The Agmon Lab is focused on developing comprehensive, multi-scale models of cells –- from their molecular underpinnings, to their integrated functions, to the organismic level with many heterogeneous cells interacting in a shared environment. The last two decades of biological research have generated abundant experimental data on the molecular composition, spatial organization, and dynamics of thousands of cell types; however, we need new tools that can transform this data into predictive models that can be used for scientific discovery. Rather than building isolated models that capture a narrow range of cellular behavior with a single class of representation, the next generation of computational models will need to combine multi-source and multi-level data with diverse, meaningful representations of biological mechanisms into integrative multi-scale simulations. These simulations will be used to interpret the input datasets, make experimental predictions, identify medical solutions, and help us understand fundamental principles of biological organization.

To support this vision, the Agmon lab is building Vivarium –- an open-source ecosystem of modular biological models. We have several projects that apply Vivarium in the domains of single cell bacterial physiology, community interactions in microbiomes (both ocean microbiomes and gut microbiomes), synthetic cells, and the origins of life.

Research keywords

computational systems biology, multi-scale modeling and simulation, cell biology, machine learning, complex adaptive systems