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.

• Processes
• Composites
• Experiments
• Tutorials
  • Vivarium E. coli Processes
  • Vivarium E. coli Composites
  • Allocation using PartitionedProcess
  • E. coli Simulations
  • Colony Simulations
• Working with Documentation
  • Reading Documentation
  • Writing Documentation
• Stores
  • Bulk Molecules
  • Unique Molecules
• API Reference
  • ecoli
  • reconstruction
  • validation
  • wholecell

Warning

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.