process-bigraph 0.0.8

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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

MongoDB

We use a MongoDB database to store the data collected from running simulations via the DatabaseEmitter class. The use of this class is specified in the 'emitter' section of the instance declaration for a given process as such:

...,
'emitter': {
                '_type': 'step',
                'address': 'local:database-emitter',
                'config': {
                    'ports': {
                        'inputs': {
                            'table': 'string',

. This can be a remote server, but for this guide we will run a MongoDB server locally.

Note: MongoDB is only required if you want to store data in MongoDB or want to run experiments that do so via the declaration shown above. You don't need MongoDB to work through this guide.

Check Installation

$ mongod --version
db version v4.2.3
...

Make sure you see a version at least 3.2.

Install

If you are on macOS, you can install MongoDB using Homebrew. You will need to add the MongoDB tap following the instructions here.

If you are on Linux, see the MongoDB documentation's instructions.

Setup

You can get a MongoDB server up and running locally any number of ways. Here is one:

1. Create a folder process_bigraph_work/mongodb. This is where MongoDB will store the database We store the database here instead of at the default location in /usr/local/var/mongodb to avoid permissions issues if you are not running as an administrator.

2. Make a copy of the mongod configuration file so we can make changes:

   $ cp /usr/local/etc/mongod.conf process_bigraph_work/mongod.conf
   

   Note that your configuration file may be somewhere slightly different. Check the MongoDB documentation for your system.

3. In process_bigraph_work/mongod.conf change the path after dbPath: to point to process_bigraph_work/mongodb.

4. Create a shell script process_bigraph_work/mongo.sh with the following content:

   #!/bin/bash
   
   mongod --config mongod.conf
   

5. Make the script executable:

    $ chmod 700 process_bigraph_work/mongo.sh
   

6. Now you can launch MongoDB by running this script:

    $ process_bigraph_work/mongo.sh
   

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

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