Eran Agmon, University of Connecticut Health
Compositional Systems Biology with Vivarium: Enabling Scalable, Hybrid Simulations of Cellular Systems
As biomedical models grow in complexity, the need for modular, extensible frameworks becomes increasingly important. This talk introduces Compositional Systems Biology, a domain of systems biology focused on building multiscale biological simulations through modular, interoperable processes. Central to this approach is Vivarium, an open-source software for integrating diverse modeling formalisms—including ODEs, stochastic kinetics, constraint-based models, agent-based systems, and rule-based logic—into unified, hybrid simulations. A flagship demonstration of Vivarium’s capabilities is the implementation of a whole-cell model of Escherichia coli, which integrates over a dozen mechanistic submodels spanning metabolism, gene expression, macromolecular synthesis, and cell division. This model demonstrates Vivarium’s strengths in managing biological complexity through schema-driven composition, modular interfaces, and distributed orchestration. I will discuss design principles behind Vivarium, showcase applications, and preview emerging tools that enable collaborative, scalable, and open-ended systems biology.
1. Agmon, E. (2024). Foundations of a Compositional Systems Biology. ArXiv, arXiv-2408. https://arxiv.org/abs/2408.00942
2. Agmon, E., Spangler, R. K., Skalnik, C. J., Poole, W., Peirce, S. M., Morrison, J. H., & Covert, M. W. (2022). Vivarium: an interface and engine for integrative multiscale modeling in computational biology. Bioinformatics, 38(7), 1972-1979. https://academic.oup.com/bioinformatics/article/38/7/1972/6522109
The presentation slides are available here.
The YouTube video is here.