Availability

Products

A Demonstration Version of ShellSIM with limited capability is available online, subject to User Registration alone, using the Software as a Service (SaaS) approach that enables the User to run ShellSIM remotely from anywhere with an internet connection, accessing ShellSIM behind a firewall on server at Plymouth Marine Laboratory.

The Full Version of ShellSIM with complete capability is available as executable code within a software program compiled as Dynamic Link Library (DLL) using the Microsoft.NET framework, thereby ensuring easy linkage with other programs using any of the many software languages supported by .NET (e.g. C#, Visual Basic, Java). Availability of that Full Version is subject to Plymouth Marine Laboratory's (PML) Licence Agreement for nominal fee of £50 within the context of collaborative work, and which fee is negotiable within commercial contexts, subject to any required training from PML.

The Table below summarizes differences between the Demonstration and Full Versions of ShellSIM.

Feature

Demonstration Version

Licensed Versions

Availability

Remote access through http://www.shellsim.com/demo.aspx

Available from Dr A. J. S. (Tony) Hawkins of Plymouth Marine Laboratory (Email; ajsh@pml.ac.uk) as a software program in the form of Dynamic Link Library (DLL) compiled using the Microsoft.NET framework, allowing Users to readily link with ShellSIM using any of the many software languages supported by .NET (APL, Fortran, Pascal, C#.NET, VB.NET etc)

Cost

Free to use web demo

Subject to License Agreement for nominal fee of £50

Ease of Use

User friendly intuitive interface, facilitated by Tool Tips and Graphical Outputs

Clear Guidelines, with comprehensive Class Library User Instructions

Customer Service

Feedback and suggestions are welcomed, with support available upon request

Collaboration with Plymouth Marine Laboratory, with any Training as required, will enable:
(i) use of portable experimental equipment and/or streamlined protocols for efficient and cost effective calibration of ShellSIM in further shellfish species
(ii) the Licensed User to apply ShellSIM for validated species at new sites

Culture Area

Users are restricted to a maximum of two sectors each with two populations within

Users may use an unrestricted number of sectors each with an unrestricted number of populations within.

Initialisation Options

Execution limited up to 1095 days (i.e. 3 years) at fixed intervals of 1 day
Physiological outputs are standardised to an individual shellfish of 1 g dry soft tissue
Nitrogen and phosphorous to carbon rations are fixed as the Redfield stoichiometric ratio

Floating timestep between 1 and 0.01 day (i.e. 24 h to 14.4 min) helps to optimise model coupling
User can define the soft dry tissue weight to which physiological outputs are standardised
User can define elemental ratios for predictions of nitrogen and/or phosphorous from carbon

Environmental Conditions

User selects constant values for forcing functions that include aerial exposure, current speed, water temperature, salinity, dissolved oxygen and suspended particles available as food measured as total particulate matter, particulate organic matter, chlorophyll a and particulate organic carbon

User can input time series defining time-dependencies for each of the same forcing functions as in the Demo Version

Shellfish species

Choice of two representative shellfish species calibrated for ShellSIM

Choice of 13 commonly-cultured species calibrated and validated for ShellSIM, the User being able to populate each Culture Area Sector with one or more of any of these Species

Ploidy status

User defines each population as diploid, triploids induced at meiosis I or triploids induced at meiosis I

Same as Demo Version

Seeding regime

User defines the number of individual shellfish deployed within each Population to each Sector upon the entered Start Day, and also the number of shellfish deployed each day following the Start Day ( i.e. “Subsequent Seeding”)
User defines size upon seeding of each population either as (i) Initial Shell Length (cm) or (ii) Initial Total Fresh Weight (g; the mass of whole live shellfish, including water remaining in the shell cavity)

User can input time-series for Subsequent Seeding of each Population to each Sector, thus allowing one-off deployment, or simulating the consequences of separate seeding events, including the settlement of natural spat (recruitment)
User can, in addition to either Initial Shell Length or Initial Total Fresh Weight, define Initial Dry Tissue Weight (g; the mass of all dry soft tissues, excluding shell), thereby affording control of initial shellfish condition

Mortality

For each population, the User selects values for Mortality Fraction, as fraction of shellfish that die when < 1 and > 1, 2, 3, 4 and 5 cm Shell Length

User can input time-series for Mortality Fraction, thus allowing seasonal size-dependent predation as may occur upon shellfish by starfish

Harvest Regime

For each Population, the User can select values of Harvestable Size between 0.1 and 25 g Total Fresh Weight (TFW), including the fraction of animals of Harvestable size that are actually harvested per d (i.e. “Harvest Fraction”, enabling ShellSIM to resolve population consequences of different seeding, mortality and harvest regimes

In addition to selecting Harvestable Size, the User can input time-series for Harvest Fraction, thus allowing a one off harvest per annum, a constant mortality per time step, or a temporal pattern of harvest

Simulations of Individual Shellfish Growth, Size and Condition

For each Population, simulates:

  • total fresh weight (g/individual)
  • shell length (cm/individual)
  • dry soft tissue weight (g dry soft tissue/individual)
  • dry condition index (dry soft tissue weight * 100 / dry shell weight)

In addition to Demo Version outputs, simulates:

  • soft tissue weight change (change in g dry soft tissue/individual/d)
  • wet condition index (wet meat weight*100/total fresh weight)

Simulations of Weight-Standardised Physiological Rates

Available in Licenced version only

Licenced version simulates:

  • clearance rate (l cleared of particles/individual of standard dry soft tissue weight/h)
  • filtration of total particulate matter (mg filtered/individual of standard dry soft tissue weight/h)
  • oxygen volume uptake (ml/individual of standard dry soft tissue weight/h)
  • oxygen mass uptake (mg/individual of standard dry soft tissue weight/h)
  • nitrogen excretion (µg N-NH4 /individual of standard dry soft tissue weight/h)
  • ammonium loss (µmol N-NH4 /individual of standard dry soft tissue weight/h)
  • net energy balance (J/individual of standard dry soft tissue weight/h)
  • dry shell growth (mg/individual of standard dry soft tissue weight/h)
  • wet shell growth (mg/individual of standard dry soft tissue weight/h)
  • dry soft tissue growth (mg/individual of standard dry soft tissue weight/h)
  • dry soft tissue growth per day (% change in dry soft tissue/ individual of standard dry soft tissue weight/d)
  • wet soft tissue growth (mg/individual of standard dry soft tissue weight/h)
  • total fresh weight growth (mg/individual of standard dry soft tissue weight/h)
  • total fresh weight growth per day (g/individual of standard dry soft tissue weight/d)

Simulations of Cumulative Environmental Impacts of Individual Shellfish

For each population, simulates:

  • clearance rate (l cleared of particles/individual)
  • oxygen volume uptake (ml/individual)
  • nitrogen excretion (µg N-NH4 /individual)
  • deposition of pseudofaeces as total particulate matter (mg/individual)
  • deposition of true faeces as total particulate matter (mg/individual)
  • deposition of pseudofaeces as organic C (mg/individual)
  • deposition of true faeces as organic C (mg/individual)

In addition to Demo Version outputs, simulates:

  • filtration of organic C (mg/individual)
  • filtration of organic N (mg/individual)
  • filtration of organic P (mg/individual)
  • filtration of chlorophyll (µg filtered/individual)
  • filtration of secondary organics (mg filtered/individual)
  • filtration of total organics (mg filtered/individual)
  • filtration of particulate inorganic matter (mg filtered/individual)
  • filtration of total particulate matter (mg filtered/individual)
  • ammonium loss (µmol N-NH4 /individual), total aerobic and anaerobic heat losses (J/individual)
  • deposition of true faeces as organic N (mg/individual)
  • deposition of true faeces as organic P (mg/individual)
  • deposition of pseudofaeces as organic N (mg/individual)
  • deposition of pseudofaeces as organic P (mg/individual)
  • deposition of pseudofaeces as particulate organic matter (mg/individual)
  • deposition of true faeces as particulate organic matter (mg/individual)
  • total deposition as particulate organic matter (mg/individual)
  • total deposition as total particulate matter (mg/individual)

Simulations of Population Dynamics

For each population, simulates:

  • number of shellfish harvested (number of shellfish harvested)

In addition to Demo Version outputs, simulates:

  •  biomass of shellfish harvested from each population (biomass of shellfish harvested)

Simulations of Density Dependent Environmental Impacts per Shellfish Population

Available in Licenced version only

Licenced version simulates:

  • clearance rate (l cleared of particles/l/d)
  • filtration of organic C (mg organic carbon/l/d)
  • filtration of organic N (mg organic nitrogen/l/d)
  • filtration of organic P (mg organic phosphorous/l/d)
  • filtration of chlorophyll (µg filtered/l/d)
  • filtration of secondary organics (mg filtered/l/d)
  • filtration of total organic matter (mg filtered/l/d)
  • deposition of pseudofaeces as total particulate matter (mg/l/d)
  • deposition of true faeces as total particulate matter (mg/l/d)
  • nitrogen excretion (µg N-NH4 /l/d)
  • filtration of particulate inorganic matter (mg filtered/l/d)
  • filtration of total particulate matter (mg filtered/l/d)
  • ammonium loss (µmol N-NH4 /m3/d; note per m3 here is correct, contra per litre for all other outputs)
  • oxygen volume uptake (ml/l/d)
  • total aerobic and anaerobic heat losses (J/l/day)
  • deposition of true faeces as organic C (mg/l/d)
  • deposition of true faeces as organic N (mg/l/d)
  • deposition of true faeces as organic P (mg/l/d)
  • deposition of pseudofaeces as organic C (mg/l/d)
  • deposition of pseudofaeces as organic N (mg/l/d)
  • deposition of pseudofaeces as organic P (mg/l/d)
  • deposition of pseudofaeces as particulate organic matter (mg/l/d)
  • deposition of true faeces as particulate organic matter (mg/l/d)
  • total deposition as particulate organic matter (mg/l/d)
  • total deposition as total particulate matter (mg/l/d)

Simulations of Marketable Produce

Separately for Representative Shellfish Species 1 and Representative Shellfish Species 2,  combining each population from all Sectors, simulates:

  • total biomass harvested from Culture Area as a whole (total number)
  • total carbon harvested as shellfish biomass (including both soft tissue and shell) from Culture Area as a whole (g)
  • total nitrogen harvested as shellfish biomass (including both soft tissue and shell) from Culture Area as a whole (g)
  • average physical product (APP; biomass harvested/total biomass seeded) for  shellfish harvested from Culture Area as a whole (ratio)

In addition to Demo Version outputs, simulates:

  • total number of shellfish harvested from Culture Area as a whole (total number)
  • total phosphorous harvested as shellfish biomass (including both soft tissue and shell) from Culture Area as a whole (g)

Simulations of Water Quality Impact

For the Culture Area as a whole, simulates:

  • output concentration of Chlorophyll a (mg/m3)
  • output concentration of Particulate Organic Matter (POM) (mg/m3)
  • output concentration of Ammonium (mg/m3)
  • output concentration of Dissolved Oxygen (mg/m3)
  • fractional change in concentration of Chlorophyll a from beginning to end of Culture Area (fraction)
  • fractional change in concentration of Particulate Organic Matter from beginning to end of Culture Area (fraction)
  • fractional change in concentration of Ammonium from beginning to end of Culture Area (fraction)
  • fractional change in concentration of Dissolved Oxygen (DO) from beginning to end of Culture Area (fraction)

In addition to Demo Version outputs, for the Culture Area as a whole, simulates:

  • input concentration of Chlorophyll a (mg/m3)
  • input concentration of Particulate Organic Matter (mg/m3)
  • input concentration of Particulate Inorganic (mg/m3)
  • input concentration of Ammonium (mg/m3)
  • input concentration of Dissolved (mg/m3)
  • output concentration of Particulate Inorganic (mg/m3)
  • absolute change in concentration of Chlorophyll a from beginning to end of Culture Area (mg/m3)
  • absolute change in concentration of Particulate Organic Matter from beginning to end of Culture Area (mg/m3)
  • absolute change in concentration of Particulate Inorganic Matter from beginning to end of Culture Area (mg/m3)
  • absolute change in concentration of Ammonium from beginning to end of Culture Area (mg/m3)
  • absolute change in concentration of Dissolved Oxygen from beginning to end of Culture Area (mg/m3)
  • fractional change in concentration of Particulate Inorganic Matter from beginning to end of Culture Area (fraction)

Further Information

Learn more about ShellSIM at http://www.shellsim.com

Learn more about C#.NET (compiler for the ShellSIM DLL) at http://msdn.microsoft.com/en-us/vcsharp/default.aspx and http://en.wikipedia.org/wiki/C_Sharp_(programming_language)

Consultation with Plymouth Marine Laboratory will enable the Licensed User to apply ShellSIM for validated species at new sites, and/or the collaborative application of standardised protocols that enable efficient and cost effective calibration and validation of ShellSIM for new shellfish species. If you are interested in either of the above, including variations thereof, talk to us!

Requirements for use

Calibration

Calibration of ShellSIM in new species ideally requires information describing:

(i)  responses to changes in seawater temperature, food availability, food composition, salinity, aerial exposure, dissolved oxygen and current speed;

(ii)  relative relations between shell length, shell weight and tissue weight; and

(iii)  average organic carbon or energy contents of tissue and shell.

Some of the above information is likely to be known, or might be assumed. However, where new measures are necessary for calibration, then protocols have been established, and portable equipment designed that enables study under natural conditions (illustrated below).

 

Standardised methods

Initialisation

Before ShellSIM can be run, the User defines the culture area, environmental conditions and details of shellfish husbandry, all described under Initialisation Options on the Description page.

Forcing (i.e. driver) data are required that define the time-dependency of environmental conditions, also as described under Initialisation Options. Among those forcing data, it is essential that CHL, TPM, POM and PIM are measured according to standardised protocols that have consistently been used during calibration of ShellSIM to date. If ShellSIM is driven by data measured using different protocols, there can be no guarantee that feeding, growth and other responses will be accurately simulated. Certainly, incompatible driver data may compromise comparisons of relative performance, whether in the same or separate species.

Validation

To validate ShellSIM, data are required describing shellfish growth and/or environmental impact at each site, and which should ideally have been measured coincident in space and time with the above driver data.

Training

Plymouth Marine Laboratory can provide advice and/or training in measurements of driver data (i.e. forcing functions) and shellfish growth.

 

Clew Bay September 2005

Conditions of use

Full conditions of use are described on the Legal page of this website.

ShellSIM uses state-of-the-art equations to simulate shellfish responses, but is neither infallible nor fool proof. Therefore, neither Dr. A. J. S. Hawkins nor Plymouth Marine Laboratory can accept any liability for losses or consequential damages due to its application.