RT Journal Article
SR Electronic
T1 Hybrid Automata Library: A modular platform for efficient hybrid modeling with real-time visualization
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 411538
DO 10.1101/411538
A1 Rafael Bravo
A1 Etienne Baratchart
A1 Jeffrey West
A1 Ryan O. Schenck
A1 Anna Miller
A1 Jill Gallaher
A1 Chandler Gatenbee
A1 David Basanta
A1 Mark Robertson-Tessi
A1 Alexander R. A. Anderson
YR 2018
UL http://biorxiv.org/content/early/2018/12/19/411538.abstract
AB The Hybrid Automata Library (HAL) is a Java Library developed for use in mathematical oncology modeling. It is 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). 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/MathOnco/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.Author Summary In this paper we introduce the Hybrid Automata Library (HAL) with the purpose of simplifying the implementation and sharing of hybrid models for use in mathematical oncology. Hybrid modeling is used in oncology to create spatial models of tissue, typically by modeling cells using agent-based techniques, and by modeling diffusible chemicals using partial differential equations (PDEs). HAL’s key components are designed to run agent-based models, PDEs, and visualization. The components are standardized and are completely decoupled, so models can be built with any combination of them. We first explore the philosophy behind HAL, then summarize the components. Lastly we demonstrate how the components work together with an example of a hybrid model, and a walk-through of the code used to construct it. HAL is open-source and will produce identical results on any machine that supports Java 8 and above, making it highly portable. We recommend HAL to modelers interested in spatial dynamics, even those outside of mathematical oncology, as the components are general enough to facilitate a variety of model types. A community page that provides a download link and online documentation can be found at https://halloworld.org [1].