dc.contributor.author | Christensen, Asbjørn | |
dc.contributor.author | Mariani, Patrizio | |
dc.contributor.author | Payne, Mark R. | |
dc.date.accessioned | 2019-02-28T13:27:09Z | |
dc.date.available | 2019-02-28T13:27:09Z | |
dc.date.issued | 2018 | |
dc.identifier.citation | Christensen.A.; Mariani, P. and Payne, M.R. (2018) A generic framework for individual-based modelling and physical-biological interaction. PLoS ONE 13(1): e0189956 [24pp.]. DOI:10.1371/journal.pone.0189956 | en_US |
dc.identifier.uri | http://hdl.handle.net/11329/863 | |
dc.identifier.uri | http://dx.doi.org/10.25607/OBP-410 | |
dc.description.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. | en_US |
dc.language.iso | en | en_US |
dc.rights | Attribution 4.0 | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.subject.other | Coupled ocean circulation model | en_US |
dc.subject.other | Biological-physical modelling | en_US |
dc.subject.other | IBMlib | |
dc.title | A generic framework for individual-based modelling and physical-biological interaction. | en_US |
dc.type | Journal Contribution | en_US |
dc.description.refereed | Refereed | en_US |
dc.format.pagerange | e0189956 [24pp.] | en_US |
dc.identifier.doi | 10.1371/ journal.pone.0189956 | |
dc.subject.parameterDiscipline | Parameter Discipline::Biological oceanography | en_US |
dc.subject.parameterDiscipline | Parameter Discipline::Physical oceanography | |
dc.subject.dmProcesses | Data Management Practices::Data analysis | en_US |
dc.bibliographicCitation.title | PLoS ONE | en_US |
dc.bibliographicCitation.volume | 13 | en_US |
dc.bibliographicCitation.issue | 1 | en_US |
dc.description.sdg | 14.A | en_US |
dc.description.bptype | Best Practice | en_US |
dc.description.bptype | Guide | en_US |
obps.contact.contactemail | asc@aqua.dtu.dk | |
obps.resourceurl.publisher | https://doi.org/10.1371/journal.pone.0189956 | en_US |