Welcome to Vivarium E. coli’s documentation!

Vivarium E. coli project is a port of the Covert Lab’s E. coli Whole Cell Model to the Vivarium framework.

A graph with blue, database symbol nodes at the top and orange, square nodes on the bottom. The blue nodes are connected by solid edges, while the orange nodes are connected to the blue nodes by broken edges.


This documentation is very much a work in progress. It likely contains errors and poor formatting.

The scope of this project is to migrate the Whole Cell Model’s processes, and therefore takes the model’s sim_data as its starting point in the simulation pipeline. sim_data is a large configuration object created by the parameter calculator (ParCa). For this reason the reconstruction/ and wholecell/utils/ folders have been duplicated here as they are necessary to unpickle the serialized sim_data object. If a new sim_data object is required to be read, the corresponding wcEcoli folders will have to be synchronized.

All state handling (previously handled by Bulk- and UniqueMolecules states/containers/views) and the actual running of the simulation (previously wholecell.sim.Simulation) are now handled entirely by Vivarium’s core engine and process interface.

The new process classes can be found in ecoli/processes/* and are linked together using a Vivarium topology that is generated in ecoli/experiments/ecoli_master_sim.py.