PT  - JOURNAL ARTICLE
AU  - Rafael Bravo
AU  - Mark Robertson-Tessi
AU  - Alexander R. A. Anderson
TI  - Hybrid Automata Library
AID  - 10.1101/411538
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 411538
4099  - http://biorxiv.org/content/early/2018/09/10/411538.short
4100  - http://biorxiv.org/content/early/2018/09/10/411538.full
AB  - The Hybrid Automata Library (HAL) is a Java Library made of simple, efficient, generic components that can be used to model complex spatial systems. HAL’s components can broadly be classified into: on- and off-lattice agent containers, finite difference diffusion fields, a Gui building system, and additional tools and utilities for computation and data collection. These components are designed to operate independently and are standardized to make them easy to interface with one another. As a demonstration of how modeling can be simplified using our approach, we have included a complete example of a hybrid model (a spatial model with interacting agent-based and PDE components, commonly used for oncology modeling). HAL is a useful asset for researchers who wish to build efficient 1D, 2D and 3D hybrid models in Java, while not starting entirely from scratch. It is available on github at https://github.com/torococo/HAL under the MIT License. HAL requires at least Java 8 or later to run, and the java jdk version 1.8 or later to compile the source code.