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.

Warning

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

Tip

Any text formatted like workflow is a clickable link to detailed API documentation.

• Stores
  • Bulk Molecules
  • Unique Molecules
  • Listeners
• Processes
  • Registration
  • Parameters
  • Partitioned Processes
  • Connecting to Stores
  • Time Steps
• Composites
  • Partitioning Modifications
  • Division Modifications
  • Log Updates
  • Initial State
• Experiments
  • Configuration
  • JSON Config Files
  • Output
  • Schema Overrides
  • Colony Simulations
  • Create Your Own
• Workflows
  • ParCa
  • Variants
  • Simulations
  • Analyses
  • Workflows
  • Sherlock
  • Progress
  • Fault Tolerance
  • Output
  • Troubleshooting
• Output
  • Stores to Emit
  • Serializing Emits
  • In-Memory Emitter
  • Parquet Emitter
  • Other Workflow Output
• Tutorial
  • New Process
  • New Variant
  • New Analysis
  • Run Workflow
• Documentation
  • Reading Documentation
  • Writing Documentation
• API Reference
  • ecoli
  • reconstruction
  • runscripts
  • validation
  • wholecell