Vivarium-ecoli is now public
Vivarium-ecoli is the Covert lab’s new version of the E. coli whole-cell model, built entirely with the Vivarium framework. This combines over a dozen independent sub-models, which have been fitted with the Vivarium interface to make them into reusable modules – these can now be recombined in alternate models, and will be a valuable resource for the modeling community and for future research. In addition to modularizing the whole-cell model, we combined agent-based modeling to support running multiple heterogeneous E. coli models in parallel within a shared environment. The result was a multiscale model that facilitates the study of emergent population-level behaviors with single-cell molecular resolution. Paper coming soon.