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.

Written on September 25, 2021