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Modelling Trichodesmium photophysiology in the Great Barrier Reef using the eReefs models

The research is important for the Great Barrier Reef (GBR) water quality management. The data was collected for the parameterisation of the variation of Trichodesmium phycobilipigments under varying light conditions in the GBR. Linux operating system, C compiler and NETCDF library were used to build the modified EMS applications on AIMS HPC. The EMS version used is 1.2.1. The modified EMS was derived from the eReefs model (https://ereefs.org.au/ereefs) and the model descriptions are found in Baird et al. (2020). Methods for collecting the data include the following:

Hydrodynamic model forcing available in https://research.csiro.au/ereefs/models/models-about/models-hydrodynamics/; Biogeochemical (BGC) model forcing (Simulated hydrodynamic model output, regional wave model data, 2019 catchment conditions of nutrient and sediment loads available in https://svnserv.csiro.au/svn/CEM/projects/eReefs/model/gbr4_bgc_hindcast/gbr4_H2p0_B3p2_Cb/); Initialisation file: GBR4 BGC 3p1 initialisation data.              

The 4km resolution grid of the EMS was run on AIMS HPC from 1/12/2010 to 30/11/2012 and the data was collected on 26/06/2023. Software-specific information needed to interpret the data are R Software version 3.5.1, GNU Compiler Collection (GCC) version 6.1.0, network Common Data Form (NetCDF-cxx) version 4.2.1, Open Message Passing Interface (OpenMPI-gcc) version 1.10.2 and NetCDF Operators (NCO) version 4.5.5.

R scripts and MATLAB scripts for post-processing simulated data are available: https://github.com/Chinenyeani1986/Trichodesmium-buoyancy 

 
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    Data Record Details
    Data record related to this publication Modelling Trichodesmium photophysiology in the Great Barrier Reef using the eReefs models
    Data Publication title Modelling Trichodesmium photophysiology in the Great Barrier Reef using the eReefs models
  • Description

    The research is important for the Great Barrier Reef (GBR) water quality management. The data was collected for the parameterisation of the variation of Trichodesmium phycobilipigments under varying light conditions in the GBR. Linux operating system, C compiler and NETCDF library were used to build the modified EMS applications on AIMS HPC. The EMS version used is 1.2.1. The modified EMS was derived from the eReefs model (https://ereefs.org.au/ereefs) and the model descriptions are found in Baird et al. (2020). Methods for collecting the data include the following:

    Hydrodynamic model forcing available in https://research.csiro.au/ereefs/models/models-about/models-hydrodynamics/; Biogeochemical (BGC) model forcing (Simulated hydrodynamic model output, regional wave model data, 2019 catchment conditions of nutrient and sediment loads available in https://svnserv.csiro.au/svn/CEM/projects/eReefs/model/gbr4_bgc_hindcast/gbr4_H2p0_B3p2_Cb/); Initialisation file: GBR4 BGC 3p1 initialisation data.              

    The 4km resolution grid of the EMS was run on AIMS HPC from 1/12/2010 to 30/11/2012 and the data was collected on 26/06/2023. Software-specific information needed to interpret the data are R Software version 3.5.1, GNU Compiler Collection (GCC) version 6.1.0, network Common Data Form (NetCDF-cxx) version 4.2.1, Open Message Passing Interface (OpenMPI-gcc) version 1.10.2 and NetCDF Operators (NCO) version 4.5.5.

    R scripts and MATLAB scripts for post-processing simulated data are available: https://github.com/Chinenyeani1986/Trichodesmium-buoyancy 

     

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  • Other Descriptors
    • Descriptor
      • Descriptor type
    • Data type dataset
  • Keywords
    • eReefs
    • CSIRO-EMS
    • Trichodesmium
    • Phycobilipigments
    • Great Barrier Reef
  • Funding source
  • Research grant(s)/Scheme name(s)
    • -
    • Research themes
    Tropical Ecosystems, Conservation and Climate Change
    FoR Codes (*)
    • 410203 - Ecosystem function
    • 410402 - Environmental assessment and monitoring
    SEO Codes
    • 180201 - Assessment and management of coastal and estuarine ecosystems
    • 190504 - Effects of climate change on Australia (excl. social impacts)
- Specify coverage
    Specify spatial or temporal setting of the data
    Temporal (time) coverage
  • Start Date 2010/12/01
  • End Date 2012/11/30
    • Time Period
    Spatial (location) coverage
  • Locations
    • Great Barrier Reef
- Data
    Data Locations

    Type Location Notes
    URL https://github.com/Chinenyeani1986/Trichodesmium-phycobilipigments Metadata and scripts for analysing data
    Physical Location Australian Institute of Marine Science (AIMS), Cape Cleveland 4810, QLD eReefs datasets permanently stored on the AIMS Pearl - High Performance Computer (Restricted Access)
    The Data Manager is: Barbara Robson
    College or Centre College of Science & Engineering
    Access conditions Open: free access under license
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    • Data record size
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- License
    Select or add a licence for the data
    The data will be licensed under CC BY 4.0: Attribution 4.0 International
  • Other Licence
    • Statement of rights in data
  • Data owners
      Chinenye Ani
      Australian Institute of Marine Science
- Citation
    Citation Ani, Chinenye; Robson, Barbara; Lewis, Stephen; Smithers, Scott (2023): Modelling Trichodesmium photophysiology in the Great Barrier Reef using the eReefs models. James Cook University. https://doi.org/10.25903/550s-tj34