General Description

ShellSIM simulates interrelations between suspension-feeding bivalve shellfish and the environment, with outputs that quantify consequences for shellfish production, water quality and ecological status.

This is a dynamic model, based upon common principles of energy balance (illustrated below), using differential equations that define functional physiological responses to environmental change. Time-varying rates of feeding and metabolism are simulated as component processes in the prediction of individual growth, reproduction and condition, the individual being treated as an input-output system with size and energy content as state variables.

Net Energy Balance

Population dynamics are simulated using a standard conservation equation to calculate transitions between weight classes, accounting for seeding, settlement, harvesting and/or mortality as defined by the User.

Options have been integrated within a single tool to analyse consequences of culture practise; with ability for the User to define spatial distribution, environmental conditions and the relative composition of up to 14 commonly-cultured shellfish species, whether located on the bottom, rope, pole or trestle.

Notably, whereas past models have been calibrated and optimized per species per site, ShellSIM is the first common model structure to simulate effectively upon calibration in separate species, and which can then be applied using the same calibration for each species reared in contrasting environments, thereby saving significant time and resources (Hawkins et al., 2012, 2013a, 2013c).

Shellfish may selectively ingest and/or digest different particle types, whilst effecting compensatory adjustments that may help to maximize the utilization of particles rich in chlorophyll (Hawkins et al., 1999, 2001; Pascoe et al., 2009). A main advance enabling ShellSIM to be both robust and adaptable across both species and environments includes resolving the separate processing of organic matter within living phytoplankton, remaining non-phytoplankton organics (i.e. bacteria, protozoans, colloids and detritus) and inorganic matter (Hawkins 2012, Hawkins et al., 2013b). For each of these dietary components, a separate functional relation simulates filtration, pre-ingestive rejection and ingestion, affording prediction of absorption on the basis of the resulting organic content of ingested matter.

In contrast, previous models of shellfish growth have not resolved any differential filtration of separate dietary components (e.g. van Haren and Kooijman, 1993; Ross and Nisbet, 1990; Brylinkski and Sephton, 1991; Powell et al., 1992; Barillé et al., 1997; Scholten and Smaal, 1998; Solidoro et al., 2000). Others, although in some cases resolving the availability of living phytoplankton from remaining detrital organics, are without functional relations to simulate the highly responsive processes whereby living phytoplankton, remaining detrital organics and inorganic matter are differentially selected, rejected and/or absorbed (e.g. Raillard et al., 1993; Campbell and Newell, 1998; Grant and Bacher, 1998; Ren and Ross, 2001; Pouvreau et al., 2000, 2006).

Phyto versus Detrital organics

By these means, ShellSIM is able to simulate feeding and growth over a broad range of circumstances, whether in response to short-term tidal influences, seasonal effects or spatial differences such as occur between open water and estuarine environments (Hawkins et al., 2012, 2013a, 2013c). Furthermore, coincident simulation of the dynamic consequences of seston composition and other environmental variations for particle clearance rate, ammonium loss, faecal loss and oxygen uptake (illustrated below) enables ShellSIM to help undertake effective temporal and spatial analyses of the complex feedbacks, both positive and negative, whereby suspension feeding shellfish interact with ecosystem properties and processes.

Dynamic interactions with ecosystem processes

Scales to which applicable

Available as a single User-friendly software tool, ShellSIM quantifies animal-environment interrelations according to optional scales and types of culture: the User defining any combination of up to 14 shellfish species, including explicit definition of associated spatial distributions (i.e. farm layout, illustrated below) and practice (i.e. seeding, mortality and harvesting), whether suspended or on the bottom.

Spatial layout

In addition, as exemplified within Applications, ShellSIM is readily integrated within geographic information systems (GIS), or linked with separate hydrodynamic and/or biogeochemical models, thereby enabling analyses at both local and system (i.e. bay, biotope) scales.

Initialisation options

Initialisation of ShellSIM is undertaken at 3 basic levels:

  1. Output Specification; specifying Timestep, Start Day, Stop Day, Standard Dry Soft Tissue Weight for which physiological outputs will be computed and conversion ratios for nitrogen to carbon and phosphorous to carbon;
  2. Culture Area and Conditions; specifying Culture Area Length, Width and Depth, the number of any vertical divisions resulting in separate Sectors to be modelled such that any current flows in laminar series through each Sector within that Culture Area, and forcing data describing the time-dependencies of environmental conditions (Forcing Functions) such as may include Current Speed, Temperature, Salinity, Dissolved Oxygen, Food Availability (Total Particulate Mass, Particulate Organic Matter, Chlorophyll a and/or Particulate Organic Carbon, all per litre of seawater) and any Aerial Exposure at the upstream boundary of that Culture Area over time; plus
  3. Shellfish; specifying up to two shellfish species for each Sector within the Culture Area, including for each resulting population the Ploidy Status, Culture Type (suspended, trestle or bottom), time when shellfish are introduced (Seeding Regime), size of shellfish deployed (Seed Size), expected Mortality during culture, Size of Harvestable Shellfish and proportion of harvestable shellfish that are harvested (Harvest Regime).

For explicit definition of these Initialisation Options, refer to Guidelines available online here with the Demo Version of ShellSIM.

Note that these options collectively afford the User opportunity for analyses at different levels of complexity that range from:

  1. an individual shellfish deployed as a Population of one within a single Sector;
  2. a Population within single Sector;
  3. more than one Species competing within the same Sector; and
  4. consequences of shellfish culture practise for growth and water quality as water passes downstream through defined Sectors.


ShellSIM predicts 6 types of output:

  1. Individual Shellfish Growth, Size and Condition per individual shellfish at each Timestep.
  2. Weight-Standardised Physiological Rates are computed at each Timestep for an Individual Shellfish of Standard Dry Soft Tissue Weight, as defined under Initialisation Options.
  3. Cumulative Environmental Impacts of Individual Shellfish are those effected by each Individual Shellfish, summing impacts over all Timesteps from the Start Day.
  4. Density-dependent Environmental Impacts per Shellfish Population are computed per day at each time Timestep as the combined effects (i.e. fluxes) by all Individuals within that Population standardised per litre or cubic meter of water.
  5. Population Dynamics are computed as the number of Individual Shellfish within Weight Classes comprising that Population, for which ShellSIM determines the number of Weight Classes such first Weight Class will have an average total fresh weight equal to the Seed Size, adding as many Weight Classes at intervals of 10 g total fresh weight as may be required to reach the Size of Harvestable Shellfish. This allows calculation of the total biomass in each Weight Class, including the number and biomass of shellfish harvested, according to Seeding Regime, Seed Size, Mortality, Size of Harvestable Shellfish and Harvest Regime as entered under Initialisation Options.
  6. Culture Practise Outputs are expressed as shellfish number and biomass harvested for each Species in each Sector, including associated net impacts on water quality, all summed for the Culture Area as a whole, together with marginal analyses of profitability.

For explicit definition of these Outputs, refer to Guidelines available online here with the Demo Version of ShellSIM.