process-bigraph 1.0.5

protocol and execution for compositional systems biology

Process-Bigraph

Process-Bigraph is an extension of the bigraph-schema library, offering a computational framework that integrates process modules into bigraphs. This allows for the representation of complex, multiscale systems, that combine the structural capabilities of bigraphs with modular dynamic processes. It serves as a tool for creating, simulating, and analyzing intricate and dynamic models, fostering a more comprehensive understanding of complex systems.

What are Process Bigraphs?

Process Bigraphs are based on a mathematical formalism introduced by Robin Milner, which was expanded in Vivarium with the addition of Processes, and standardized with the introduction of the Schema format. Bigraphs provide a powerful framework for compositional modeling due to their ability to represent complex systems through hierarchical structures and flexible reconfigurations, thus enabling the seamless composition and decomposition of system components. Variables are contained in Stores (circles), which can be embedded in the place graph hierarchy, represented by the dark edges. Instead of hyperedges, CBS employs Processes (the rectangles) which have ports (solid black dots) connect via wires (dashed edges) to variables within the Stores. Processes are functions that read and write to variables through their ports. They can be used to rewrite the bigraph by adding new structure and new processes.

Getting Started

Installation

You can install process-bigraph using pip:

pip install process-bigraph

Tutorial

To get started with Bigraph-viz, explore our resources:

• Process Bigraphs Intro.
• Bigraph Schema Basics Tutorial. For an introduction to the basic elements of process-bigraph schema.
• Formatting Tutorial for examples about how to adjust the final look of your bigraph figure.
• Ecoli for the wiring diagraph of a whole-cell E. coli model.

License

process-bigraph is open-source software released under the Apache 2 License.