Welcome to the documentation for Vivarium Core!¶
The Vivarium Core library provides the Vivarium interface and engine for composing and simulating integrative, multiscale models.
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 building biological systems in-silico.
Vivarium does not include any specific modeling frameworks, but instead focuses on the interface between such frameworks, and provides a powerful multiscale simulation engine that combines and runs them. Users of Vivarium can therefore implement any type of model module they prefer – whether it is a custom module of a specific biophysical system, a configurable model with its own standard format, or a wrapper for an off-the-shelf library. The multiscale engine supports complex agents operating at multiple timescales, and facilitates parallel computation across multiple CPUs.
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.
- Please use the following reference when citing Vivarium:
Agmon, E., Spangler, R.K., Skalnik, C.J., Poole, W., Morrison, J.H., Peirce, S.M., and Covert, M.W. (2022). Vivarium: an interface and engine for integrative multiscale modeling in computational biology. Bioinformatics, btac049. link to article