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

by West, Jeffrey , Anderson, Alexander R. A. , Baratchart, Etienne , Basanta, David , Robertson-Tessi, Mark , Schenck, Ryan O. , Miller, Anna K. , Gallaher, Jill , Gatenbee, Chandler D. , Bravo, Rafael R.

in Algorithms / Automata theory / Biology and Life Sciences / Cancer / Computational Biology - methods / Computer and Information Sciences / Computers / Containers / Data collection / Decentralization / Design / Engineering and Technology / Finite difference method / Gene Library / Graphical user interface / Java (Computer program language) / Java (Programming language) / Libraries / Mathematical models / Medicine and Health Sciences / Models, Biological / Models, Theoretical / Oncology / Partial differential equations / Physical Sciences / Reagents / Research and Analysis Methods / Robots / Social Sciences / Software / Source code / Three dimensional models / Time / Two dimensional models / User-Computer Interface / Utilities

2020

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2020

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2020

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Journal Article

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

West, Jeffrey,

Anderson, Alexander R. A.,

Baratchart, Etienne,

Basanta, David,

Robertson-Tessi, Mark,

Schenck, Ryan O.,

Miller, Anna K.,

Gallaher, Jill,

Gatenbee, Chandler D.,

Bravo, Rafael R.

2020

Overview

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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Publisher

Public Library of Science,Public Library of Science (PLoS)

Subject

Algorithms

/ Automata theory

/ Biology and Life Sciences

/ Cancer

/ Computational Biology - methods

/ Computer and Information Sciences

/ Computers