bigraph-viz 2.0.1

A visualization method for displaying the structure of process bigraphs

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

Notebooks

All notebooks are tested in CI and published as HTML to GitHub Pages: Browse all notebooks

Notebook	Description
Basics	Tutorial covering stores, processes, wires, and composites
Basics2	Extended basics with cell structure example
Basics Pres	Presentation-style examples
Bigraph Example	Transcription/translation and multicellular models
Cell Atlas	Kidney glomerulus model
Ecoli	Whole-cell E. coli wiring diagram
Ecoli hybrid	E. coli hybrid framework
Format	Styling options for bigraph figures
Gut Microbiome	Multi-region gut model with cdFBA-CRM
Ccb	CCB model (source only)

License

Bigraph-viz is open-source software released under the Apache 2 License.