TY  - JOUR
A1  - Mooij, Wolf M.
A1  - Brederveld, Robert J.
A1  - de Klein, Jeroen J. M.
A1  - DeAngelis, Don L.
A1  - Downing, Andrea S.
A1  - Faber, Michiel
A1  - Gerla, Daan J.
A1  - Hipsey, Matthew R.
A1  - Janse, Jan H.
A1  - Janssen, Annette B. G.
A1  - Jeuken, Michel
A1  - Kooi, Bob W.
A1  - Lischke, Betty
A1  - Petzoldt, Thomas
A1  - Postma, Leo
A1  - Schep, Sebastiaan A.
A1  - Scholten, Huub
A1  - Teurlincx, Sven
A1  - Thiange, Christophe
A1  - Trolle, Dennis
A1  - van Dam, Anne A.
A1  - van Gerven, Luuk P. A.
A1  - van Nes, Egbert H.
A1  - Kuiper, Jan J.
T1  - Serving many at once: How a database approach can create unity in dynamical ecosystem modelling
JF  - Environmental modelling & software with environment data news
N2  - 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. (C) 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).
KW  - Modelling framework
KW  - Programming language
KW  - Differential equation
KW  - Community-based modelling
KW  - Database approach to modelling
KW  - DATM
Y1  - 2014
U6  - https://doi.org/10.1016/j.envsoft.2014.04.004
SN  - 1364-8152
SN  - 1873-6726
VL  - 61
SP  - 266
EP  - 273
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Janssen, Annette B. G.
A1  - Arhonditsis, George B.
A1  - Beusen, Arthur
A1  - Bolding, Karsten
A1  - Bruce, Louise
A1  - Bruggeman, Jorn
A1  - Couture, Raoul-Marie
A1  - Downing, Andrea S.
A1  - Elliott, J. Alex
A1  - Frassl, Marieke A.
A1  - Gal, Gideon
A1  - Gerla, Daan J.
A1  - Hipsey, Matthew R.
A1  - Hu, Fenjuan
A1  - Ives, Stephen C.
A1  - Janse, Jan H.
A1  - Jeppesen, Erik
A1  - Joehnk, Klaus D.
A1  - Kneis, David
A1  - Kong, Xiangzhen
A1  - Kuiper, Jan J.
A1  - Lehmann, Moritz K.
A1  - Lemmen, Carsten
A1  - Oezkundakci, Deniz
A1  - Petzoldt, Thomas
A1  - Rinke, Karsten
A1  - Robson, Barbara J.
A1  - Sachse, Rene
A1  - Schep, Sebastiaan A.
A1  - Schmid, Martin
A1  - Scholten, Huub
A1  - Teurlincx, Sven
A1  - Trolle, Dennis
A1  - Troost, Tineke A.
A1  - Van Dam, Anne A.
A1  - Van Gerven, Luuk P. A.
A1  - Weijerman, Mariska
A1  - Wells, Scott A.
A1  - Mooij, Wolf M.
T1  - Exploring, exploiting and evolving diversity of aquatic ecosystem models: a community perspective
JF  - Aquatic ecology : the international forum covering research in freshwater and marine environments
N2  - Here, we present a community perspective on how to explore, exploit and evolve the diversity in aquatic ecosystem models. These models play an important role in understanding the functioning of aquatic ecosystems, filling in observation gaps and developing effective strategies for water quality management. In this spirit, numerous models have been developed since the 1970s. We set off to explore model diversity by making an inventory among 42 aquatic ecosystem modellers, by categorizing the resulting set of models and by analysing them for diversity. We then focus on how to exploit model diversity by comparing and combining different aspects of existing models. Finally, we discuss how model diversity came about in the past and could evolve in the future. Throughout our study, we use analogies from biodiversity research to analyse and interpret model diversity. We recommend to make models publicly available through open-source policies, to standardize documentation and technical implementation of models, and to compare models through ensemble modelling and interdisciplinary approaches. We end with our perspective on how the field of aquatic ecosystem modelling might develop in the next 5-10 years. To strive for clarity and to improve readability for non-modellers, we include a glossary.
KW  - Water quality
KW  - Ecology
KW  - Geochemistry
KW  - Hydrology
KW  - Hydraulics
KW  - Hydrodynamics
KW  - Physical environment
KW  - Socio-economics
KW  - Model availability
KW  - Standardization
KW  - Linking
Y1  - 2015
U6  - https://doi.org/10.1007/s10452-015-9544-1
SN  - 1386-2588
SN  - 1573-5125
VL  - 49
IS  - 4
SP  - 513
EP  - 548
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - van Gerven, Luuk P. A.
A1  - Brederveld, Robert J.
A1  - de Klein, Jeroen J. M.
A1  - DeAngelis, Don L.
A1  - Downing, Andrea S.
A1  - Faber, Michiel
A1  - Gerla, Daan J.
A1  - Janse, Jan H.
A1  - Janssen, Annette B. G.
A1  - Jeuken, Michel
A1  - Kooi, Bob W.
A1  - Kuiper, Jan J.
A1  - Lischke, Betty
A1  - Liu, Sien
A1  - Petzoldt, Thomas
A1  - Schep, Sebastiaan A.
A1  - Teurlincx, Sven
A1  - Thiange, Christophe
A1  - Trolle, Dennis
A1  - van Nes, Egbert H.
A1  - Mooij, Wolf M.
T1  - Advantages of concurrent use of multiple software frameworks in water quality modelling using a database approach
JF  - Fundamental and applied limnology : official journal of the International Association of Theoretical and Applied Limnology
N2  - Water quality modelling deals with multidisciplinary questions ranging from fundamental to applied. Addressing this broad range of questions requires multiple analysis techniques and therefore multiple frameworks. Through the recently developed database approach to modelling (DATM), it has become possible to run a model in multiple software frameworks without much overhead. Here we apply DATM to the ecosystem model for ditches PCDitch and its twin model for shallow lakes PCLake. Using DATM, we run these models in six frameworks (ACSL, DELWAQ, DUFLOW, GRIND for MATLAB, OSIRIS and R), and report on the possible model analyses with tools provided by each framework. We conclude that the dynamic link between frameworks and models resulting from DATM has the following main advantages: it allows one to use the framework one is familiar with for most model analyses and eases switching between frameworks for complementary model analyses, including the switch between a 0-D and 1-D to 3-D setting. Moreover, the strength of each framework - including runtime performance - can now be easily exploited. We envision that a community-based further development of the concept can contribute to the future development of water quality modelling, not only by addressing multidisciplinary questions but also by facilitating the exchange of models and process formulations within the community of water quality modellers.
KW  - Database Approach To Modelling
KW  - DATM
KW  - PCLake
KW  - PCDitch
KW  - OSIRIS
KW  - ACSL
KW  - R
KW  - GRIND
KW  - DUFLOW
KW  - DELWAQ
KW  - Modelling Framework
KW  - Model Implementation
KW  - Model Analysis
KW  - Differential Equations
KW  - Community-based Modelling
Y1  - 2015
U6  - https://doi.org/10.1127/fal/2015/0631
SN  - 1863-9135
VL  - 186
IS  - 1-2
SP  - 5
EP  - 20
PB  - Schweizerbart
CY  - Stuttgart
ER  - 
TY  - JOUR
A1  - Lischke, Betty
A1  - Hilt, Sabine
A1  - Janse, Jan H.
A1  - Kuiper, Jan J.
A1  - Mehner, Thomas
A1  - Mooij, Wolf M.
A1  - Gaedke, Ursula
T1  - Enhanced input of terrestrial particulate organic matter reduces the resilience of the clear-water state of shallow lakes: A model study
JF  - Ecosystems
N2  - The amount of terrestrial particulate organic matter (t-POM) entering lakes is predicted to increase as a result of climate change. This may especially alter the structure and functioning of ecosystems in small, shallow lakes which can rapidly shift from a clear-water, macrophyte-dominated into a turbid, phytoplankton-dominated state. We used the integrative ecosystem model PCLake to predict how rising t-POM inputs affect the resilience of the clear-water state. PCLake links a pelagic and benthic food chain with abiotic components by a number of direct and indirect effects. We focused on three pathways (zoobenthos, zooplankton, light availability) by which elevated t-POM inputs (with and without additional nutrients) may modify the critical nutrient loading thresholds at which a clear-water lake becomes turbid and vice versa. Our model results show that (1) increased zoobenthos biomass due to the enhanced food availability results in more benthivorous fish which reduce light availability due to bioturbation, (2) zooplankton biomass does not change, but suspended t-POM reduces the consumption of autochthonous particulate organic matter which increases the turbidity, and (3) the suspended t-POM reduces the light availability for submerged macrophytes. Therefore, light availability is the key process that is indirectly or directly changed by t-POM input. This strikingly resembles the deteriorating effect of terrestrial dissolved organic matter on the light climate of lakes. In all scenarios, the resilience of the clear-water state is reduced thus making the turbid state more likely at a given nutrient loading. Therefore, our study suggests that rising t-POM input can add to the effects of climate warming making reductions in nutrient loadings even more urgent.
KW  - climate change
KW  - PCLake
KW  - bistability
KW  - alternative stable states
KW  - critical nutrient loading
KW  - ecosystem modeling
KW  - allochthony
KW  - t-POM
Y1  - 2014
U6  - https://doi.org/10.1007/s10021-014-9747-7
SN  - 1432-9840
SN  - 1435-0629
VL  - 17
IS  - 4
SP  - 616
EP  - 626
PB  - Springer
CY  - New York
ER  -