Serving many at once: How a database approach can create unity in dynamical ecosystem modelling

Simulation modelling in ecology is a field that is becoming increasingly compartmentalized. Here we propose a Database Approach To Modelling (DATM) to create unity in dynamical ecosystem modelling with differential equations. In this approach the storage of ecological knowledge is independent of the language and platform in which the model will be run. To create an instance of the model, the information in the database is translated and augmented with the language and platform specifics. This process is automated so that a new instance can be created each time the database is updated. We describe the approach using the simple Lotka-Volterra model and the complex ecosystem model for shallow lakes PCLake, which we automatically implement in the frameworks OSIRIS, GRIND for MATLAB, ACSL, R, DUFLOW and DELWAQ. A clear advantage of working in a database is the overview it provides. The simplicity of the approach only adds to its elegance. Scientific and educational experience with the proposed Database Approach To Modelling (DATM) shows the following:It facilitated overview of and insight in the model by developers and users.Allowed for a much more dynamic scientific development of the model.Allowed for a direct implementation of these developments in multiple platforms.

[1]  David P. Hamilton,et al.  A community-based framework for aquatic ecosystem , 2012 .

[2]  Wolf M. Mooij,et al.  An object-oriented simulation framework for individual-based simulations (OSIRIS): Daphnia population dynamics as an example , 1996 .

[3]  Marten Scheffer,et al.  A strategy to improve the contribution of complex simulation models to ecological theory , 2005 .

[4]  Marten Scheffer,et al.  Ecological models and the pitfalls of causality , 1994, Hydrobiologia.

[5]  Marten Scheffer,et al.  Critical phosphorus loading of different types of shallow lakes and the consequences for management estimated with the ecosystem model PCLake , 2008 .

[6]  Willy Govaerts,et al.  MATCONT: A MATLAB package for numerical bifurcation analysis of ODEs , 2003, TOMS.

[7]  Adrie J. M. Beulens,et al.  A methodology to support multidisciplinary model-based water management , 2007, Environ. Model. Softw..

[8]  Gideon Gal,et al.  Testing the Impact of Management Scenarios on Water Quality Using an Ecosystem Model , 2004 .

[9]  A. J. Lotka.  UNDAMPED OSCILLATIONS DERIVED FROM THE LAW OF MASS ACTION. , 1920 .

[10]  David P. Hamilton,et al.  A community-based framework for aquatic ecosystem models , 2011, Hydrobiologia.

[11]  V. Volterra.  Variations and Fluctuations of the Number of Individuals in Animal Species living together , 1928 .

[12]  George H. Leavesley,et al.  A modular approach to addressing model design, scale, and parameter estimation issues in distributed hydrological modelling , 2002 .

[13]  Damaris Zurell,et al.  How can we bring together empiricists and modellers in functional biodiversity research , 2013 .

[14]  David P. Hamilton,et al.  Challenges and opportunities for integrating lake ecosystem modelling approaches , 2010, Aquatic Ecology.

[15]  P. Reichert.  AQUASIM-a tool for simulation and data analysis of aquatic systems , 1994 .

[16]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[17]  Robert Muetzelfeldt,et al.  The Simile visual modelling environment , 2003 .

[18]  A. J. Clemmens,et al.  Description and Evaluation of Program: DUFLOW , 1991 .

[19]  Karline Soetaert,et al.  Solving Differential Equations in R: Package deSolve , 2010 .

[20]  J. Janse,et al.  A model of ditch vegetation in relation to eutrophication , 1998 .

[21]  E. E. Mitchell,et al.  Advanced Continuous Simulation Language (ACSL) , 1976 .

[22]  Jan H. Janse,et al.  Setting critical nutrient values for ditches using the eutrophication model PCDitch , 2007, Aquatic Ecology.

[23]  Karline Soetaert,et al.  Inverse Modelling, Sensitivity and Monte Carlo Analysis in R Using Package FME , 2010 .

[24]  H. Scholten,et al.  The Smart approach to modelling and simulation , 2001 .

[25]  Friedrich Recknagel,et al.  Process-based simulation library SALMO-OO for lake ecosystems. Part 1: Object-oriented implementation and validation , 2008, Ecol. Informatics.

[26]  Marten Scheffer,et al.  Estimating the critical phosphorus loading of shallow lakes with the ecosystem model PCLake: Sensitivity, calibration and uncertainty , 2010 .