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

Wolf M. Mooij; Robert J. Brederveld; Jeroen J.M. de Klein; Don L. DeAngelis; Andrea S. Downing; Michiel Faber; Daan J. Gerla; Matthew R. Hipsey; Jochem 't Hoen; Jan H. Janse; Annette B.G. Janssen; Michel Jeuken; Bob W. Kooi; Betty Lischke; Thomas Petzoldt; Leo Postma; Sebastiaan A. Schep; Huub Scholten; Sven Teurlincx; Christophe Thiange; Dennis Trolle; Anne A. van Dam; Luuk P.A. van Gerven; Egbert H. van Nes; Jan J. Kuiper

doi:10.1016/j.envsoft.2014.04.004

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

Wolf M. Mooij, Robert J. Brederveld, Jeroen J.M. de Klein, Don L. DeAngelis, Andrea S. Downing, Michiel Faber, Daan J. Gerla, Matthew R. Hipsey, Jochem 't Hoen, Jan H. Janse, Annette B.G. Janssen, Michel Jeuken, Bob W. Kooi, Betty Lischke, Thomas Petzoldt, Leo Postma, Sebastiaan A. Schep, Huub Scholten, Sven Teurlincx, Christophe ThiangeDennis Trolle, Anne A. van Dam, Luuk P.A. van Gerven, Egbert H. van Nes, Jan J. Kuiper

Biology

Research output: Contribution to journal › Article

23 Scopus citations

Abstract

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.

Original language	English (US)
Pages (from-to)	266-273
Number of pages	8
Journal	Environmental Modelling and Software
Volume	61
DOIs	https://doi.org/10.1016/j.envsoft.2014.04.004
State	Published - Nov 1 2014

Keywords

Community-based modelling
Database approach to modelling
DATM
Differential equation
Modelling framework
Programming language

ASJC Scopus subject areas

Ecological Modeling
Environmental Engineering
Software

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Mooij, W. M., Brederveld, R. J., de Klein, J. J. M., DeAngelis, D. L., Downing, A. S., Faber, M., Gerla, D. J., Hipsey, M. R., 't Hoen, J., Janse, J. H., Janssen, A. B. G., Jeuken, M., Kooi, B. W., Lischke, B., Petzoldt, T., Postma, L., Schep, S. A., Scholten, H., Teurlincx, S., ... Kuiper, J. J. (2014). Serving many at once: How a database approach can create unity in dynamical ecosystem modelling. Environmental Modelling and Software, 61, 266-273. https://doi.org/10.1016/j.envsoft.2014.04.004

Serving many at once : How a database approach can create unity in dynamical ecosystem modelling. / Mooij, Wolf M.; Brederveld, Robert J.; de Klein, Jeroen J.M.; DeAngelis, Don L.; Downing, Andrea S.; Faber, Michiel; Gerla, Daan J.; Hipsey, Matthew R.; 't Hoen, Jochem; Janse, Jan H.; Janssen, Annette B.G.; Jeuken, Michel; Kooi, Bob W.; Lischke, Betty; Petzoldt, Thomas; Postma, Leo; Schep, Sebastiaan A.; Scholten, Huub; Teurlincx, Sven; Thiange, Christophe; Trolle, Dennis; van Dam, Anne A.; van Gerven, Luuk P.A.; van Nes, Egbert H.; Kuiper, Jan J.

In: Environmental Modelling and Software, Vol. 61, 01.11.2014, p. 266-273.

Research output: Contribution to journal › Article

Mooij, WM, Brederveld, RJ, de Klein, JJM, DeAngelis, DL, Downing, AS, Faber, M, Gerla, DJ, Hipsey, MR, 't Hoen, J, Janse, JH, Janssen, ABG, Jeuken, M, Kooi, BW, Lischke, B, Petzoldt, T, Postma, L, Schep, SA, Scholten, H, Teurlincx, S, Thiange, C, Trolle, D, van Dam, AA, van Gerven, LPA, van Nes, EH & Kuiper, JJ 2014, 'Serving many at once: How a database approach can create unity in dynamical ecosystem modelling', Environmental Modelling and Software, vol. 61, pp. 266-273. https://doi.org/10.1016/j.envsoft.2014.04.004

Mooij, Wolf M. ; Brederveld, Robert J. ; de Klein, Jeroen J.M. ; DeAngelis, Don L. ; Downing, Andrea S. ; Faber, Michiel ; Gerla, Daan J. ; Hipsey, Matthew R. ; 't Hoen, Jochem ; Janse, Jan H. ; Janssen, Annette B.G. ; Jeuken, Michel ; Kooi, Bob W. ; Lischke, Betty ; Petzoldt, Thomas ; Postma, Leo ; Schep, Sebastiaan A. ; Scholten, Huub ; Teurlincx, Sven ; Thiange, Christophe ; Trolle, Dennis ; van Dam, Anne A. ; van Gerven, Luuk P.A. ; van Nes, Egbert H. ; Kuiper, Jan J. / Serving many at once : How a database approach can create unity in dynamical ecosystem modelling. In: Environmental Modelling and Software. 2014 ; Vol. 61. pp. 266-273.

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AU - Trolle, Dennis

AU - van Dam, Anne A.

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