Compositional Systems Biology: An Executable Framework for Connecting Models Across Scales

Abstract: Biological systems are organized across interacting scales, from molecular networks and metabolic pathways to cells, tissues, microbial communities, and their environments, yet many computational models remain difficult to connect, reuse, or extend beyond the scale or formalism for which they were originally built. In this talk, I will introduce Compositional Systems Biology, an approach for building multiscale biological models from interoperable processes with explicit interfaces, shared state representations, and well-defined orchestration patterns governing when and how model components are executed. At the core of this work is Vivarium, an open-source platform for multiscale simulation that integrates diverse modeling formalisms -- including ODEs, stochastic kinetics, constraint-based models, agent-based dynamics, and rule-based logic -- within a unified execution framework. I will describe how this framework has been used in whole-cell modeling, including vEcoli, a comprehensive model of E. coli integrating mechanistic submodels of metabolism, transcription, translation, macromolecular synthesis, and cell division, and then discuss how the same compositional principles are being extended toward microbial systems, host-microbiome interactions, and spatially resolved multicellular tissue models. Throughout the talk, I will emphasize how executable composition can link biological structure to function, support transparent model reuse and validation, and create new opportunities for collaborative modeling across systems biology, computational medicine, and tissue-scale simulation. Bio: Eran Agmon is an Assistant Professor at the University of Connecticut School of Medicine and a member of the Center for Cell Analysis and Modeling. His research focuses on software infrastructure and theory for compositional, multiscale biological modeling, motivated by a longstanding interest in cells as both integrated molecular systems and adaptive agents that function within, respond to, and reshape their environments. He is a Principal Investigator on DARPA's Simulating Microbial Systems program, where his group is developing hybrid simulations of E. coli that integrate mechanistic, agent-based, and constraint-based models, and a co-Investigator with the Center for Reproducible Biomedical Modeling, contributing to community standards, reusable simulation pipelines, and infrastructure for interoperable computational biology.