Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization

Area of Science:

• Computational Biology
• Mathematical Oncology
• Software Engineering

Background:

• Mathematical modeling is crucial for understanding complex biological systems.
• Developing hybrid models (agent-based and PDE) presents significant challenges.
• Existing tools may lack the flexibility for diverse spatial modeling needs.

Purpose of the Study:

• To introduce the Hybrid Automata Library (HAL), a Java-based software library.
• To provide researchers with a framework for building efficient, generic spatial models.
• To facilitate the creation of complex hybrid models in mathematical oncology.

Main Methods:

• HAL offers modular components: on/off-lattice agent containers, diffusion fields, and GUI tools.
• Components are designed for independent operation and easy interfacing.
• A complete hybrid model example demonstrates the library's utility.

Main Results:

• HAL enables the development of performant 1D, 2D, and 3D hybrid models.
• The library simplifies the process of building complex spatial simulations.
• It provides a standardized approach for integrating agent-based and PDE components.

Conclusions:

• HAL is a valuable asset for researchers in mathematical oncology and spatial modeling.
• The library reduces the barrier to entry for creating sophisticated hybrid models.
• HAL promotes efficient and flexible model development in Java.