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Further reading

 

eReefs modelling group’s publications

BAIRD, M. E., ADAMS, M. P., BABCOCK, R. C., OUBELKHEIR, K., MONGIN, M., WILD-ALLEN, K. A., SKERRATT, J., ROBSON, B., PETROU, K., RALPH, P. J., O’BRIEN, K. R., CARTER, A. B., JARVIS, J. C. & RASHEED, M. A. 2016 A physical representation of seagrass growth for application in a complex shallow-water biogeochemical model Ecological Modelling. 325, 13-27.

BAIRD, M. E., CHERUKURU, N., JONES, E. M., MARGVELASHVILI, N., MONGIN, M., OUBELKHEIR, K., RALPH, P. J., RIZWI, F., ROBSON, B., SCHROEDER, T., SKERRATT, J., STEVEN, A. D. L. & WILD-ALLEN, K. A. 2016. Remote-sensing reflectance and true colour produced by a coupled hydrodynamic, optical, sediment, biogeochemical model of the Great Barrier Reef, Australia: comparison with remotely-sensed data Environmental Modelling and Software 78, 79-96.

GILLIBRAND, P. A. & HERZFELD, M. 2016 A mass-conserving advection scheme for offline simulation of tracer transport in coastal ocean models. Ocean Modelling. 101,1-16.

HERZFELD, M. 2015. Methods for freshwater riverine input into regional ocean models. Ocean Modelling, 90, 1-15.

HERZFELD, M. & GILLIBRAND, P. A. 2015. Active open boundary forcing using dual relaxation time-scales in downscaled ocean models. Ocean Modelling, 89, 71-83.

JONES, E. M., DOBLIN, M. A., MATEAR, R. & KING, E. 2015. Assessing and evaluating the ocean-colour footprint of a regional observing system. Journal of Marine Systems, 143, 49-61.

Jones, E., M. Baird, M. Mongin, J. Parslow, J. Skerratt, Lovell, J. N. Margvelashvili, R. Matear, K. Wild-Allen, B. Robson, F. Rizwi, P. Oke, E. King, T. Schroeder, A. Steven, and J. Taylor (2016) Use of remote-sensing reflectance to constrain a data assimilating marine biogeochemical model of the Great Barrier Reef. Biogeosciences 13, 6441–6469.

MARGVELASHVILI, N., ANDREWARTHA, J., HERZFELD, M., ROBSON, B. & BRANDO, V. 2013. Satellite data assimilation and estimation of a 3d coastal sediment transport model using error-subspace emulators. Environmental Modelling and Software Journal 40, 191-201.

MARGVELASHVILI, N., CAMPBELL, E., MURRAY, L. & JONES, E. M. 2014. Hierarchical emulation and data assimilation into the sediment transport model. Procedia Computer Science, 29, 2121-2126.

MARGVELASHVILI, N., HERZFELD, M., F. RIZWI, M. M., M. E. BAIRD, E. JONES, , E. KING, T. SCHROEDE, RIZWI, F., MONGIN, M., BAIRD, M. E., JONES, E. M., SCHAFFELKE, B., KING, E. & SCHROEDER, T. 2016. Emulator-assisted data assimilation in complex models. . Ocean Dynamics 66, 1109-1124.

MONGIN, M. & BAIRD, M. 2014. The impact of photosynthesis, calcification and water circulation on carbon chemistry variability above a coral reef: a modelling study. Ecological Modelling, 284, 19-34.

MONGIN, M., BAIRD, M. E., TILBROOK, B., MATEAR, R., LENTON, A., HERZFELD, M., WILD-ALLEN, K. A., SKERRATT, J., MARGVELASHVILI, N., ROBSON, B., DUARTE, C. M., GUSTAFSSON, M. S. M., RALPH, P. J. & STEVEN, A. D. L. 2016. The exposure of the Great Barrier Reef to ocean acidification. Nature Communications 7:10732.

MONGIN, M., BAIRD, M. E., LENTON, A & HADLEY, S. 2016. Optimising reef-scale CO2 removal by seaweed to buffer ocean acidification. Environ. Res. Lett. 11 034023.

OKE, P. R., LARNICOL, G., JONES, E. M., KOURAFALOU, V., SPERREVIK, A. K., CARSE, F., TANAJURA, C. A. S., MOURRE, B., TONANI, M., BRASSINGTON, G. B., LE HENAFF, M., HALLIWELL, J., GEORGE R., ATLAS, R., MOORE, A. M., EDWARDS, C. A., MARTIN, M. J., SELLAR, A. A., ALVAREZ, A., DE MEY, P. & ISKANDARANI, M. 2014. Assessing the impact of observations on ocean forecasts and reanalyses: Part 2, Regional applications. Journal of Operational Oceanography, issue?

ROBSON, B. 2014. When do aquatic systems models provide useful predictions, what is changing, and what is next? Environmental Modelling & Software, 61, 287-296.

ROBSON, B. J., BAIRD, M. & WILD-ALLEN, K. 2013. A physiological model for the marine cyanobacteria, Trichodesmium. MODSIM2013, 20th International Congress on Modelling and Simulation, Modelling and Simulation Society of Australia and New Zealand, 1652-1658.

ROBSON, B. J. & DOURDET, V. 2015. Prediction of sediment, particulate nutrient and dissolved nutrient concentrations in a dry tropical river to provide input to a mechanistic coastal water quality model. Environmental Modelling & Software, 63, 97-108.

ROBSON, B. J., SKERRATT, J., MONGIN, M., WILD-ALLEN, K. A. & BAIRD, M. E. 2014. Varying the temporal resolution of river nutrient boundary conditions to a coupled hydrodynamic-biogeochemical model of a coastal system has surprisingly little impact on model results. Proceedings – 7th International Congress on Environmental Modelling and Software: Bold Visions for Environmental Modeling, iEMSs Vol 1, 533-539.

SCHILLER, A., HERZFELD, M., BRINKMAN, R., RIZWI, F. & ANDREWARTHA, J. 2015. Cross-shelf exchanges between the Coral Sea and the Great Barrier Reef lagoon determined from a regional-scale numerical model. Continental Shelf Research, 109, 150-163.

SCHILLER, A., HERZFELD, M., BRINKMAN, R. & STUART, G. 2014. Monitoring, Predicting, and Managing One of the Seven Natural Wonders of the World. Bulletin of the American Meteorological Society, 95, 23-30.

STEVEN, A. D. L., HODGE, J., CANNARD, T., CARLIN, G., FRANKLIN, H., MCJANNET, D., MOESENEDER, C. & SEARLE, R. 2015. Continuous Water Quality Monitoring on the Great Barrier Reef. CSIRO Final Report to Great Barrier Reef Foundation. CSIRO, 159pp.

WEIJERMAN, M., FULTON, E. A., JANSSEN, A. B. G., KUIPER, J. J., LEEMANS, R., ROBSON, B. J., VAN DE LEEMPUT, I. A. & MOOIJ, W. M. 2015. How models can support ecosystem-based management of coral reefs. Progress in Oceanography.

References

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Brodie, J., Furnas, M., 2001. Status of nutrient and sediment inputs from Great Barrier Reef catchments and impacts on the Reef Proceedings of the 2nd National Conference on Aquatic Environments: Sustaining Our Aquatic Environments – Implementing Solutions. 20-23 November, 2001, Townsville, 14 p.

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Fabricius K., Logan M., Weeks S., Brodie J. 2014. The effects of river run-off on water clarity across the central Great Barrier Reef Marine Pollution Bulletin 84, 191–200

Furnas, M.J., (1991). Net in situ growth rates of phytoplankton in an oligotrophic, tropical shelf ecosystem. Limnol. Oceanogr., 36(1): 13-29.

Furnas, M.  2003. Catchments and corals: terrestrial runoff to the Great Barrier Ref. Australian Institute of Marine Science, Queen land., 334 p.

Furnas, M., Mitchell, A., Skuza, M. and Brodie, J., (2005).  In the other 90%: phytoplankton responses to enhanced nutrient availability in the Great Barrier Reef Lagoon.  Mar. Poll. Bull., 51: 253-265.

Furnas, M and Mitchell, A.W., (1986). Phytoplankton dynamics in the central Great Barrier Reef – I. Seasonal changes in biomass and community structure and therir relation to intrusive activity. Continental Shelf Res., 6(3): 363-384.

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Griffin, D. A. and J. H. Middleton, 1986. Coastal trapped waves behind a large continental shelf island, southern Great Barrier Reef. J. Phys. Oceanogr., 16, 1651 – 1664.

Griffin, D. A., J. H. Middleton and L. Bode, 1987. The tidal and longer-period circulation of Capricornia, souther Great Barrier Reef. Aust. J. Mar. Freshw. Res., 38, 461 – 474.

Harris, P.T., Hughes, M.G., Baker, E.K., Dalrymple, R.W., Keene, J.B., 2004. Sediment transport in distributary channels and its export to the pro-deltaic environment in a tidally-dominated delta: Fly River, Papua New Guinea. Continental Shelf Research, 24, 2431-2454.

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Larcombe, P., Carter, R. 2004. Cyclone pumping,sediment partitioning and the development of the Great Barrier Reef shelf system: a review. Quaternary Science Reviews 23, 107–135

Lewis S., Olley J., Furuichi T., Sharma A., Burton J. 2014. Complex sediment deposition history on a wide continental shelf: Implications for the calculation of accumulation rates on the Great Barrier Reef. Earth and Planetary Science Letters 393, 146–158

Madsen, O.S., 1994. Spectral wave-current bottom boundary layer flows, in Coastal Engineering 1994 Proceedings, 24th International Conference Coastal Engineering Research Council/ASCE, pp. 384-398.

Margvelashvili, N., Saint-Cast, F., Condie, S., 2008. Numerical modelling of the suspended sediment transport in Torres Strait. Continental Shelf Research 28, 2241-2256.

Neil D., Orpin, A., Ridd, P., Yu, B. 2002. Sediment yield and impacts from river catchments to the Great Barrier Reef lagoon. Mar. Freshwater Res. 53, 733-752.

Olley J., Brooks A., Spencer J., Pietsch T., Borombovits D., Howley C., Curwen G. (2013) “Geochemistry and provenance of sediments from Princess Charlotte Bay, Northern Great Barrier Reef”,  Appendix 12 of the Australian Rivers Institute and Griffith University report “An Empirically-based sediment budget for the Normanby Basin: Sediment Sources, Sinks & Drivers on the Cape York Savannah”, Australian Government Caring for our Country – Reef Rescue initiative (http://www.capeyorkwaterquality.info/references/cywq-229)

Orpin , A.R., Ridd, P.V. and Stewart, L.K. (1999) Assessment of the relative importance of major sediment-transport mechanisms in the central Great Barrier Reef lagoon. Australian Journal of Earth Science 46: 883 – 896.

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Thompson A., Schroeder T., Brando V., Schaffelke B. 2014. Coral community responses to declining water quality: Whitsunday Islands, Great Barrier Reef, Australia. Coral Reefs DOI 10.1007/s00338-014-1201-y

Webster I., Brinkman R., Parslow J., Prange J., Steven A., Waterhouse J. 2008. Review and gap analysis of receiving-water water quality modelling in the Great Barrier Reef. CSIRO Report to Department of Environment, Water, Heritage and the Arts, 150 p.

Wolanski, E., Spagnol, S. (2000). Sticky waters in the Great Barrier Reef. Estuarine, Coastal and Shelf Science 50, 27-32

Wolanski, E., Fabricius, K., Cooper, T., Humphrey, C. 2008 Wet season fine sediment dynamics on the inner shelf of the Great Barrier Reef. Estuarine, Coastal and Shelf Science