This dataset contains data collected by the Australian Continuous Plankton Recorder (AusCPR) survey and is funded by IMOS (Ships of Opportunity sub-facility) and CSIRO. The aims of the AusCPR survey are to: * map plankton biodiversity and distribution * develop the first long-term plankton baseline for Australian waters * document plankton changes in response to climate change * provide indices for fisheries management * detect harmful algal blooms * validate satellite remote sensing * initialise and test ecosystem models. The survey conducts repeat tows in the GBR, the East Australian Current and down to the Southern Ocean Time Series Mooring (SOTS). Other routes are conducted on an adhoc nature around Australia. The dataset also contains phytoplankton data from the UTAS / AAD led Southern Ocean CPR (SOCPR) project which is also funded by IMOS. The datasets available in this collection include Phytoplankton Colour Index (an estimate of chlorophyll in the water), phytoplankton abundance, zooplankton abundance and a biomass index from AusCPR and phytoplankton abundance from SOCPR. This data are freely available through the AODN portal: https://portal.aodn.org.au. This data is freely available but please acknowledge all relevant parties, as detailed in acknowledgement section.

Contaminants were modelled as nested sets of polygons representing plumes of differing concentrations spreading from their source. Nodes of the polygons were advected by the currents and 'diffused' at each time step until the contour became so dilute that it was eliminated because the concentrations reached the lower threshold for tracking. Nodes of the plume were also excised if the plume became so thin that the nodes were very close to each other. The temporal spatial footprint is presented as an image time series.

The model used to compute the currents on the North West Shelf was developed within CSIRO Marine Research and is referred to as MECO (Model for Estuaries and Coastal Oceans). It is a general-purpose finite difference hydrodynamic model applicable to scales ranging from estuaries to ocean basins. It has found previous applications in systems such as the Derwent and Huon Estuaries in Tasmania, Gippsland Lakes, Port Phillip Bay (Walker 1999), Bass Strait, the Great Australian Bight and South-eastern Australia (Bruce et al. 2001), and the Gulf of Carpentaria (Condie et al. 1999). A full description of the circulation model as applied to North West Shelf and descriptions of the spatial and temporal characteristics of the circulation and connectivity can be found in Condie(2004).

The iconic species examined in the MSE are turtles and sharks. For both groups the populations are represented by the animal agent model for post-larval stages and spatial dynamics and the blastula agent for reproduction and spatial dynamics of very early life history stages. This representation enables density dependent processes to apply to natural mortality at larval and post-larval stages and to egg production. It allows spatially explicit treatment of larval and post-larval stages, but there is no explicit spatial structure at the egg stage other than eggs being confined to their suitable habitat. Biological parameter values for the species were taken from the literature and modified slightly during model calibration to give plausible biomass levels under the levels of fishing pressure or catch recorded from the North West Shelf.

The daily rainfall time series were constructed from records on the rainfall at the Karratha and Port Hedland airports supplied by the National Climate Centre in the Head Office of the Bureau of Meteorology (P. Reid pers. comm.). These data sets ran from 14/12/1971 for Karratha and from 17/7/1942 for Port Hedland. These data sets were merged using: - an average where a valid entry existed for both time series - the data as supplied if only one valid entry was present - the long term average (through multiple years) if no valid entry for that day in that year in either time series. The resulting combined rainfall series was then converted into a time series of 90 day running sums. Sums rather than averages were used as overall input to the system. These systems are of particular importance for recruitment in the prawn fisheries of the North West Shelf region.

Cyclone tracks were constructed using data supplied by the National Climate Centre in the Head Office of the Bureau of Meteorology. These records contained information on the timing, route and intensity of the cyclone, though prior to the advent of GPS and automated monitoring, some of this information was approximate at best. The final footprint of the cyclone used by the Catastrophe agents in NWS-InVitro was constructed by mapping a polygon over each leg of a cyclone's route, with the track as the centreline and a width of 30km on either side of that central track. These footprints and an intensity index were stored in the Cyclone.data and Disaster.data files for use in NWS-InVitro.

The application of the MSE modelling approach to the North West Shelf required three scenarios, for currents and contaminants, each spanning four decades to be simulated for many model runs. These scenarios were loosely defined as: 'high winds' to simulate the potential effect of stronger than normal winds; 'normal' where the distributional property of the winds were the same as those experienced currently; 'low winds' where winds were weaker than current conditions. Three-dimensional simulations of currents and the distributions of contaminants for such periods, at temporal resolutions of at least one hour, would require many months of computer time and, in addition, would generate large quantities of current data which would be impractical to incorporate into the agent-based simulation system InVitro. An alternate approach was required that was: 1) relatively fast, 2) made efficient use of limited computational resources and, 3) accurately represented the modelled currents throughout the study region. We chose to statistically model the currents by recognizing that near the coast the currents were primarily driven by the tides and elsewhere from a combination of tides, winds and boundary forcing. Tide and wind data were available but unfortunately we did not have ready access to the boundary forcing information - this is required in nesting the higher-resolution North West Shelf model within a coarse global circulation model. This was not considered to be a major deficiency as the boundary forcing (derived from a global General Circulation Model) was of coarse resolution with inadequate local representation of winds, bathymetry and water mass structure (Scott Condie, pers. Comm.). Our analyses were therefore focused on statistically modelling the currents and contaminants forced by local tides and winds.

This study collects information on intertidal seagrass meadows at Thursday and Horn Island, Torres Strait. Data is collected by scientists and trained students/ community volunteers using the standard Seagrass-Watch protocols (see www.seagrasswatch.org). Three permanently marked sites (50mx 50m) are monitored 3 - times a year. Data is submitted to Seagrass-Watch HQ for QAQC and submission to the main Seagrass-Watch MSAccess database (Northern Fisheries Centre, DPI&F custodians). Summary data and anaylis is presented in quarterly newsletters and available on the web as part of State of teh Environment reporting.