Welcome to Vivarium E. coli’s documentation!

Vivarium E. coli is a port of the Covert Lab’s E. coli Whole Cell Model to the Vivarium framework. For more scientific modeling details, refer to the documentation for the original model as well its corresponding publication (10.1126/science.aav3751). This website covers how the model was implemented using Vivarium and describes the user interface for developing and running the model. We recommend new users read through the sections below in order.

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

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