vivarium-core 0.2.1

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 define the functions that update the system's state variables.They declare parameters, ports, and an update function. (b) Stores hold the state variables and map each process' variable names to their values. They have a schema that determines how the variables are handled with properties such as units, updaters, dividers, emitters, and more. (c) Topology is a bipartite graph of processes connected to stores through their ports. Shared stores aggregate the processes' required variables, and couple the processes as they unfold in time. (d) Processes and Stores can be linked together with a topology in a single level called a compartment, and across compartments by way of boundary stores. (e) Compartments are embedded within each other in a hierarchy -- depicted here as a place graph with outer compartments at the top and inner compartments below them.