Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America.
Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
PLoS Comput Biol. 2020 Mar 10;16(3):e1007635. doi: 10.1371/journal.pcbi.1007635. eCollection 2020 Mar.
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.
混合自动机库 (HAL) 是一个用 Java 开发的库，用于数学肿瘤学建模。它由简单、高效、通用的组件组成，可以用于对复杂的空间系统进行建模。HAL 的组件大致可分为：格子和非格子代理容器、有限差分扩散场、GUI 构建系统，以及用于计算和数据收集的其他工具和实用程序。这些组件旨在独立运行，并进行了标准化，以便于彼此接口。为了展示如何使用我们的方法简化建模，我们提供了一个混合模型（具有交互基于代理和偏微分方程组件的空间模型）的完整示例。HAL 对于希望在 Java 中构建高性能的 1D、2D 和 3D 混合模型的研究人员来说是一个有用的资源，同时也不必完全从头开始。它可在 GitHub 上的 https://github.com/MathOnco/HAL 获得，根据 MIT 许可证使用。HAL 需要 Java JDK 版本 1.8 或更高版本才能编译和运行源代码。
