IMAG/MSM WG Multiscale Modeling and Viral Pandemics Zoom

To join the meeting:  
https://iu.zoom.us/meeting/register/tZYqd-2srD8tGtCXDem4Cka08rBz5fDW0EQR

Please feel free to forward this invitation to anyone you think would be interested.

Thursday May 15, 2025 at 10:00PM (EST)

We are moving the seminar time from 3pm EST to 10 am EST STARTING MAY 15th.

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.