model. He is a proponent of open access, a business model focused on making science accessible.

“Science is a very competitive business, and I think part of it is going to be to change that competition model into more of a collaborative model,” Bourne said.

Bourne said the 3D Virtual Cell is more than just a technological advancement — it is about changing how science works by increasing productivity through collaboration.

“Science is very inefficient,” Bourne said. “90 percent of research time is spent getting ready for the results, and only 10 percent is getting the actual results.”

Bourne wants to increase productivity in the earlier stages of research. He said that time could be better allocated if the scientific process were available to everyone, because much of the setup process that competing groups go through is the same.

He said the biggest challenge that he and his team face in their approach is the lack of community among scientists, because scientists often focus only on one specific area of expertise.

“When you’re looking at a virtual cell, you’re looking at many biological scales,” Bourne said. “Someone looks at molecules, someone looks at organelles, someone looks at whole cells. And they don’t communicate very well with each other, and they’re definitely not [a] community.”

Bourne and his team received $600,000 in seed funding from the NSF for initial planning of the project and conference. He estimates the project will need a minimum of $2 million per year to be sustained.

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