ARCADE: Agent-based Representation of Cells And Dynamic Environments

ARCADE is a flexible, extensible, interface-based Java framework for agent-based modeling of biological systems.

ARCADE is a lightweight agent-based modeling framework that uses the MASON library for multi-agent scheduling and simulation.

Existing implementations of the core interfaces can be used to run simulations via highly configurable setup files. ARCADE currently has two major implementation:

patch represents one or more agents in each environmental patch location
potts represents agents as a collection of connected voxels (Cellular Potts modeling)

New implementations of these interfaces can be easily integrated with existing functionality to develop models for different biological systems or questions of interest.

The ARCADE v3 patch implementation is actively under development and not yet at parity with ARCADE v2. You can track progress using the migration: v2 to v3 tag.

What’s new in v3.3.0 - 2024-12-16

Compare with v3.2.0

Features

Add getString method to Parameters class by @Jannetty in #115
Update minibox filter function to support multiple tag separators by @Jannetty in #112

Features: `patch`

Implement cell cycle length tracking by @pohaoc2 in #97
Add apoptosis age to induce change to apoptotic state by @cainja in #114

Features: `potts`

Add rotateVectorAroundAxis function to Plane class with tests by @Jannetty in #117

Documentation

Add publication abstracts to docs by @jessicasyu in #118
Add emulation paper to publications by @cainja in #124
Add setup file documentation by @jessicasyu in #119

Admin

Bump action versions and update docs workflow trigger by @jessicasyu in #129

Getting started

Coming soon!

About the project

ARCADE v2 is © 2020-2023 Bagheri Lab at Northwestern University. ARCADE v3 is © 2022-2024, Bagheri Lab at the University of Washington Seattle and Jessica S. Yu at the Allen Institute for Cell Science.

License

ARCADE v2 is distributed under a GPL 3 license. ARCADE v3 is distributed under a BSD 3-Clause license.