The Auslig 250k series 1 Topograpic data (Geoscience Australia 2000) was used along with a North West Shelf coastline contour to generate a 0.008 degree grid using the ArcInfo topogrid command. This was merged with the AGSO bathymetric 30 second grid (Geoscience Australia) to form a complete bathymetric and topographic grid at 0.008 degree resolution for the complete North West Shelf study area. Finally this grid was projected to a Lambert Conformal Conic projection for use by the model. Conformal projections, ensure that scale is invariant in all directions locally, but large grids/areas will be distorted because of differential 'stretching' of areas across large scales.

This Ecopath with Ecosim (EwE) model was developed for the North West Shelf and the food web upon which it is based. The fishery of the area has been variable over the years. Bulman attempts to capture the trophic flows and biomasses during the late 1980s. At this time, the foreign fishery had reduced considerably following closures and the domestic fisheries were expanding. Fifteen years of catch and effort data were used to tune the model, i.e., annual fishing effort data were input in order to try to recreate the actual changes in the system caused by fishing.

This group of files are the configuration files used in the NWSJEMS MSE runs. A start or end time of 0 indicates that the agent will commence (or end) with the entire simulation rather than on a specific date. The configuration parameters typically include the latitude and longitude of their starting position or extent, whether they are to be tracked, their periodicity of output and a sting list of other agent types they may be interested in.

This group of links are the input data used in the NWSJEMS MSE runs. This metadata record contains the links to all the metadata records for the input data. Access to input data for InVitro is controlled through the input data source.

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 benthic habitats represented in the MSE include continental shelf seabed habitats, coastal seagrass meadows and mangrove forests. A metapopulation model was used. Due to availability of historical data, models were most fully developed for the continental shelf seabed habitats. Parameter values for the remaining habitat types were derived from available NWS data and scientific literature. Historical extent data was augmented by personal communication through workshops and interviews with residents, divers and scientists with long term NWS experience. Each of the habitat types was modelled using the benthic agent model structure.

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.