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

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

doi:10.1371/journal.pcbi.1007635

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.

Highlights

The Hybrid Automata Library (HAL) was created to assist the growing mathematical oncology community with a common framework to facilitate building and visualizing hybrid models
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
To make better progress in this endeavor, it is helpful to have a set of highly generic tools that encapsulate the key components of spatial modeling so that researchers can produce efficient models quickly without being constrained in their approach, nor in the complexity of the systems that they can produce

Summary

Introduction

The Hybrid Automata Library (HAL) was created to assist the growing mathematical oncology community with a common framework to facilitate building and visualizing hybrid models. Hybrid models in oncology usually represent cells (both of the tumor and of the surrounding tissue) using agent-based modeling (ABMs) and the concentrations of relevant chemicals (drugs, resources and signaling molecules) as continuous partial differential equations (PDEs). These models can simulate local interactions between cells with complex internal dynamics and decision-making processes while allowing cells to interact with the PDE concentration fields in their local environment. A unique strength of the hybrid modeling approach is that it allows for a mechanistic understanding of the ecological feedback between the cancer cells and their tissue environment. Further realism can be incorporated by initializing spatial models with clinical or histological data [20, 21]

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