Welcome to the documentation for Vivarium Core!

Vivarium is a multiscale platform for simulating cells in dynamic environments, within which they can grow, divide, and thrive.

A sequence of six frames showing simulated *E. coli* colony growth. The colony grows from a single cell in the leftmost frame to around 100 in the rightmost.

Introduction

A vivarium, literally a “place of life,” is a controlled environment in which organisms can be studied. You might have encountered examples of vivaria like an aquarium or a terrarium. The Vivarium project provides a framework for creating a computational vivarium which can simulate colonies of cells in shared, dynamic environments.

The platform’s framework is a novel synthesis of several modeling methodologies:

  1. Whole-cell modeling, to simulate hybrid models of cells with complex internal organization.

  2. Agent-based modeling, to simulate the interactions of many cells in a shared environment.

  3. Multiscale simulation, to solve problems with multiple scales of time and space.

  4. Wirable model modules, to streamline model development by decomposing computational representations into modules that can be reconfigured and recombined.

This project, Vivarium Core, is the core engine that can simulate models built using the Vivarium interface.

Using This Documentation

If you want to run Vivarium, start with our getting started guide, which will walk you through getting Vivarium up and running.

For step-by-step instructions, check out our tutorials.

For a technical deep-dive into the important concepts in Vivarium, check out our topic guides.

If you want to look something up like the configuration options for some process or the definition of a word, see our reference information.