bigraph-viz 0.0.23

A graphviz-based plotting tool for compositional bigraph schema

Bigraph-viz

Bigraph-viz is an easy-to-use plotting tool for compositional bigraph schema, built on top of Graphviz.

Compositional Schemas and Milner Bigraphs

Compositional Bigraph Schemas (CBS) are based on a mathematical formalism introduced by Robin Milner in 2009 , and used in Vivarium. Bigraphs consist of networks with embeddable nodes that can be placed within other nodes and dynamically restructured. CBS reimagines the bigraph concept. Variables are contained within Stores (the circles in the figure), which can be embedded in a hierarchy, as shown by the dark edges. Instead of Milner's hyperedges, CBS employs Processes (the rectangles) which connect via wires (dashed edges) to shared variables within the Stores. Processes and Stores form a type of bipartite graph, as illustrated by the dashed edges.

In Vivarium, the CBS is used to structure a modular multiscale simulation. Bigraph-viz is part of an effort to standardize this structure, so that it can be used as an exchange format for multiscale simulations.

Getting Started

Dependencies

Before installing bigraph-viz, make sure you have Graphviz.

Ubuntu/Debian

sudo apt-get install -y graphviz

macOS

brew install graphviz

Windows

Download and install the Graphviz installer from the official website. Make sure to add the Graphviz bin directory to your system's PATH.

Installation

Once Graphviz is installed, you can install bigraph-viz using pip:

pip install bigraph-viz

Tutorial

To get started with Bigraph-viz, explore the Bigraph Schema Basics Tutorial.

See the Formatting Tutorial for examples about how to adjust the final look of your bigraph figure.

See Ecoli for the wiring diagraph of a whole-cell E. coli model.