eReefs Software Outputs
The following open-source software has been created or extensively updated by the eReefs development teams for use in eReefs research and is available to be re-used in other applications:
CSIRO EMS
CSIRO’s Environmental Modelling Suite (EMS) is the software used to generate the eReefs GBR4, GBR1 and RECOM data products. EMS includes the C code for CSIRO’s Sparse Hydrodynamic Ocean Code (SHOC) hydrodynamic model and the related river-tracer and biogeochemistry and sediments models.
EMS was created by CSIRO’s Coastal Environmental Modelling team and has been reused in many applications in addition to eReefs. It is freely available for re-use under an open-source license, with users encouraged to register with the EMS development team for additional assistance and updates.
- EMS documentation: https://research.csiro.au/cem/software/ems/
- EMS source code: https://github.com/csiro-coasts/ems
CSIRO emsarray
CSIRO’s emsarray library is an extension to the xarray Python Package that adds support for datasets with the CSIRO EMS geometry conventions, including the results of the eReefs GBR4 and GBR1 models with their curvilinear grids. It supports:
- one- or two-dimensional grids that use the Climate and Forecasting (CF) metadata conventions
- staggered (structured) grids for EMS-SHOC (i.e. eReefs GBR4, GBR1 and RECOM )
- unstructured grids for EMS-COMPAS
- (additional conventions via plugins)
emsarray can be used to:
- locate a geographic point within the dataset
- subset the dataset to a collection of points
- clip a dataset to a geographic region
- export the dataset geometry to alternate formats
- draw basic plots
- render basic animations
The emsarray library was created in 2021 as an eReefs deliverable, but is a generic tool which can be used with any EMS or similar datasets, not just the eReefs ones. It is freely reusable under a a BSD-3-clause Open Source Licence.
- emsarray documentation: https://emsarray.readthedocs.io/en/stable/
- emsarray source code: https://github.com/csiro-coasts/emsarray
- emsarray package repositories: PyPi or CondaForge
eReefs-related Software
The following open-source software was not created specifically for eReefs, but is may be useful for people working with eReefs data products:
RRAP Coral Bleaching Model
This is a Matlab version of the C-language coral bleaching model from the CSIRO Environmental Modelling Suite (EMS).
It contains a mechanistic model of the coral-symbiont relationship that considers temperature-mediated build-up of reactive oxygen species due to excess light, leading to zooxanthellae expulsion. The model explicitly represents the coral host biomass, as well as zooxanthellae biomass, intracellular pigment concentration, nutrient status, and the state of reaction centres and the xanthophyll cycle.
This software was created as an output of the Reef Restoration and Adaptation Program (RRAP) and is freely reusable under a MIT Licence.
- RRAP Coral Bleaching Model source code: https://github.com/gbrrestoration/coral-bleaching-model