Speaker
Description
Multicellular biological systems span many spatial and temporal scales, yet models of these systems are often developed in isolation, using different assumptions, algorithms, and software frameworks. Vivarium is an open-source compositional framework designed to make these models interoperable by allowing independently developed components to be connected through standardized interfaces and shared state variables. Rather than building monolithic simulations, Vivarium enables researchers to assemble complex models by composing modular processes representing different biological functions and modeling formalisms, including agent-based models, differential equations, flux balance analysis, and spatial simulators. In this talk, I will introduce the core ideas behind Vivarium and show how this compositional approach supports multiscale simulations of microbial and multicellular systems while enabling integration with existing modeling tools. By focusing on modularity, explicit interfaces, and reusable components, Vivarium aims to lower the barrier to composing large biological simulations and to support a more collaborative ecosystem for building and connecting models across the community.
