Omphalos brings AI-assisted mechanistic modeling to McMaster University

From May 6 to June 17, 2026, Omphalos hosted McMaster University biology students for a seven-week internship through SCIENCE 3XR3: Collaborative Immune System Modeling and Simulation. Students trained in biological system modeling, using an AI-assisted L++ workflow to build mechanistic disease models that could be run as simulations.

Student teams developed four integrated L++ models covering Huntington's disease, rheumatoid arthritis, pulmonary fibrosis, and hantavirus infection. They learned to test biological hypotheses through simulation, collaborate on GitHub, and present their work to an industry review panel. Dr. Elly Zhou of the University of Toronto and University Health Network joined as a guest speaker. She is the first author of a recent Nature Biotechnology paper on digital twins of ex vivo human lungs.

The collaboration gave Omphalos an opportunity to evaluate its technology and learn how students use it. It showed how AI-assisted modeling can make computational biology more accessible while maintaining rigorous scientific reasoning. Students described AI as a useful tool for implementing models and emphasized that researchers remain responsible for the scientific validity of their work.