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2 changes: 1 addition & 1 deletion .nojekyll
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117 changes: 108 additions & 9 deletions about.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.3.450">
<meta name="generator" content="quarto-1.3.433">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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<div class="navbar-container container-fluid">
<div class="navbar-brand-container">
<a href="./index.html" class="navbar-brand navbar-brand-logo">
<img src="./images/AIMS-logo.png" alt="" class="navbar-logo">
<img src="./images/ereefs_logo.png" alt="" class="navbar-logo">
</a>
<a class="navbar-brand" href="./index.html">
<span class="navbar-title">AIMS eReefs</span>
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</a>
<ul class="dropdown-menu" aria-labelledby="nav-menu-ereefs-websites">
<li>
<a class="dropdown-item" href="https://www.ereefs.org.au/platform/" rel="" target="">
<span class="dropdown-text">whose is this?</span></a>
<a class="dropdown-item" href="https://www.ereefs.org.au/" rel="" target="">
<span class="dropdown-text">Project Website</span></a>
</li>
<li>
<a class="dropdown-item" href="https://research.csiro.au/ereefs/" rel="" target="">
<span class="dropdown-text">CSIRO</span></a>
</li>
<li>
<a class="dropdown-item" href="./index.html" rel="" target="">
<span class="dropdown-text">What other sites are there?</span></a>
<a class="dropdown-item" href="http://www.bom.gov.au/environment/activities/reeftemp/reeftemp.shtml" rel="" target="">
<span class="dropdown-text">ReefTemp</span></a>
</li>
<li>
<a class="dropdown-item" href="https://portal.ereefs.info/map" rel="" target="">
<span class="dropdown-text">Interactive Data Portal</span></a>
</li>
</ul>
</li>
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<ul class="dropdown-menu" aria-labelledby="nav-menu-visualisation-portal">
<li>
<a class="dropdown-item" href="./index.html" rel="" target="">
<span class="dropdown-text">AIMS eReefs Visualisation Portal</span></a>
<span class="dropdown-text">Visualisation Portal</span></a>
</li>
<li>
<a class="dropdown-item" href="./index.html#ereefs-csiro-hydrodynamic-model" rel="" target="">
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<!-- margin-sidebar -->

<!-- main -->
<main class="content" id="quarto-document-content">
<main class="content page-columns page-full" id="quarto-document-content">

<header id="title-block-header" class="quarto-title-block default">
<div class="quarto-title">
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</header>

<p>About this site</p>
<section id="about-aims-ereefs-platform" class="level1 page-columns page-full">
<h1>About AIMS eReefs platform</h1>
<p>The eReefs research project is a collaboration between the <a href="https://www.barrierreef.org/">Great Barrier Reef Foundation</a>, <a href="https://www.csiro.au/">CSIRO</a>, the <a href="https://www.aims.gov.au/">Australian Institute of Marine Science</a>, <a href="http://www.bom.gov.au/">Bureau of Meteorology</a>, and <a href="https://www.qld.gov.au/">Queensland Government</a>. It aims to develop a platform that will provide a picture of what is currently happening on the reef and what has happened in the past. This website provides visualisations and aggregations of the eReefs hydrodynamic and biogeochemical models allowing easy access to the current and historic environmental conditions on the Great Barrier Reef.</p>
<section id="about-the-ereefs-models" class="level2">
<h2 class="anchored" data-anchor-id="about-the-ereefs-models">About the eReefs models</h2>
<p>The <a href="https://research.csiro.au/ereefs/models/models-about/models-hydrodynamics/">eReefs hydrodynamic model</a> predicts the movement of marine waters, as well as key physical environmental conditions such as water temperature and salinity. This model is a deterministic physics based model that evolves based on equations of conversation of momentum, continuity and conservation of heat and salt driven externally by wind, atmospheric pressure gradients, surface heat and water fluxes and open-boundary conditions such as tides and low frequency ocean currents. The external boundary of CSIRO hydrodynamic model are forced by the <a href="http://www.bom.gov.au/australia/charts/about/about_access.shtml">BOM Access-R weather models</a> and <a href="http://www.bom.gov.au/oceanography/forecasts/">BOM OMAP for boundary currents</a>. The GBR1 1 km model is nested inside the GBR4 4 km model, with the GBR4 acting as the boundary of the GBR1 model.</p>
<p>The hydrodynamic model results allow us to better understand the effect of cyclones, the location of potentially damaging heat waves that can cause coral bleaching, the ocean currents that disperse larve of corals and Crown-of-Thorns starfish, and fresh water plumes from flooded rivers that can damage inshore reefs.</p>
<p>The <a href="https://research.csiro.au/ereefs/models/models-about/models-biogeochemistry/">eReefs BioGeoChemical (BGC) and sediment model</a> uses the results of the hydrodynamic model to track the movement and concentration of nutrients and sediments. It models the effects of land run off into the marine space and the nutrient recycling processes associated with plankton, seagrass and coral.</p>
<p>More information: <a href="https://doi.org/10.1080/1755876X.2019.1650589"><em>eReefs</em>: An operational information system for managing the Great Barrier Reef</a>.</p>
</section>
<section id="what-does-this-website-show" class="level2">
<h2 class="anchored" data-anchor-id="what-does-this-website-show">What does this website show?</h2>
<p>This site presents visualisations of key variables from both the eReefs Hydrodynamic and BGC models. The raw model outputs are available publicly via the <a href="https://dapds00.nci.org.au/thredds/catalogs/fx3/catalog.html">National Computing Infrastructure (NCI) THREDDS data service</a> and are described in more detail on the <a href="https://research.csiro.au/ereefs/models/model-outputs/access-to-raw-model-output/">Access to raw model output</a> page on the CSIRO eReefs site. The problem is that using the raw model data directly can be a huge challenge due to their huge data size (~ 19 TB). The raw model data uses files that have a curvilinear grid, that helps the efficiency of the model, but prevents the data from being directly viewable in GIS applications such as QGIS or ArcGIS. Another significant challenge is that the model data has over 10's of millions of individual map layers making it very difficult to understand the processes looking at them one at a time. The AIMS eReefs platform aims to solve these problems by:</p>
<ul>
<li>Presenting visualisations using pre-rendered videos. These videos provide rapid viewing of the eReefs data. These videos show multiple related variables, to allow the connections between key processes to be easily seen,</li>
<li>Generating aggregations over time (daily, months, seasonal, annual) of the model data to show longer time scale spatial patterns of variables, whilst shrinking the data to a more manageable size,</li>
<li>Regridding the model data from curvilinear data to a rectangular grid so that it can be used in a desktop GIS applications,</li>
<li>Providing a <a href="https://extraction.ereefs.aims.gov.au/">data extraction service</a> that allows time series data of locations of interest to be easily downloaded,</li>
<li>Providing <a href="https://thredds.ereefs.aims.gov.au/thredds/s3catalogue/aims-ereefs-public-prod/derived/ncaggregate/ereefs/catalog.html">data services</a> of all the generated derived data so that it can be accessed programmatically to facilitate reproducible science.</li>
<li>Generating exposures maps to identify regions where organisms are being exposed to harsh conditions that might adversely affect their health.</li>
</ul>
<p>The products on this website are updated in near real time from the NCI data services. As CSIRO updates the model data this site regenerates and updates the visualisation and data services available.</p>
</section>
<section id="how-are-the-map-products-on-this-website-generated" class="level2 page-columns page-full">
<h2 class="anchored" data-anchor-id="how-are-the-map-products-on-this-website-generated">How are the map products on this website generated?</h2>
<p>Two new tools were developed to process and visualise the eReefs model data. These were a tool for processing the model outputs to calculate time aggregates and exposures (Ncaggregate), and a tool for automatically generating maps and videos from the data (Ncanimate). Along with these tools a host of smaller coordinating tools were developed. These were to automate the mirroring of data, to coordinate the processing workflow and for presenting of the thousands of products on the website.</p>
<div class="media-image mediaframe_wikipedia wysiwyg-media-file column-page">
<div class="image">
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
<p><img src="images/AIMS-eReefs-platform-overview.png" class="media-image img-fluid figure-img"></p>
<figcaption class="figure-caption">AIMS eReefs platform overview</figcaption>
</figure>
</div>
</div>
<div class="metadata" style="width: 1000px; ">
<p><span class="title">AIMS eReefs platform overview</span></p>
<div class="description">
<p>The GBR4 and GBR1 model data is generated by CSIRO. It is then push to the National Computing Intrastructure (NCI) where it is made available publicly as a data service. The AIMS eReefs platform creates a local partial mirror of the data, stripping off unused variables to save on space. This data is then processed to produce regridded aggregation data with daily, monthly and annual aggregations. This data is made available as data services to allow data download, programmatic access to the data and as a web mapping service to link in with the CSIRO eReefs Vis Portal. The raw model data, along with the aggregated data is visualised as maps and map videos. These are made available via the AIMSeReefs visualisation portal. The final component is the data extraction tool. Requests from users trigger&nbsp;the extraction process. These extractions can take a while and so users are emailed back when there extractions are complete.</p>
</div>
<p><span class="license"><a href="http://creativecommons.org/licenses/by-sa/3.0/au/"><img src="../../images/cc.png" class="cc" width="15" height="15" alt="CC BY SA"></a> by <a href="//eatlas.org.au/node/2">AIMS</a></span></p>
</div>
</div>
</section>
<section id="how-do-i-access-the-data-used-in-the-visualisations" class="level2">
<h2 class="anchored" data-anchor-id="how-do-i-access-the-data-used-in-the-visualisations">How do I access the data used in the visualisations?</h2>
<p>All the dataset used to create the visualisations on this site are made available in NetCDF format from our <strong><a href="https://thredds.ereefs.aims.gov.au/">AIMS eAtlas THREDDS server</a></strong>.</p>
<p>These correspond to all the aggregate products generated by this project. This corresponds to daily, monthly, annual aggregates. These files have been regridded to a regular grid to allow them to be loaded into a standard GIS application such as ArcMap. You can do this by following the <a href="https://desktop.arcgis.com/en/arcmap/10.3/manage-data/netcdf/reading-netcdf-data-as-a-raster-layer.htm">Reading netCDF as a raster layer</a> guide.</p>
</section>
<section id="how-do-i-access-the-data-programmatically" class="level2">
<h2 class="anchored" data-anchor-id="how-do-i-access-the-data-programmatically">How do I access the data programmatically?</h2>
<p>All the data used in the visualisations are available programmatically via the <strong><a href="https://thredds.ereefs.aims.gov.au/">AIMS eAtlas THREDDS server</a></strong> by either download the full NetCDF data or by using libraries to access the data using the OPeNDAP data protocol. The following are tutorials in using these services in a range of languages.</p>
<table class="table">
<thead>
<tr class="header">
<th style="text-align: left;">Language</th>
<th style="text-align: left;">Description</th>
<th style="text-align: left;">Data source</th>
<th style="text-align: left;">Notebook</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td style="text-align: left;">Python</td>
<td style="text-align: left;"><a href="http://github.com/aims-ks/ereefs-python-scripts/blob/master/notebooks/1-plot-aims-ereefs-map-data.ipynb">1. Plot AIMS eReefs data as a map from OpeNDAP service</a></td>
<td style="text-align: left;">AIMS eReefs aggregate model data</td>
<td style="text-align: left;"><a href="https://github.com/aims-ks/ereefs-python-scripts/blob/master/notebooks/1-plot-aims-ereefs-map-data.ipynb">Notebook (Jupyter)</a></td>
</tr>
<tr class="even">
<td style="text-align: left;">Python</td>
<td style="text-align: left;"><a href="http://github.com/aims-ks/ereefs-python-scripts/blob/master/notebooks/2-plot-aims-ereefs-time-plot.ipynb">2. Plot AIMS eReefs time plot from OpeNDAP service</a></td>
<td style="text-align: left;">AIMS eReefs aggregate model data</td>
<td style="text-align: left;"><a href="https://github.com/aims-ks/ereefs-python-scripts/blob/master/notebooks/2-plot-aims-ereefs-time-plot.ipynb">Notebook (Jupyter)</a></td>
</tr>
<tr class="odd">
<td style="text-align: left;">Python</td>
<td style="text-align: left;"><a href="http://github.com/aims-ks/ereefs-python-scripts/blob/master/notebooks/3-extraction-tool-data-wind-vs-current.ipynb">3. Processing the data from the AIMS eReefs extraction tool - Wind and currents</a></td>
<td style="text-align: left;">AIMS eReefs data extraction tool</td>
<td style="text-align: left;"><a href="https://github.com/aims-ks/ereefs-python-scripts/blob/master/notebooks/3-extraction-tool-data-wind-vs-current.ipynb">Notebook (Jupyter)</a></td>
</tr>
<tr class="even">
<td style="text-align: left;">R</td>
<td style="text-align: left;"><a href="http://ereefs.aims.gov.au/ereefs-aims/help/how-to-plot-aims-ereefs-data-with-r">How to plot AIMS eReefs data with R</a></td>
<td style="text-align: left;">AIMS eReefs aggregate model data</td>
<td style="text-align: left;"><a href="https://ereefs.aims.gov.au/ereefs-aims/help/how-to-plot-aims-ereefs-data-with-r">R</a> <a href="https://github.com/aims-ks/ereefs-r-scripts/blob/master/notebooks/1-plot-aims-ereefs-data.Rmd">markdown</a></td>
</tr>
<tr class="odd">
<td style="text-align: left;">R</td>
<td style="text-align: left;"><a href="https://research.csiro.au/ereefs/models/models-about/r-package-plotting-ereefs-data/">R package to facilitate extracting and visualising eReefs model output data</a></td>
<td style="text-align: left;">CISRO eReefs raw model data</td>
<td style="text-align: left;"><a href="https://github.com/AIMS/ereefs">R library</a></td>
</tr>
</tbody>
</table>


</section>
</section>

</main> <!-- /main -->
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.ncanimate-products {
justify-content: center
}

/* trying to make the navbar static
.headroom--pinned,
.headroom--unpinned,
.headroom--top,
.headroom--not-top {
position: block !important;
}
*/
19 changes: 12 additions & 7 deletions gbr1/current-magnitude-average/index.html
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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.3.450">
<meta name="generator" content="quarto-1.3.433">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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<div class="navbar-container container-fluid">
<div class="navbar-brand-container">
<a href="../../index.html" class="navbar-brand navbar-brand-logo">
<img src="../../images/AIMS-logo.png" alt="" class="navbar-logo">
<img src="../../images/ereefs_logo.png" alt="" class="navbar-logo">
</a>
<a class="navbar-brand" href="../../index.html">
<span class="navbar-title">AIMS eReefs</span>
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</a>
<ul class="dropdown-menu" aria-labelledby="nav-menu-ereefs-websites">
<li>
<a class="dropdown-item" href="https://www.ereefs.org.au/platform/" rel="" target="">
<span class="dropdown-text">whose is this?</span></a>
<a class="dropdown-item" href="https://www.ereefs.org.au/" rel="" target="">
<span class="dropdown-text">Project Website</span></a>
</li>
<li>
<a class="dropdown-item" href="https://research.csiro.au/ereefs/" rel="" target="">
<span class="dropdown-text">CSIRO</span></a>
</li>
<li>
<a class="dropdown-item" href="../../index.html" rel="" target="">
<span class="dropdown-text">What other sites are there?</span></a>
<a class="dropdown-item" href="http://www.bom.gov.au/environment/activities/reeftemp/reeftemp.shtml" rel="" target="">
<span class="dropdown-text">ReefTemp</span></a>
</li>
<li>
<a class="dropdown-item" href="https://portal.ereefs.info/map" rel="" target="">
<span class="dropdown-text">Interactive Data Portal</span></a>
</li>
</ul>
</li>
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<ul class="dropdown-menu" aria-labelledby="nav-menu-visualisation-portal">
<li>
<a class="dropdown-item" href="../../index.html" rel="" target="">
<span class="dropdown-text">AIMS eReefs Visualisation Portal</span></a>
<span class="dropdown-text">Visualisation Portal</span></a>
</li>
<li>
<a class="dropdown-item" href="../../index.html#ereefs-csiro-hydrodynamic-model" rel="" target="">
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</div></div></div>
</div>
</div>
<p><br></p>
<p>This page shows the magnitude of the surface sea water current on the Great Barrier Reef based on the <a href="https://research.csiro.au/ereefs/models/">1km eReefs Hydrodynamic model</a>.</p>
<p>The magnitude shown in these videos and images tells you the speed of the water, but with no indication of the direction. In shallow areas this information can be useful in understanding the amount of sediment mixing caused by tides and the amount of shear stress (side ways rubbing) that these areas might experience. Shallow areas that have a high current magnitude are likely to be different habitats.</p>
<p>For details of this dataset and access to the data see the <a href="https://eatlas.org.au/data/uuid/375c9dc9-70f8-4d97-a3e9-c013896a81e5">eReefs CSIRO Hydrodynamic model (Temperature, Salinity, Wind, Current) Summaries (AIMS)</a> metadata page.</p>
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