v3.3.0

🚀 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

---

Full Changelog: v3.2.0...v3.3.0

v3.2.0

🚀 Features

• Update cell make method to return container by @jessicasyu in #74
• Update cell constructors to use container by @jessicasyu in #75
• Add support for linked populations in setup file by @jessicasyu in #76
• Add support for parameter distributions by @jessicasyu in #85

Features: patch

• Add support for initialization by percentage by @jessicasyu in #53
• Add patch cell agent with random state rules by @jessicasyu in #56
• Add support for different patch initialization schemes by @jessicasyu in #81
• Pass initial glucose concentration as parameter for metabolism modules by @allison-li-1016 in #96

Features: potts

• Added class key for potts populations by @Jannetty in #11
• Make necessary PottsCell fields public, prepare for abstract setModule() function by @Jannetty in #12
• Convert PottsCell to abstract class by @Jannetty in #13
• Add support for splits with offset, direction, and split probability by @Jannetty in #16
• Add custom plane splitvoxels by @Jannetty in #46
• Refactor plane constructor to take Double3D instead of Int3D by @Jannetty in #83

🐛 Bug fixes

• Remove apoptosis checkpoint for potts cells by @jessicasyu in #18
• Replace instance of wildcard import of Module to prevent clash in Java 9 by @cainja in #65
• Fix passing in initial glucose as a parameter value by @allison-li-1016 in #99

🧪 Tests

• Remove unnecessary mocking in potts cell stem tests by @jessicasyu in #57
• Unit tests for core utilities Colors class by @cainja in #63
• Adding tests for core utilities Solver class by @cainja in #69
• Improved tests for core utilities Color class by @cainja in #73
• Adding tests for core utilities Graph class by @cainja in #64
• Adding tests for core utilities Parameter class by @cainja in #71

📁 Admin

• Update workflows conditions for main and develop branches by @jessicasyu in #10
• Change source compatibility from 1.8 to 1.11 by @jessicasyu in #66
• Migrate to JUnit 5 by @jessicasyu in #67
• Add spotless autoformatter by @jessicasyu in #68
• Update workflows for changelog releases and Jekyll docs by @jessicasyu in #100

---

Full Changelog: v3.1.4...v3.2.0

ARCADE v3.1.4

Full Changelog: v2.4...v3.1.4

ARCADE v2.4

This release contains the code associated with the article:

JS Yu & N Bagheri. (2024). Model design choices impact biological insight: Unpacking the broad landscape of spatial-temporal model development decisions. PLoS Computational Biology. doi: 10.1371/journal.pcbi.1011917

Features

• support for rectangular and hexagonal geometry
• add cycle and pulse components
• updated 3D visualization

ARCADE v2.3

This release contains the code associated with the article:

JS Yu & N Bagheri. (2021). Modular microenvironment components reproduce vascular dynamics de novo in a multi-scale agent-based model. Cell Systems. doi: 10.1016/j.cels.2021.05.007

Features

• modular environment components for defining nutrient sources
• realistic vasculature generation and exact hemodynamic calculations
• Gradle build automation

ARCADE v2.2

This release contains the code associated with the article:

JS Yu & N Bagheri. (2020). Agent-based models predict emergent behavior of heterogeneous cell populations in dynamic microenvironments. Frontiers in Bioengineering and Biotechnology. doi: 10.3389/fbioe.2020.00249

Features

• application and command line interface for running simulations
• XML-based simulation setup files
• custom interface structure for modular, extensible biological models