As of today, the Agmon Lab (also known as the Vivarium lab) is open in the Center for Cell Analysis and Modeling. Our research is twofold: 1) we are developing computational methods for combining multi-omics datasets and diverse models into multi-scale simulations, and 2) we are applying these approaches to build mechanistic simulations of whole cells and microbiomes, which span molecular to multi-cellular scales.
I am very pleased to announce that I will be rising to the ranks of Assistant Professor this July, as a faculty member at UConn Health’s Center for Cell Analysis and Modeling, and the Molecular Biology and Biophysics Department. See news release: Eran Agmon joins CCAM
The paper on the Vivarium framework, “Vivarium: an interface and engine for integrative multi-scale modeling in computational biology,” has been accepted for publication at Bioinformatics. Check it out here.
As an undergrad at UCSD’s Dept of Cognitive Science, I was deeply influenced by Gilles Fauconnier and am saddened to learn of his passing earlier this year. In revisting his landmark book, The Way We Think, I am excited to see just how much his notion of conceptual blending still resonates with my research. The figure below illustrates “double-scope integration”, in which two input conceptual frames are brought together into a blended frame that can lead to novel insights. This is what I aim to systematize with integrative modeling software – the capacity to blend models of different biological properties, and through their integration to reveal novel biology.
Combine simulations @Vivarium! We’re in the BioSimulators pipeline: https://biosimulators.org. BioSimulators is a free registry of biosimulation tools, with a standardized interface. The simulators support a broad range of frameworks (e.g., logical, kinetic), simulation algorithms (e.g., FBA, SSA), and formats (e.g., BNGL, CellML, NeuroML/LEMS, SBML, Smoldyn). And with Vivarium, they can now be combined to create novel multi-scale simulations.
This dives into the code – how to make a simulation process, a simulation composite, and how to run co-simulations across hierarchies and at different scales. https://vivarium-core.readthedocs.io/en/latest/tutorials.html
Vivarium-ecoli documentation I have been working with a talented team of students to migrate the Covert Lab’s E. coli Whole Cell Model to the Vivarium framework. This took the models of cellular subprocesses (such as metabolism, transcription, and chromosome replication) modularized them, refactored their parameter handling, and rewired them together into a composite model. These can now be recombined in alternate models, and built upon by wiring in different models of mechanisms. We are excited to see how it will be used by the computational systems biology community.
I’m excited to join NASA’s Center for the Emergence of Life as a research affiliate – see here. I’ve been working on a project with Gabrielle Cohn, Andrew Pohorille, Milena Popovic, and Mark Ditzler to use machine learning to characterize RNA function from sequence and structure. The results promise to reveal the fitness landscape and evolution of early life in the RNA world.
The Vivarium Collective website is up. This is a central forum for posting vivarium projects, providing a friendly front-end to the internet.
The Vivarium preprint is out! Available here