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

W.M. Mooij, R.J. Brederveld, J.M. de Klein, D.L. DeAngelis, A.S. Downing, M. Faber, D.J. Gerla, M.R. Hipsey, J. 't Hoen, J.H. Janse, A.B.G. Janssen, M. Jeuken, B.W. Kooi, B. Lischke, T. Petzoldt, L. Postma, S.A. Schep, H. Scholten, S. Teurlincx, C. Thiange & 5 others D. Trolle, A.A. van Dam, L.P.A. van Gerven, E.H. van Nes, J.J. Kuiper

Research output: Contribution to JournalArticleAcademicpeer-review

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 languageEnglish
Pages (from-to)266-273
JournalEnvironmental Modelling & Software
Volume61
DOIs
Publication statusPublished - 2014

Fingerprint

ecosystem modeling
Ecosystems
Lotka-Volterra model
OSIRIS
Ecology
MATLAB
modeling
Lakes
Differential equations
ecology
ecosystem
Computer simulation
lake
simulation

Cite this

Mooij, W. M., Brederveld, R. J., de Klein, J. M., DeAngelis, D. L., Downing, A. S., Faber, M., ... Kuiper, J. J. (2014). Serving many at once: How a database approach can create unity in dynamical ecosystem modelling. Environmental Modelling & Software, 61, 266-273. https://doi.org/10.1016/j.envsoft.2014.04.004
Mooij, W.M. ; Brederveld, R.J. ; de Klein, 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. ; Thiange, C. ; Trolle, D. ; van Dam, A.A. ; van Gerven, L.P.A. ; van Nes, E.H. ; Kuiper, J.J. / Serving many at once: How a database approach can create unity in dynamical ecosystem modelling. In: Environmental Modelling & Software. 2014 ; Vol. 61. pp. 266-273.
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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.",
author = "W.M. Mooij and R.J. Brederveld and {de Klein}, J.M. and D.L. DeAngelis and A.S. Downing and M. Faber and D.J. Gerla and M.R. Hipsey and {'t Hoen}, J. and J.H. Janse and A.B.G. Janssen and M. Jeuken and B.W. Kooi and B. Lischke and T. Petzoldt and L. Postma and S.A. Schep and H. Scholten and S. Teurlincx and C. Thiange and D. Trolle and {van Dam}, A.A. and {van Gerven}, L.P.A. and {van Nes}, E.H. and J.J. Kuiper",
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Mooij, WM, Brederveld, RJ, de Klein, JM, 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 & Software, vol. 61, pp. 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, W.M.; Brederveld, R.J.; de Klein, 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.; Thiange, C.; Trolle, D.; van Dam, A.A.; van Gerven, L.P.A.; van Nes, E.H.; Kuiper, J.J.

In: Environmental Modelling & Software, Vol. 61, 2014, p. 266-273.

Research output: Contribution to JournalArticleAcademicpeer-review

TY - JOUR

T1 - Serving many at once: How a database approach can create unity in dynamical ecosystem modelling

AU - Mooij, W.M.

AU - Brederveld, R.J.

AU - de Klein, J.M.

AU - DeAngelis, D.L.

AU - Downing, A.S.

AU - Faber, M.

AU - Gerla, D.J.

AU - Hipsey, M.R.

AU - 't Hoen, J.

AU - Janse, J.H.

AU - Janssen, A.B.G.

AU - Jeuken, M.

AU - Kooi, B.W.

AU - Lischke, B.

AU - Petzoldt, T.

AU - Postma, L.

AU - Schep, S.A.

AU - Scholten, H.

AU - Teurlincx, S.

AU - Thiange, C.

AU - Trolle, D.

AU - van Dam, A.A.

AU - van Gerven, L.P.A.

AU - van Nes, E.H.

AU - Kuiper, J.J.

PY - 2014

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AB - 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.

U2 - 10.1016/j.envsoft.2014.04.004

DO - 10.1016/j.envsoft.2014.04.004

M3 - Article

VL - 61

SP - 266

EP - 273

JO - Environmental Modelling & Software

JF - Environmental Modelling & Software

SN - 1364-8152

ER -