A general framework for aquatic biogeochemical models

Environmental Modelling and Software

Volumn 61, Issue , 2014, Pages 249-265

  Bruggeman, Jorn ^a,b   Bolding, Karsten ^a  

^a Bolding and Burchard ApS   (Denmark)

^b PLYMOUTH MARINE LABORATORY   (United Kingdom)

Author keywords

Biogeochemical modelling; Coupling; Ecological modelling; Framework; Hydrodynamics

Indexed keywords

HYDRODYNAMICS;

BIOGEOCHEMICAL MODELLING; BIOGEOCHEMICAL MODELS; ECOLOGICAL MODELLING; FRAMEWORK;

COUPLINGS;

BIOGEOCHEMICAL CYCLE; BIOGEOCHEMISTRY; CHEMOSTAT; ECOLOGICAL MODELING; HYDRODYNAMICS; SOFTWARE; THREE-DIMENSIONAL FLOW;

EID: 84908262412     PISSN: 13648152     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.envsoft.2014.04.002     Document Type: Article

References (51)

1. Alexandrov G.A., Ames D., Bellocchi G., Bruen M., Crout N., Erechtchoukova M., Hildebrandt A., Hoffman F., Jackisch C., Khaiter P., Mannina G., Matsunaga T., Purucker S.T., Rivington M., Samaniego L. Technical assessment and evaluation of environmental models and software: letter to the editor. Environ. Model. Softw. 2011, 26(3):328-336.
2. Artioli Y., Blackford J.C., Butenschon M., Holt J.T., Wakelin S.L., Thomas H., Borges A.V., Allen J.I. The carbonate system in the North Sea: sensitivity and model validation. J.Mar. Syst. 2012, 102:1-13.
3. Aumont O., Bopp L. Globalizing results from ocean in situ iron fertilization studies. Global Biogeochem. Cycles 2006, 20(2).
4. Baretta J.W., Ebenhöh W., Ruardij P. The European regional seas ecosystem model, a complex marine ecosystem model. Netherlands J. Sea Res. 1995, 33(3-4):233-246.
5. Bennett N.D., Croke B.F.W., Guariso G., Guillaume J.H.A., Hamilton S.H., Jakeman A.J., Marsili-Libelli S., Newham L.T.H., Norton J.P., Perrin C., Pierce S.A., Robson B., Seppelt R., Voinov A.A., Fath B.D., Andreassian V. Characterising performance of environmental models. Environ. Model. Softw. 2013, 40:1-20.
6. 2 induced acidification in the North Sea. J.Mar. Syst. 2007, 64(1-4):229-241.
7. Burchard H., Bolding K. GETM: A General Estuarine Transport Model 2002, Scientific documentation, Tech. Rep., EUR 20253 EN, European Commission.
8. Burchard H., Bolding K., Kühn W., Meister A., Neumann T., Umlauf L. Description of a flexible and extendable physical-biogeochemical model system for the water column. J.Mar. Syst. 2006, 61(3-4):180-211.
9. Burchard H., Bolding K., Ruiz Villarreal M. GOTM - a General Ocean Turbulence Model. Theory, Applications and Test Cases 1999, Tech. Rep. EUR 18745 EN, European Commission.
10. Burchard H., Deleersnijder E., Meister A. Application of modified Patankar schemes to stiff biogeochemical models for the water column. Ocean Dyn. 2005, 55(3-4):326-337.
11. Charnock H. Wind Stress on a water surface. Q.J. R. Meteorol. Soc. 1955, 81(350):639-640.
12. Delworth T.L., Broccoli A.J., Rosati A., Stouffer R.J., Balaji V., Beesley J.A., Cooke W.F., Dixon K.W., Dunne J., Dunne K.A., Durachta J.W., Findell K.L., Ginoux P., Gnanadesikan A., Gordon C.T., Griffies S.M., Gudgel R., Harrison M.J., Held I.M., Hemler R.S., Horowitz L.W., Klein S.A., Knutson T.R., Kushner P.J., Langenhorst A.R., Lee H.C., Lin S.J., Lu J., Malyshev S.L., Milly P.C.D., Ramaswamy V., Russell J., Schwarzkopf M.D., Shevliakova E., Sirutis J.J., Spelman M.J., Stern W.F., Winton M., Wittenberg A.T., Wyman B., Zeng F., Zhang R. GFDL's CM2 global coupled climate models. Part I: Formulation and simulation characteristics. J.Clim. 2006, 19(5):643-674.
13. Edwards K.P., Barciela R., Butenschön M. Validation of the NEMO-ERSEM operational ecosystem model for the North West European Continental Shelf. Ocean Sci. 2012, 8(6):983-1000.
14. Fasham M.J.R., Ducklow H.W., McKelvie S.M. Anitrogen-based model of plankton dynamics in the oceanic mixed layer. J.Mar. Res. 1990, 48(3):591-639.
15. Fennel W., Neumann T. The mesoscale variability of nutrients and plankton as seen in a coupled model. German J. Hydrogr. 1996, 48(1).
16. Follows M.J., Dutkiewicz S., Grant S., Chisholm S.W. Emergent biogeography of microbial communities in a model ocean. Science 2007, 315(5820):1843-1846.
17. Galbraith E.D., Gnanadesikan A., Dunne J.P., Hiscock M.R. Regional impacts of iron-light colimitation in a global biogeochemical model. Biogeosciences 2010, 7(3):1043-1064.
18. Galbraith E.D., Kwon E.Y., Gnanadesikan A., Rodgers K.B., Griffies S.M., Bianchi D., Sarmiento J.L., Dunne J.P., Simeon J., Slater R.D., Wittenberg A.T., Held I.M. Climate variability and radiocarbon in the CM2Mc earth system model. J.Clim. 2011, 24(16):4230-4254.
19. Garcia H.E., Locarnini R.A., Boyer T.P., Antonov J.I., Zweng M.M., Baranova O.K., Johnson D.R. World Ocean Atlas 2009, volume 4: nutrients (phosphate, nitrate, silicate). NOAA Atlas NESDIS 71 2010, 398. U.S. Government Printing Office, Washington, DC. S. Levitus (Ed.).
20. Gregersen J.B., Gijsbers P.J.A., Westen S.J.P. OpenMI: open modelling interface. J.Hydroinform. 2007, 9(3):175-191.
21. Griffies S.M. Elements of MOM4p1 2009, 444. GFDL Ocean Group Technical Report No. 6, NOAA/Geophysical Fluid Dynamics Laboratory.
22. Griffies S.M., Biastoch A., Boning C., Bryan F., Danabasoglu G., Chassignet E.P., England M.H., Gerdes R., Haak H., Hallberg R.W., Hazeleger W., Jungclaus J., Large W.G., Madec G., Pirani A., Samuels B.L., Scheinert M., Sen Gupta A., Severijns C.A., Simmons H.L., Treguier A.M., Winton M., Yeager S., Yin J.J. Coordinated ocean-ice reference experiments (COREs). Ocean Model. 2009, 26(1-2):1-46.
23. Griffies S.M., Gnanadesikan A., Dixon K.W., Dunne J.P., Gerdes R., Harrison M.J., Rosati A., Russell J.L., Samuels B.L., Spelman M.J., Winton M., Zhang R. Formulation of an ocean model for global climate simulations. Ocean Sci. 2005, 1:45-79.
24. Hemmings J.C.P., Challenor P.G. Addressing the impact of environmental uncertainty in plankton model calibration with a dedicated software system: the Marine Model Optimization Testbed (MarMOT 1.1 alpha). Geosci. Model Dev. 2012, 5(2):471-498.
25. Hill C., DeLuca C., Balaji, Suarez M., da Silva A. The architecture of the earth system modeling framework. Comput. Sci. Eng. 2004, 6(1):18-28.
26. Hipsey M.R., Bruce L.C., Hamilton D.P. Aquatic EcoDynamics (AED) Model Library Science Manual 2013, 34. The University of Western Australia Technical Manual, Perth, Australia.
27. Hipsey M.R., Bruce L.C., Hamilton D.P. GLM General Lake Model. Model Overview and User Information 2013, 20. The University of Western Australia Technical Manual, Perth, Australia.
28. Huse G., Johansen G.O., Bogstad L., Gjosaeter H. Studying spatial and trophic interactions between capelin and cod using individual-based modelling. ICES J. Mar. Sci. 2004, 61(7):1201-1213.
29. Jöckel P., Kerkweg A., Buchholz-Dietsch J., Tost H., Sander R., Pozzer A. Technical note: coupling of chemical processes with the modular earth submodel system (MESSy) submodel TRACER. Atmos. Chem. Phys. 2008, 8(6):1677-1687.
30. Jöckel P., Sander R., Kerkweg A., Tost H., Lelieveld J. Technical note: the Modular Earth Submodel System (MESSy) - a new approach towards Earth System Modeling. Atmos. Chem. Phys. 2005, 5:433-444.
31. Jørgensen S.E. Areview of recent developments in lake modelling. Ecol. Model. 2010, 221(4):689-692.
32. Key R.M., Kozyr A., Sabine C.L., Lee K., Wanninkhof R., Bullister J.L., Feely R.A., Millero F.J., Mordy C., Peng T.H. Aglobal ocean carbon climatology: results from global data analysis project (GLODAP). Global biogeochemical cycles 2004, 18(4).
33. Kim T., Khangaonkar T. An offline unstructured biogeochemical model (UBM) for complex estuarine and coastal environments. Environ. Model. Softw. 2012, 31:47-63.
34. Larson J., Jacob R., Ong E. The Model Coupling Toolkit: a new fortran90 toolkit for building multiphysics parallel coupled models. Int. J. High Perform. Comput. Appl. 2005, 19(3):277-292.
35. Madec G. NEMO ocean engine, Note du Pole de modélisation 2008, Institut Pierre-Simon Laplace (IPSL), France.
36. Millero F.J., Lee K., Roche M. Distribution of alkalinity in the surface waters of the major oceans. Mar. Chem. 1998, 60(1-2):111-130.
37. Muetzelfeldt R. Declarative Modelling in Ecological and Environmental Research 2004, European Commission, EUR 20918.
38. Neumann T. Towards a 3D-ecosystem model of the Baltic Sea. J.Mar. Syst. 2000, 25(3-4):405-419.
39. Pereira A., Duarte P., Norro A. Different modelling tools of aquatic ecosystems: a proposal for a unified approach. Ecol. Inform. 2006, 1(4):407-421.
40. Ridgwell A., Hargreaves J.C., Edwards N.R., Annan J.D., Lenton T.M., Marsh R., Yool A., Watson A. Marine geochemical data assimilation in an efficient Earth System Model of global biogeochemical cycling. Biogeosciences 2007, 4(1):87-104.
41. Robson B.J., Hamilton D.P., Webster I.T., Chan T. Ten steps applied to development and evaluation of process-based biogeochemical models of estuaries. Environ. Model. Softw. 2008, 23(4):369-384.
42. Soetaert K., Meysman F. Reactive transport in aquatic ecosystems: rapid model prototyping in the open source software R. Environ. Model. Softw. 2012, 32:49-60.
43. Sonntag S., Hense I. Phytoplankton behavior affects ocean mixed layer dynamics through biological-physical feedback mechanisms. Geophys. Res. Lett. 2011, 38.
44. 2 flux over the global oceans. Deep-Sea Res. Part Ii-Topical Stud. Oceanogr. 2009, 56(8-10):554-577.
45. Travers M., Shin Y.J., Jennings S., Cury P. Towards end-to-end models for investigating the effects of climate and fishing in marine ecosystems. Prog. Oceanogr. 2007, 75(4):751-770.
46. Trolle D., Hamilton D.P., Hipsey M.R., Bolding K., Bruggeman J., Mooij W.M., Janse J.H., Nielsen A., Jeppesen E., Elliott A., Makler-Pick V., Petzoldt T., Rinke K., Flindt M.R., Arhonditsis G.B., Gal G., Bjerring R., Tominaga K., 't Hoen J., Downing A.S., Marques D.M., Fragoso C.R.J., Søndergaard M., Hanson P.C. Acommunity-based framework for aquatic ecosystem models. Hydrobiologia 2012, 683:25-34.
47. Valcke S. The OASIS3 coupler: a European climate modelling community software. Geosci. Model Dev. 2013, 6(2):373-388.
48. Valcke S., Craig T., Coquart L. OASIS3-MCT User Guide, OASIS3-MCT 2.0 2013, CERFACS/CNRS SUC URA No 1875: Toulouse, France.
49. Villa F., Athanasiadis I.N., Rizzoli A.E. Modelling with knowledge: a review of emerging semantic approaches to environmental modelling. Environ. Model. Softw. 2009, 24(5):577-587.
50. Warner J.C., Perlin N., Skyllingstad E.D. Using the Model Coupling Toolkit to couple earth system models. Environ. Model. Softw. 2008, 23(10-11):1240-1249.
51. Woods J.D. The Lagrangian Ensemble metamodel for simulating plankton ecosystems. Prog. Oceanogr. 2005, 67(1-2):84-159.