Researchers at UConn Health's Virtual Cell Project say they have made it easier for cell biologists to build complex biological models. Details on the updates to their VCell software program were published earlier this week in the Biophysical Journal.
The Virtual Cell, or VCell, reportedly offers a comprehensive set of modeling and simulation capabilities for cell biology. It allows biologists without strong math or computer programming skills to build models and simulate how a cell functions. VCell first came online almost 20 years ago, and the UConn Health team headed by biophysicist Leslie Loew has developed and maintained it since.
Expectations have changed in this age of iPhones and computers you can navigate with swipe and click. Unfortunately rule-based modeling remained complex and catching mistakes in thousands of lines of repetitive, almost-but-not-quite-identical code was maddening. Cell biology models quickly get so unwieldy that only an experienced modeler or programmer can handle them.
Loew and the VCell team decided to make things easier for cell biologists. In their new paper, they describe a user interface for VCell that uses colored shapes to represent molecules. Bubbles show binding sites, and lines show links between molecules. The links can also be different colors and shapes to represent different interactions. A simple model describing hemoglobin resembles a map or wiring diagram.
Instead of writing thousands of lines of code, biologists using VCell can now just define their molecules and explain to VCell how they can interact with each other. The biologist doesn't have to worry about the combinatorial explosion. The computer, all 60 teraflops, 3,000 processors, and 2 petabytes of storage hosted at UConn Health's Cell and Genome building, handles it.
Loew believes the new version of VCell will dramatically expand the number of people who can use rule-based modeling because it facilitates use of the comprehensive set of simulation methods available in VCell in a single, unified, user-friendly software environment.