A generic framework for individual-based modelling and physical-biological interaction

Authored by Asbjorn Christensen, Patrizio Mariani, Mark R Payne

Date Published: 2018

DOI: 10.1371/journal.pone.0189956

Sponsors: European Union

Platforms: Fortran

Model Documentation: Other Narrative Flow charts Mathematical description

Model Code URLs: https://github.com/IBMlib/IBMlib

Abstract

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 opensource 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.

Tags

Dynamics Mortality Ecosystem Variability Transport Particle-tracking North-sea Larval European continental-shelf Herring spawning components