wcEcoli colonies paper is out on PLoS CB
The first paper on vivarium-ecoli is out! Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses has been published in PLoS Computational Biology. This project used Vivarium to reconstruct an existing E. coli whole-cell model, expand it with several new submodels, and nest it within a spatial environment shared by many independent whole-cell E. coli models running in parallel. This effectively connects molecular-level events with colony-level phenonema. Perhaps the most multiscale model ever?