Scientists Develop Virtual Cell Modeling Program to Simulate Biological Behavior

Scientists Develop Virtual Cell Modeling Program to Simulate Biological Behavior
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A collaborative team of scientists from Indiana University, Johns Hopkins Medicine, the University of Maryland School of Medicine, and Oregon Health & Science University has developed an advanced computer program capable of simulating the behavior of human and animal cells. Published July 25 in Cell, the research aims to improve predictions of cell behavior, drug responses, and disease progression—potentially reducing the need for early-stage live cell experiments.

The program builds on previous software called PhysiCell, created by Indiana University professor Paul Macklin, and uses agent-based modeling to replicate cellular activity. Each cell type is represented by a “math robot” agent, which operates based on rules tied to genetic and environmental conditions.

This allows researchers to simulate complex biological processes, such as tumor development or brain cell organization. Unlike traditional modeling tools, the updated software is designed for accessibility. Using a simple spreadsheet format, scientists without advanced programming skills can match cell types to readable rules, which are then translated into mathematical models.

This innovation enables rapid model creation and supports spatial transcriptomics—mapping how cells function within 3D tissue environments. The program has already been used to replicate cancer and brain development scenarios, including modeling tumor cell responses to immune system activity. These digital simulations closely mirrored laboratory findings, validating the software’s predictive capabilities.

Ultimately, researchers envision the program as a “digital twin” of living systems, helping to prioritize hypotheses and guide laboratory research. Ongoing development includes integrating artificial intelligence to enhance model generation and data interpretation.