Christensen Asbjørn, Mariani Patrizio, Payne Mark R
DTU Aqua, Technical University of Denmark, Kgs. Lyngby, Denmark.
PLoS One. 2018 Jan 19;13(1):e0189956. doi: 10.1371/journal.pone.0189956. eCollection 2018.
The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems.
全球高分辨率海洋数据的可用性不断提高，使得对物理-生物相互作用及其对生态系统影响的分析更加详细。我们展示了IBMlib，它是一个通用、便携且计算高效的框架，用于在海洋环境中进行拉格朗日模拟。该框架的目的是处理复杂的个体水平生物模型，结合描述生物环境的现实三维海洋物理和生物地球化学模型，而无需对空间或时间尺度进行假设。这个开源框架具有一个最小化的稳健接口，以促进个体水平生物模型与海洋模型之间的耦合，并且我们提供了应用示例，包括向前/向后模拟、栖息地连通性计算、评估海洋状况、物理环流模型比较、模型集合运行以及最近使用IBMlib框架的后验欧拉模拟。我们展示了代码长寿背后的代码设计理念、我们的实现经验以及代码性能基准测试。该框架可能会对海洋生态系统的表征、理解、预测以及最终管理方面的进展做出重大贡献。
