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

PLoS Computational Biology
Rafael R BravoAlexander R. A. Anderson

Abstract

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 performant 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 the Java JDK version 1.8 or later to compile and run the source code.

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Citations

Jan 17, 2021·Proceedings of the National Academy of Sciences of the United States of America·Mehdi DamaghiRobert J Gillies
Jan 20, 2021·Nature Ecology & Evolution·Daria MiroshnychenkoAndriy Marusyk
Feb 11, 2021·PLoS Computational Biology·Juan Jiménez-SánchezVíctor M Pérez-García
Apr 8, 2021·Nature Communications·Jeffrey WestAlexander R A Anderson
Nov 6, 2021·Royal Society Open Science·Sadegh MarzbanGergely Röst

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Software Mentioned

NumPy
Cancer Crusade
Clojure
Hybrid Automata Library ( HAL )
MASON
Repast
Morpheus
MapHood
AgentList
DrawModel

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