AMSA IMOS Data workshop 2019

How to access and use IMOS data for your Research

Workshop Sunday July 7th 1000 – 1700

IMOS is looking forward to hosting this workshop in Fremantle as part of the 2019 AMSA Conference, “Marine Science for a Blue Economy”.

The workshop will be held at Tannock Hall, Notre Dame University, Fremantle Building ND4 Room 701, Corner of Croke St and Cliff St.

Get directions with Google Maps

Contact me at any stage if you have workshop related questions:

Craig Steinberg e: c.steinberg(at)aims.gov.au m: 041 824 8067

Since 2006, IMOS has been routinely operating a wide range of observing equipment throughout Australia’s coastal and open oceans, making all of its data accessible to the marine and climate science community, other stakeholders and users, and international collaborators. This workshop is to assist the scientific community to discover, access, download, use and understand the potential of the data.

Presentations will be made by key leaders responsible for the collection and dissemination of the data with examples of how they have used the data sets to further their research. Hands on guided tutorials will be show how the AODN portal can be used and a summary of tools that are available to analyse the data. Short abstracts can be found further down this document.

Bring your own device as some of the presentations will be interactive.

Agenda

Sunday July 7th 1000 – 1700  Tannock Hall, Notre Dame University, Fremantle Building ND4 Room 701, Corner of Croke St and Cliff St

1000 – 1005

Welcome and housekeeping

Craig Steinberg, AIMS.

1005 – 1015

IMOS Overview

Sebastien Mancini, AODN

1015 – 1025

WAIMOS Overview

Nicole Jones, UWA

1025-1040

Introduction to the AODN portal

Sebastien Mancini, AODN

1040 – 1055

Using IMOS plankton data from the NRS and AusCPR surveys

Claire Davies, CSIRO and Jason Everett, UQ

1055 – 1110

Gliderscope & NetCDF Ninja: Tools for exploring and using Ocean Glider Data

Mun Woo and Paul Thomson, UWA

1110  – 1125

Sensor network

Scott Bainbridge, AIMS

1125  – 1140

Moorings network

Ming Feng, CSIRO and Craig Steinberg, AIMS

1140 – 1155

Which SST product should I use?

Pallavi Govekar, BoM

1155 – 1210

BoM seasonal marine forecasting products

Claire Spillman, BoM

1210 – 1300

Break – Lunch provided

 

1300 – 1315 Monitoring Australian Seas with IMOS OceanCurrent Madeleine Cahill, CSIRO
1315 – 1400 Hands on: AODN Portal tutorial Sebastien Mancini, AODN
1400 – 1430 Hands on: IMOS Biology component of the biogeochemical : Microbes, Zoo & phyto- plankton data & fish. Applications in R. Claire Davies, CSIRO and Jason Everett, UQ
1430 – 1445 Afternoon tea  
1445 – 1500 Hands on: Visualising an IMOS glider data set using GliderScope Paul Thomson and Mun Woo, UWA
1500 – 1600 Hands on: AODN Moorings/SRS/SOOP All presenters
1600 – 1700 Hands on: Free range IMOS data wrangling All presenters

Preparation

Bring your own device as some of the presentations will be interactive.

Data Portal

Your main access to marine and climate data is through the AODN Portal.

Data Tools

http://imos.org.au/data/data/imosdatatools/ from here you can download Gliderscope and other tools.

Ocean Data View 
Ocean Data View (ODV) is a program designed for the interactive graphical display of oceanographic data. The software is freely available for Windows, Mac OS X, Linux, and UNIX systems. To download ODV you must register for free on the website http://odv.awi.de (go to the ‘Software’ tab). 

Download the Ocean Data View Manual v1.3.
The Manual was prepared by the Coastal and Regional Oceanography Lab at UNSW.

Applications of IMOS Biological Data in R

R is a popular statistical language commonly used by biologists for the wrangling and analysis of biological datasets. In the IMOS Biology Session, we will highlight applications of the IMOS plankton data and demonstrate some of these using R. Due to time constraints we won’t be teaching R or delving deeply into the code, but if you would like to code along with us, or play with the data, please come prepared with both `R` and `RStudio` installed (links below). 

We also suggest you install the following packages: “tidyverse”, “vegan” and “lubridate” (If you are an R user you will know how). If you are not an R user, then never fear. We will be focussing on the application of the data and the questions we can ask of it. So you will learn just as much without using R. We will provide all the code for those who are interested.

R: https://cran.csiro.au

RStudio: https://www.rstudio.com/products/rstudio/download/#download

Location

The workshop will be held at Tannock Hall, Notre Dame University, Fremantle Building ND4 Room 701, Corner of Croke St and Cliff St.

See map for details.

Get directions with Google Maps

Abstracts

Introduction to the AODN data Portal

Sebastien Mancini, Australian Ocean Data Network, Hobart, Tas

email:Sebastien.Mancini@utas.edu.au

The Australian Ocean Data Network (AODN) Portal provides access to all available Australian marine and climate science data including Integrated Marine Observing System (IMOS) data. These marine data collections are made freely available to the public. Data covers a wide range of parameters in different ocean environments collected from ocean-going ships, autonomous vehicles, moorings and other platforms. The scope of observations, geographically spanning ocean to coast, and across disciplines (physical, biogeochemical, biological), provides a challenge to deliver an intuitive easy-to-use robust information infrastructure enabling users to efficiently obtain the data they need. This presentation will be a live demonstration highlighting the main features and services the AODN Portal can offer in order to discover, visualize and access datasets. An afternoon tutorial will follow.


Observational data from across our tropical northern seas & WA

Craig Steinberg, Australian Institute of Marine Science, Townsville, QLD & Ming Feng, CSIRO. Perth, WA

email: c.steinberg(at)aims.gov.au & ming.feng@csiro.au

AIMS operates a number of IMOS platforms across the tropical north of Australia. There a mooring arrays on the northwest shelf and along the Great Barrier Reef, National Reference Stations in Darwin and at the Yongala wreck near Townsville, a reef based sensor network and underway shipborne observations on two Research Vessels. CSIRO operates a moorings array in the temperate regions of WA.  This presentation will show how you can access descriptions of all the mooring deployments, and near real time observational pages from a variety of sources.  Recent funding will allow the relocation of the ITF shelf array along the northwest shelf and also the re-introduction of a Mooring off Ningaloo Reef thanks to funding from the WA Government.


Gliderscope & NetCDF Ninja: Tools for exploring and using Ocean Glider Data

Mun Woo & Paul Thompson, University of Western Australia, Perth, WA

email: mun.woo(at)uwa.edu.au

Software introduced include Gliderscope, an elegant visualisation and analysis software developed specifically for ocean glider data; and the newly released NetCDF Ninja, an interactive graphical user interface that allows users to explore and edit all the metadata and data contained in NetCDF files. Using these tools, the workshop exercises will familiarise users with the types of data collected by ocean gliders, the ways data can be analysed and interpreted, as well as help them explore key principles of physical and biological oceanography.


Using IMOS plankton data from the NRS and AusCPR surveys

Claire Davies. CSIRO, Hobart, TAS & Jason Everett. UQ, Brisbane, QLD

email: claire.davies(at)csiro.au

With the IMOS National Reference Stations and AusCPR surveys researchers now have two consistently sampled and analysed ten year plankton time series. The data from both these surveys can be matched to environmental variables from other IMOS products to make statistically powerful datasets. The data can be used for bioregional monitoring, productivity indicators, linkages of trophic groups and measures of ecosystem health. Combined with historical data, dating back over 100 years, these data can be used to demonstrate species distribution changes over many decades and using climate forecasting, predictions for future. 


Which SST Product Should I Use?

Pallavi Govekar, Bureau of Meteorology, Docklands, Vic

email:helen.beggs(at)bom.gov.au

There are a large number and range of remotely sensed sea surface temperature (SST) products available from the Integrated Marine Observing System (IMOS) that cover the Australian region at varying ocean depths, spatial and temporal resolutions (http://imos.org.au/sstproducts.html).  This presentation will guide users through selecting the most appropriate IMOS satellite SST product for their application, and how to benefit from the additional attributes in the Group for High Resolution SST (GHRSST) format files, such as quality level and Sensor Specific Error Statistics.  Some examples will be briefly shown of applications that use IMOS GHRSST products, and how one might find and extract the appropriate level of SST data for an application.


Monitoring Australian Seas with IMOS OceanCurrent

Madeleine Cahill, CSIRO, Hobart, TAS

email:madeleine.cahill(at)csiro.au

OceanCurrent brings together the latest ocean observations from around Australia to provide context for marine studies and help you find IMOS data to support your work.

The satellite observations include sea surface temperature (SST), ocean colour (as a proxy for Chlorophyll), sea level anomaly and geostrophic surface currents. Different types of sea surface temperature are provided at a range of scales to cater for different requirements:

  • snapshots that give instantaneous images,
  • 4-hour composites,
  • 6-day SST composites with percentiles,
  • monthly SST and
  • SSTAARS climatology.

IMOS in-water data, including glider profiles, current meter data, Argo profiles, SealCTDs, HF radar velocities and research vessel underway data are plotted on all images and also in more much more detail on additional pages. We have begun making images clickable to make the IMOS data easier to view and to find on the AODN. In this workshop we’ll demonstrate how the website can work for you and would appreciate any feedback users may have.


Seasonal marine forecasting products

The Bureau of Meteorology's new seasonal prediction system ACCESS-S

Claire Spillman, Bureau of Meteorology, Docklands, Vic

email:claire.spillman(at)bom.gov.au

ACCESS-S is the new operational seasonal prediction system at the Bureau of Meteorology, which has been running in realtime since late 2018. ACCESS-S is a global dynamical coupled ocean-atmosphere model, producing gridded atmosphere and ocean forecasts for up to 6 months into the future. The ocean model grid in ACCESS-S is 25km by 25km in the horizontal and 1-200m in the vertical, substantially finer than its predecessor POAMA. Simulated ocean variables include sea surface temperature (SST), temperature at depth, salinity, sea level and currents.

A retrospective forecast (hindcast) data set exists for 1990-2012 which is used to both create model climatologies and assess model performance in predicting past events during the period. Hindcast ocean data is available on the NCI, with mechanisms in place at the Bureau to deliver operational realtime forecast data to key collaborators.  Monthly SST and thermal stress forecast products from ACCESS-S for around Australia are also available online at (http://www.bom.gov.au/oceanography/oceantemp/sst-outlook-map.shtml).