vivarium-core 0.1.1

Engine for composing and simulating computational biology models with the Vivarium interface.

Vivarium-core

Vivarium-core provides a process interface and simulation engine for composing and executing multi-scale computational biology models.

Documentation and Tutorials

Visit Vivarium documentation

Installation

vivarium-core can be used as a python library. To install:

$ pip install vivarium-core

Concept

Vivarium addresses computational biology's dual challenges of model reuse and multi-scale integration by explicitly separating the interface that connects models from the frameworks that implement them. The modular "process" interface allows different models to be assembled within a hierarchy of embedded compartments, and then run by the engine as integrated, multi-scale simulations.

(a) Processes and stores are the framework's basic elements. Processes declare parameters, ports that connect to stores, and an update function that computes how the state variables unfold over time. Stores hold the variables' states and determine how process updates are handled with units, updaters, dividers, emitters, properties such as molecular weight, and more. (b) A compartment is a composite of processes created with a bipartite graph called a topology, which declares how processes connect to stores through their ports. Boundary stores reach outside of the compartment, allowing it to connect with other compartments above or below. (c) A hierarchy of embedded compartments is a place graph with the higher compartments containing those below. (d) Two coupled processes operating at different time scales, showing their separated updates of a shared store, and an advancing temporal front. (e) A topology update shows the addition of a compartment in the time-step after a division update message is sent---other topology updates might include merging, engulfing, deleting, or adding.