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BFM bibliography file

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@article{Carniel2007,
	Abstract = { This paper investigates the impacts of different turbulence models on the biological state at an ocean station in the northern Adriatic sea, named S3, comparing them with other uncertainties inherent to coupled physical--biological simulations. The numerical tool is a 1-D model resulting from the coupling of two advanced numerical models. The hydrodynamic part is modelled using the General Ocean Turbulence Model (www.gotm.net), in a version adopting state-of-the-art second-moment Turbulence Closure Models (TCMs). Marine biogeochemistry is parameterized with the Biogeochemical Flux Model (http://www.bo.ingv.it/bfm), which is a direct descendant of ERSEM (European Regional Sea Ecosystem Model). Results, obtained by forcing the model with hourly wind and solar radiation data and assimilating salinity casts, are compared against monthly observations made at the station during 2000--2001. Provided that modern second-moment TCMs are employed, the comparisons indicate that both the physical and the biological dynamics are relatively insensitive to the choice of the particular scheme adopted, suggesting that TCMs have finally `converged' in recent years. As a further example, the choice of the nutrient boundary conditions has an impact on the system evolution that is more significant than the choice of the specific TCM, therefore representing a possible limitation of the 1-D model applied to stations located in a Region of Freshwater Influence. The 1-D model simulates the onset and intensity of the spring--summer bloom quite well, although the duration of the bloom is not as prolonged as in the data. Since local dynamics appears unable to sustain the bloom conditions well into summer, phytoplankton at the station was most likely influenced by river input or advection processes, an aspect that was not found when the S3 behaviour was adequately modelled using climatological forcings. When the focus is in predicting high-frequency dynamics, it is more likely that lateral advection cannot be neglected. While the physical state can be satisfactorily estimated at these short time scales, the accurate estimation of the biological state in coastal regions still appears as rather elusive. },
	Author = {Sandro Carniel and Marcello Vichi and Mauro Sclavo},
	Date-Added = {2016-11-17 10:06:01 +0000},
	Date-Modified = {2016-11-17 10:06:01 +0000},
	Doi = {10.1080/02757540701197903},
	Eprint = {http://dx.doi.org/10.1080/02757540701197903},
	Journal = {Chemistry and Ecology},
	Keywords = {Pelagic environment, Simulation, Coastal zone, Turbulent diffusion, Physical--biogeochemical modelling, BFM},
	Month = {03},
	Number = {2},
	Pages = {157-175},
	Title = {Sensitivity of a coupled physical--biological model to turbulence: high-frequency simulations in a northern Adriatic station},
	Url = {http://dx.doi.org/10.1080/02757540701197903},
	Volume = {23},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1080/02757540701197903}}

@article{Saba2010,
	Author = {Saba, Vincent S. and Friedrichs, Marjorie A. M. and Carr, Mary-Elena and Antoine, David and Armstrong, Robert A. and Asanuma, Ichio and Aumont, Olivier and Bates, Nicholas R. and Behrenfeld, Michael J. and Bennington, Val and Bopp, Laurent and Bruggeman, Jorn and Buitenhuis, Erik T. and Church, Matthew J. and Ciotti, Aurea M. and Doney, Scott C. and Dowell, Mark and Dunne, John and Dutkiewicz, Stephanie and Gregg, Watson and Hoepffner, Nicolas and Hyde, Kimberly J. W. and Ishizaka, Joji and Kameda, Takahiko and Karl, David M. and Lima, Ivan and Lomas, Michael W. and Marra, John and McKinley, Galen A. and M{\'e}lin, Fr{\'e}d{\'e}ric and Moore, J. Keith and Morel, Andr{\'e} and O'Reilly, John and Salihoglu, Baris and Scardi, Michele and Smyth, Tim J. and Tang, Shilin and Tjiputra, Jerry and Uitz, Julia and Vichi, Marcello and Waters, Kirk and Westberry, Toby K. and Yool, Andrew},
	Date-Added = {2016-11-17 10:02:09 +0000},
	Date-Modified = {2016-11-17 10:02:09 +0000},
	Doi = {10.1029/2009GB003655},
	Issn = {1944-9224},
	Journal = {Global Biogeochemical Cycles},
	Keywords = {Time series experiments, Numerical modeling, Decadal ocean variability, Ecosystems structure dynamics and modeling, marine primary productivity models, BATS HOT trends, multidecadal climate forcing},
	Month = {09},
	Note = {GB3020},
	Number = {3},
	Pages = {n/a--n/a},
	Title = {Challenges of modeling depth-integrated marine primary productivity over multiple decades: A case study at BATS and HOT},
	Url = {http://dx.doi.org/10.1029/2009GB003655},
	Volume = {24},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1029/2009GB003655}}

@article{Polimene2006,
	Author = {Polimene, L. and Pinardi, N. and Zavatarelli, M. and Colella, S.},
	Date-Added = {2016-11-17 09:59:45 +0000},
	Date-Modified = {2016-11-17 09:59:45 +0000},
	Doi = {10.1029/2005JC003260},
	Issn = {2156-2202},
	Journal = {Journal of Geophysical Research: Oceans},
	Keywords = {Ecosystems structure dynamics and modeling; Food webs structure and dynamics; Nutrients and nutrient cycling; Biogeochemical cycles processes and modeling; Adriatic Sea; ecosystem model; chlorophyll},
	Month = {12},
	Note = {C03S19},
	Number = {C3},
	Pages = {n/a--n/a},
	Title = {The Adriatic Sea ecosystem seasonal cycle: Validation of a three-dimensional numerical model},
	Url = {http://dx.doi.org/10.1029/2005JC003260},
	Volume = {111},
	Year = {2006},
	Bdsk-Url-1 = {http://dx.doi.org/10.1029/2005JC003260}}

@article{Vichi2011a,
	Author = {Vichi, Marcello and Allen, J. Icarus and Masina, Simona and Hardman-Mountford, Nicholas J.},
	Date-Added = {2016-11-17 09:57:08 +0000},
	Date-Modified = {2016-11-17 09:57:08 +0000},
	Doi = {10.1029/2010GB003867},
	Issn = {1944-9224},
	Journal = {Global Biogeochemical Cycles},
	Keywords = {Biogeochemical cycles processes and modeling; Ecosystems structure and dynamics; General circulation; Biogeochemical model; global ocean; Biogeochemical Provinces; Biogeography; PELAGOS; BFM},
	Month = {05},
	Note = {GB2005},
	Number = {2},
	Pages = {n/a--n/a},
	Title = {The emergence of ocean biogeochemical provinces: A quantitative assessment and a diagnostic for model evaluation},
	Url = {http://dx.doi.org/10.1029/2010GB003867},
	Volume = {25},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1029/2010GB003867}}

@article{Alessandri2012,
	Author = {Alessandri, A. and Fogli, P. G. and Vichi, M. and Zeng, N.},
	Date-Added = {2016-11-17 09:52:48 +0000},
	Date-Modified = {2016-11-17 09:52:48 +0000},
	Doi = {10.5194/esd-3-199-2012},
	Journal = {Earth System Dynamics},
	Keywords = {BFM; Earth System Model; climate change; hydrological cycle},
	Number = {2},
	Pages = {199--212},
	Title = {Strengthening of the hydrological cycle in future scenarios: atmospheric energy and water balance perspective},
	Url = {http://www.earth-syst-dynam.net/3/199/2012/},
	Volume = {3},
	Year = {2012},
	Bdsk-Url-1 = {http://www.earth-syst-dynam.net/3/199/2012/},
	Bdsk-Url-2 = {http://dx.doi.org/10.5194/esd-3-199-2012}}

@article{Vichi2013,
	Abstract = {Carbon dioxide removal (CDR) is the only geoengineering technique that allows negative emissions and the reduction of anthropogenic carbon in the atmosphere. Since the time scales of the global carbon cycle are largely driven by the exchanges with the natural oceanic stocks, the implementation of CDR actions is anticipated to create outgassing from the ocean that may reduce their efficiency. The adjustment of the natural carbon cycle to CDR was studied with a numerical Earth System Model, focusing on the oceanic component and considering two idealized families of CDR policies, one based on a target atmospheric concentration and one based on planned negative emissions. Results show that both actions are anticipated to release the anthropogenic carbon stored in the surface ocean, effectively increasing the required removal effort. The additional negative emissions are expected to be lower when the CDR policy is driven by planned removal rates without prescribing a target atmospheric CO2 concentration.},
	Author = {Vichi, M. and Navarra, A. and Fogli, P. G.},
	Date-Added = {2016-11-17 09:50:44 +0000},
	Date-Modified = {2016-11-17 09:50:44 +0000},
	Doi = {10.1007/s10584-012-0677-0},
	Issn = {1573-1480},
	Journal = {Climatic Change},
	Keywords = {BFM; Climate change; Earth System Model},
	Number = {1},
	Pages = {105-118},
	Title = {Adjustment of the natural ocean carbon cycle to negative emission rates},
	Url = {http://dx.doi.org/10.1007/s10584-012-0677-0},
	Volume = {118},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s10584-012-0677-0}}

@article{Fraysse2013,
	Abstract = {Terrestrial inputs (natural and anthropogenic) from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C) and nitrogen (N) cycles and a second model that also considers the phosphorus (P) cycle. Realistic simulations were performed for a period of 5 years (2007--2011). The model accuracy assessment showed that both versions of the model were able of capturing the seasonal changes and spatial characteristics of the ecosystem. The model also reproduced upwelling events and the intrusion of Rhone River water into the Bay of Marseille well. Those processes appeared to greatly impact this coastal oligotrophic area because they induced strong increases in chlorophyll-a concentrations in the surface layer. The model with the C, N and P cycles better reproduced the chlorophyll-a concentrations at the surface than did the model without the P cycle, especially for the Rhone River water. Nevertheless, the chlorophyll-a concentrations at depth were better represented by the model without the P cycle. Therefore, the complexity of the biogeochemical model introduced errors into the model results, but it also improved model results during specific events. Finally, this study suggested that in coastal oligotrophic areas, improvements in the description and quantification of the hydrodynamics and the terrestrial inputs should be preferred over increasing the complexity of the biogeochemical model.},
	Author = {Fraysse, Marion AND Pinazo, Christel AND Faure, Vincent Martin AND Fuchs, Rosalie AND Lazzari, Paolo AND Raimbault, Patrick AND Pairaud, Ivane},
	Date-Added = {2016-11-17 09:48:53 +0000},
	Date-Modified = {2016-11-17 09:48:53 +0000},
	Doi = {10.1371/journal.pone.0080012},
	Journal = {PLOS ONE},
	Keywords = {BFM; Mediterranean Sea; coastal zone},
	Month = {12},
	Number = {12},
	Pages = {1-18},
	Publisher = {Public Library of Science},
	Title = {Development of a 3D Coupled Physical-Biogeochemical Model for the Marseille Coastal Area (NW Mediterranean Sea): What Complexity Is Required in the Coastal Zone?},
	Url = {http://dx.doi.org/10.1371%2Fjournal.pone.0080012},
	Volume = {8},
	Year = {2013},
	Bdsk-Url-1 = {http://dx.doi.org/10.1371%2Fjournal.pone.0080012},
	Bdsk-Url-2 = {http://dx.doi.org/10.1371/journal.pone.0080012}}

@article{Patara2011,
	Author = {Patara, Lavinia and Visbeck, Martin and Masina, Simona and Krahmann, Gerd and Vichi, Marcello},
	Date-Added = {2016-11-17 09:43:11 +0000},
	Date-Modified = {2016-11-17 10:02:31 +0000},
	Doi = {10.1029/2010JC006785},
	Issn = {2156-2202},
	Journal = {Journal of Geophysical Research: Oceans},
	Keywords = {Climate and interannual variability, Numerical modeling, Physical and biogeochemical interactions, Decadal ocean variability, Biogeochemical cycles processes and modeling, North Atlantic Oscillation, coupled climate model, marine biogeochemistry, natural climate variability, phytoplankton bloom},
	Note = {C07023},
	Number = {C7},
	Pages = {n/a--n/a},
	Title = {Marine biogeochemical responses to the North Atlantic Oscillation in a coupled climate model},
	Url = {http://dx.doi.org/10.1029/2010JC006785},
	Volume = {116},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1029/2010JC006785}}

@article{Epicoco2016,
	Author = {Epicoco, I. and Mocavero, S. and Macchia, F. and Vichi, M. and Lovato, T. and Masina, S. and Aloisio, G.},
	Date-Modified = {2016-11-17 09:44:06 +0000},
	Doi = {10.5194/gmd-9-2115-2016},
	Journal = {Geoscientific Model Development},
	Keywords = {PELAGOS},
	Number = {6},
	Pages = {2115--2128},
	Title = {Performance and results of the high-resolution biogeochemical model PELAGOS025v1.0 within NEMO v3.4},
	Url = {http://www.geosci-model-dev.net/9/2115/2016/},
	Volume = {9},
	Year = {2016},
	Bdsk-Url-1 = {http://www.geosci-model-dev.net/9/2115/2016/},
	Bdsk-Url-2 = {http://dx.doi.org/10.5194/gmd-9-2115-2016}}

@article{Lazzari2016,
	Author = {P. Lazzari and C. Solidoro and S. Salon and G. Bolzon},
	Date-Added = {2016-11-17 09:32:35 +0000},
	Date-Modified = {2016-11-17 09:33:00 +0000},
	Doi = {http://dx.doi.org/10.1016/j.dsr.2015.12.006},
	Issn = {0967-0637},
	Journal = {Deep Sea Research Part I: Oceanographic Research Papers},
	Keywords = {Mediterranean Sea; Biogeochemical modeling; Phosphate nitrate distribution; Nutrient limitation},
	Pages = {39 - 52},
	Title = {Spatial variability of phosphate and nitrate in the Mediterranean Sea: A modeling approach},
	Url = {http://www.sciencedirect.com/science/article/pii/S0967063715301473},
	Volume = {108},
	Year = {2016},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0967063715301473},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.dsr.2015.12.006}}

@article{Visinelli2016,
	Author = {L. Visinelli and S. Masina and M. Vichi and A. Storto and T. Lovato},
	Date-Added = {2016-11-17 09:30:56 +0000},
	Date-Modified = {2016-11-17 09:31:22 +0000},
	Doi = {http://dx.doi.org/10.1016/j.jmarsys.2016.02.011},
	Issn = {0924-7963},
	Journal = {Journal of Marine Systems},
	Keywords = {Ocean biogeochemical dynamics; Data assimilation; Carbon cycle},
	Pages = {106 - 119},
	Title = {Impacts of data assimilation on the global ocean carbonate system},
	Url = {http://www.sciencedirect.com/science/article/pii/S092479631630001X},
	Volume = {158},
	Year = {2016},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S092479631630001X},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jmarsys.2016.02.011}}

@article{McKiver2015,
	Author = {McKiver, William J. and Vichi, Marcello and Lovato, Tomas and Storto, Andrea and Masina, Simona},
	Booktitle = {The variability of primary production in the ocean: From the synoptic to the global scale. The 45th International Liege Colloquium on Ocean Dynamics, Liege, Belgium, May 13-17, 2013},
	Date = {2015/7//},
	Date-Added = {2016-11-17 09:29:15 +0000},
	Date-Modified = {2016-11-17 09:29:44 +0000},
	Doi = {http://dx.doi.org/10.1016/j.jmarsys.2014.10.003},
	Isbn = {0924-7963},
	Journal = {Journal of Marine Systems},
	Keywords = {Marine plankton; Global ocean; Mesoscale processes; Chlorophyll; Nutricline},
	Month = {7},
	Pages = {153--168},
	Title = {Impact of increased grid resolution on global marine biogeochemistry},
	Ty = {JOUR},
	Url = {http://www.sciencedirect.com/science/article/pii/S0924796314002334},
	Volume = {147},
	Year = {2015},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0924796314002334},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jmarsys.2014.10.003}}

@article{Cossarini15,
	Author = {Cossarini, G. and Lazzari, P. and Solidoro, C.},
	Date-Added = {2015-09-02 15:07:34 +0000},
	Date-Modified = {2015-09-02 15:09:53 +0000},
	Doi = {10.5194/bg-12-1647-2015},
	Journal = {Biogeosciences},
	Keywords = {BFM; Mediterranean Sea; Carbonate System; Alkalinity},
	Number = {6},
	Pages = {1647--1658},
	Title = {Spatiotemporal variability of alkalinity in the Mediterranean Sea},
	Url = {http://www.biogeosciences.net/12/1647/2015/},
	Volume = {12},
	Year = {2015},
	Bdsk-Url-1 = {http://www.biogeosciences.net/12/1647/2015/},
	Bdsk-Url-2 = {http://dx.doi.org/10.5194/bg-12-1647-2015}}

@article{MelakuCanu15,
	Author = {Donata Melaku Canu and Andrea Ghermandi and Paulo A.L.D. Nunes and Paolo Lazzari and Gianpiero Cossarini and Cosimo Solidoro},
	Date-Added = {2015-09-02 15:06:24 +0000},
	Date-Modified = {2016-11-17 09:46:08 +0000},
	Doi = {http://dx.doi.org/10.1016/j.gloenvcha.2015.02.008},
	Issn = {0959-3780},
	Journal = {Global Environmental Change},
	Keywords = {Blue carbon; Carbon sequestration; Ecosystem services; Integrated assessment; Mediterranean Sea; Regulating services},
	Pages = {87 - 95},
	Title = {Estimating the value of carbon sequestration ecosystem services in the Mediterranean Sea: An ecological economics approach},
	Url = {http://www.sciencedirect.com/science/article/pii/S0959378015000278},
	Volume = {32},
	Year = {2015},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0959378015000278},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.gloenvcha.2015.02.008}}

@manual{bfn-nemo-manual,
	Author = {Vichi, M. and Lovato, T. and Gutierrez Mlot, E. and McKiver, W.},
	Date-Added = {2015-08-28 21:13:03 +0000},
	Date-Modified = {2015-08-28 21:14:19 +0000},
	Keywords = {BFM; NEMO; physical-biogeochemical coupling},
	Month = {August},
	Organization = {BFM Consortium},
	Title = {Coupling BFM with Ocean models: the NEMO model (Nucleus for the European Modelling of the Ocean)},
	Year = {2015}}

@manual{bfm-manual,
	Author = {Vichi, M. and Lovato, T. and Lazzari, P. and Cossarini, G. and Gutierrez Mlot, E. and Mattia, G. and Masina, S. and McKiver, W. J. and Pinardi, N. and Solidoro, C. and Tedesco, L. and Zavatarelli, M.},
	Date-Added = {2015-08-28 20:40:50 +0000},
	Date-Modified = {2015-08-28 20:43:26 +0000},
	Keywords = {BFM; manual; Biogeochemical Flux Model; Equation Description; User Manual},
	Month = {August},
	Organization = {BFM Consortium},
	Title = {The Biogeochemical Flux Model (BFM): Equation Description and User Manual. BFM version 5.1},
	Year = {2015}}

@article{Lazzari14,
	Author = {P. Lazzari and G. Mattia and C. Solidoro and S. Salon and A. Crise and M. Zavatarelli and P. Oddo and M. Vichi},
	Date-Added = {2015-08-28 20:06:39 +0000},
	Date-Modified = {2015-08-28 20:06:39 +0000},
	Doi = {http://dx.doi.org/10.1016/j.jmarsys.2013.06.005},
	Issn = {0924-7963},
	Journal = {Journal of Marine Systems},
	Keywords = {Scenario simulations},
	Note = {Assessing and modelling ecosystem changes in the Mediterranean and the Black Sea pelagic ecosystem - \{SESAME\}},
	Pages = {137 - 149},
	Title = {The impacts of climate change and environmental management policies on the trophic regimes in the Mediterranean Sea: Scenario analyses},
	Url = {http://www.sciencedirect.com/science/article/pii/S0924796313001425},
	Volume = {135},
	Year = {2014},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0924796313001425},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jmarsys.2013.06.005}}

@article{Ruggio13,
	Author = {Raffaele Ruggio and Marcello Vichi and Francesco Paparella and Simona Masina},
	Date-Added = {2015-08-28 20:05:20 +0000},
	Date-Modified = {2015-08-28 20:05:34 +0000},
	Doi = {http://dx.doi.org/10.1016/j.jmarsys.2013.04.001},
	Issn = {0924-7963},
	Journal = {Journal of Marine Systems},
	Keywords = {BFM; Lagrangian method},
	Pages = {11 - 23},
	Title = {Climatic trends of the equatorial undercurrent: A backup mechanism for sustaining the equatorial Pacific production},
	Url = {http://www.sciencedirect.com/science/article/pii/S0924796313000845},
	Volume = {121--122},
	Year = {2013},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0924796313000845},
	Bdsk-Url-2 = {http://dx.doi.org/10.1016/j.jmarsys.2013.04.001}}

@article{cagnazzo13,
	Author = {Cagnazzo, Chiara and Manzini, Elisa and Fogli, PierGiuseppe and Vichi, Marcello and Davini, Paolo},
	Date-Added = {2015-08-28 20:03:06 +0000},
	Date-Modified = {2015-08-28 20:04:30 +0000},
	Journal = {Climate Dynamics},
	Keywords = {BFM; Carbon Earth System Model; Stratospheric Ozone; Southern Hemisphere climate change; Ocean Carbon Cycle},
	Month = {December},
	Number = {11-12},
	Pages = {3039-3054},
	Title = {Role of stratospheric dynamics in the ozone--carbon connection in the Southern Hemisphere},
	Volume = {41},
	Year = {2013}}

@article{mattia13,
	Author = {Mattia, Gelsomina and Zavatarelli, Marco and Vichi, Marcello and Oddo, Paolo},
	Date-Added = {2015-08-28 18:46:28 +0000},
	Date-Modified = {2015-08-28 18:48:41 +0000},
	Journal = {Journal of Geophysical Research: Oceans},
	Keywords = {BFM; Decadal ocean variability; General circulation; Mediterranean Sea, Eastern Mediterranean Transient, physical-biogeochemical coupling},
	Month = {April},
	Number = {4},
	Pages = {2231-2248},
	Title = {The Eastern Mediterranean Sea biogeochemical dynamics in the 1990s: A numerical study},
	Volume = {118},
	Year = {2013}}

@article{lamon14,
	Author = {Lamon, Lara and Rizzi, Jonathan and Bonaduce, Antonio and Dubois, Clotilde and Lazzari, Paolo and Ghenim, Leila and Gana, Slim and Somot, Samuel and Li, Laurent and Canu, DonataMelaku and Solidoro, Cosimo and Pinardi, Nadia and Marcomini, Antonio},
	Date-Added = {2015-08-28 18:36:59 +0000},
	Date-Modified = {2015-08-28 18:39:07 +0000},
	Journal = {Regional Environmental Change},
	Keywords = {BFM; Models' ensemble; Model simulations; Gulf of Gabes; A1B climate change scenario; Present climate scenario},
	Number = {1},
	Pages = {31-40},
	Title = {An ensemble of models for identifying climate change scenarios in the Gulf of Gabes, Tunisia},
	Volume = {14},
	Year = {2014}}

@article{teruzzi11,
	Author = {Teruzzi, A. and Salon, S. and Bolzon, G. and Lazzari, Paolo and Ficarelli, F. and Solidoro, C. and Crise, A.},
	Date-Added = {2015-08-28 18:25:48 +0000},
	Date-Modified = {2015-08-28 18:32:35 +0000},
	Journal = {Mercator Ocean Quarterly Newsletter},
	Keywords = {BFM; Mediterranean Sea; Operational oceanography},
	Pages = {15-25},
	Read = {0},
	Title = {Operational forecasts of the biogeochemical state of Mediterranean Sea},
	Volume = {40},
	Year = {2011}}

@article{berline11,
	Author = {Berline, Leo and Stemmann, Lars and Vichi, Marcello and Lombard, Fabien and Gorsky, Gabriel},
	Date = {2011/06/01},
	Date-Added = {2011-05-02 16:47:23 +0200},
	Date-Modified = {2012-08-29 16:00:58 +0000},
	Doi = {10.1093/plankt/fbq163},
	Journal = jpr,
	Journal1 = {Journal of Plankton Research},
	Keywords = {BFM},
	Month = {06},
	Number = {6},
	Pages = {855--872},
	Title = {Impact of appendicularians on detritus and export fluxes: a model approach at DyFAMed site},
	Ty = {JOUR},
	Url = {http://plankt.oxfordjournals.org/content/33/6/855.abstract},
	Volume = {33},
	Year = {2011},
	Bdsk-Url-1 = {http://plankt.oxfordjournals.org/content/33/6/855.abstract},
	Bdsk-Url-2 = {http://dx.doi.org/10.1093/plankt/fbq163}}

@article{butenschoen12,
	Author = {Butensch{\"o}n, Momme and Zavatarelli, Marco and Vichi, Marcello},
	Date-Added = {2012-05-19 13:00:14 +0000},
	Date-Modified = {2016-11-17 09:53:03 +0000},
	Doi = {10.1016/j.ocemod.2012.04.008},
	Isbn = {1463-5003},
	Journal = {Ocean Modelling},
	Keywords = {BFM;Ecosystem Modelling; Coupling; Time Splitting; Time Scale; Biogeochemical Dynamics; Hydrodynamics},
	Pages = {36-53},
	Title = {Sensitivity of a marine coupled physical biogeochemical model to time resolution, integration scheme and time splitting method},
	Ty = {JOUR},
	Url = {http://www.sciencedirect.com/science/article/pii/S1463500312000686?v=s5},
	Volume = {52-53},
	Year = {2012},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1463500312000686?v=s5}}

@article{butenschoen12b,
	Author = {Butensch{\"o}n, Momme and Zavatarelli, Marco},
	Date = {2012/9//},
	Date-Added = {2012-08-29 16:39:31 +0000},
	Date-Modified = {2012-08-29 16:40:08 +0000},
	Doi = {10.1016/j.ocemod.2012.06.003},
	Isbn = {1463-5003},
	Journal = {Ocean Modelling},
	Keywords = {BFM;Data assimilation; Kalman Filter; Marine ecosystem model; Biogeochemical dynamics; SEEK; Comparison},
	Month = {9},
	Number = {0},
	Pages = {37--54},
	Title = {A comparison of different versions of the SEEK Filter for assimilation of biogeochemical data in numerical models of marine ecosystem dynamics},
	Ty = {JOUR},
	Url = {http://www.sciencedirect.com/science/article/pii/S1463500312000996},
	Volume = {54--55},
	Year = {2012},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S1463500312000996}}

@article{cheptsov09,
	Author = {Cheptsov, Alexey and Dichev, K. and Keller, Rainer and Lazzari, Paolo and Salon, Stefano},
	Date-Added = {2012-08-29 16:28:27 +0000},
	Date-Modified = {2012-08-29 16:29:05 +0000},
	Journal = {Computational Methods in Science and Technology},
	Keywords = {BFM;communication pattern, eco-hydrodynamic simulation, grid, mpi, performance optimization},
	Number = {1},
	Pages = {9{\textendash}19},
	Title = {Porting the {OPATM-BFM} Application to a Grid e-Infrastructure {\textendash} Optimization of Communication and I / O Patterns},
	Volume = {15},
	Year = {2009}}

@article{cheptsov12,
	Acmid = {2325184},
	Address = {Amsterdam, The Netherlands, The Netherlands},
	Author = {Cheptsov, Alexey and Koller, Bastian and Adami, Davide and Davoli, Franco and Mueller, Szymon and Meyer, Norbert and Lazzari, Paolo and Salon, Stefano and Watzl, Johannes and Schiffers, Michael and Kranzlmueller, Dieter},
	Date-Added = {2012-08-29 16:33:18 +0000},
	Date-Modified = {2012-08-29 16:33:39 +0000},
	Doi = {10.1016/j.csi.2011.10.012},
	Issn = {0920-5489},
	Issue_Date = {November, 2012},
	Journal = {Comput. Stand. Interfaces},
	Keywords = {BFM;Grid, Quality of service, Remote instrumentation, e-Infrastructure, e-Science},
	Month = nov,
	Number = {6},
	Numpages = {9},
	Pages = {476--484},
	Publisher = {Elsevier Science Publishers B. V.},
	Title = {e-Infrastructure for Remote Instrumentation},
	Url = {http://dx.doi.org/10.1016/j.csi.2011.10.012},
	Volume = {34},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.csi.2011.10.012}}

@article{lazzari10,
	Author = {Lazzari, P. and Teruzzi, A. and Salon, S. and Campagna, S. and Calonaci, C. and Colella, S. and Tonani, M. and Crise, A.},
	Date = {2010/01/21},
	Date-Added = {2011-12-13 18:51:22 +0200},
	Date-Modified = {2012-08-29 16:30:15 +0000},
	Doi = {10.5194/os-6-25-2010},
	Isbn = {1812-0792},
	J1 = {OS},
	Journal = {Ocean Sci.},
	Keywords = {BFM},
	Month = {01},
	Number = {1},
	Pages = {25--39},
	Publisher = {Copernicus Publications},
	Title = {Pre-operational short-term forecasts for {M}editerranean Sea {b}iogeochemistry},
	Ty = {JOUR},
	Url = {http://www.ocean-sci.net/6/25/2010/},
	Volume = {6},
	Year = {2010},
	Bdsk-Url-1 = {http://www.ocean-sci.net/6/25/2010/},
	Bdsk-Url-2 = {http://dx.doi.org/10.5194/os-6-25-2010}}

@article{lazzari12,
	Author = {Lazzari, P. and Solidoro, C. and Ibello, V. and Salon, S. and Teruzzi, A. and B\'eranger, K. and Colella, S. and Crise, A.},
	Date-Added = {2012-08-29 16:31:39 +0000},
	Date-Modified = {2012-08-29 16:31:53 +0000},
	Doi = {10.5194/bg-9-217-2012},
	Journal = {Biogeosciences},
	Keywords = {BFM},
	Number = {1},
	Pages = {217--233},
	Title = {Seasonal and inter-annual variability of plankton chlorophyll and primary production in the Mediterranean Sea: a modelling approach},
	Url = {http://www.biogeosciences.net/9/217/2012/},
	Volume = {9},
	Year = {2012},
	Bdsk-Url-1 = {http://www.biogeosciences.net/9/217/2012/},
	Bdsk-Url-2 = {http://dx.doi.org/10.5194/bg-9-217-2012}}

@article{macias10,
	Author = {Macias, D. and Ramirez-Romero, E. and C. M. Garcia},
	Date-Added = {2010-10-21 10:26:59 +0200},
	Date-Modified = {2012-08-29 16:29:51 +0000},
	Doi = {10.1357/002224010793078979},
	Journal = jmr,
	Keywords = {BFM},
	Number = {1},
	Pages = {119-151},
	Title = {Effect of nutrient input frequency on the structure and dynamics of the marine pelagic community: A modeling approach},
	Volume = {68},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1357/002224010793078979}}

@article{patara12,
	Author = {Patara, Lavinia and Vichi, Marcello and Masina, Simona and Fogli, Pier Giuseppe and Manzini, Elisa},
	Date-Added = {2012-04-18 08:16:16 +0000},
	Date-Modified = {2012-08-29 14:16:37 +0000},
	Doi = {10.1007/s00382-012-1300-9},
	Isbn = {0930-7575},
	Journal = cdyn,
	Keywords = {Earth and Environmental Science;BFM},
	Pages = {1--18},
	Publisher = {Springer Berlin / Heidelberg},
	Title = {Global response to solar radiation absorbed by phytoplankton in a coupled climate model},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1007/s00382-012-1300-9},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00382-012-1300-9}}

@article{patara12b,
	Author = {Patara, Lavinia and Vichi, Marcello and Masina, Simona},
	Date = {2012/10/10/},
	Date-Added = {2012-08-26 08:56:24 +0000},
	Date-Modified = {2012-08-29 16:34:16 +0000},
	Day = {10},
	Doi = {10.1016/j.ecolmodel.2012.06.012},
	Isbn = {0304-3800},
	Journal = em,
	Keywords = {BFM;Plankton model; Biogeochemistry; Physiological stoichiometry; Natural climate variability; Climate change; North Pacific; Earth System Model; BFM},
	Month = {10},
	Pages = {132--147},
	Title = {Impacts of natural and anthropogenic climate variations on North Pacific plankton in an Earth System Model},
	Ty = {JOUR},
	Url = {http://www.sciencedirect.com/science/article/pii/S0304380012002840},
	Volume = {244},
	Year = {2012},
	Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/pii/S0304380012002840}}

@article{Polimene2007,
	Abstract = {A mechanistic explanation for the accumulation of dissolved organic carbon (DOC), observed in coastal seas such as the Northern Adriatic Sea, is proposed here on the basis of numerical simulations of the marine ecosystem dynamics carried out with a coupled biogeochemical-circulation model. The biogeochemical model is based on the European Regional Seas Ecosystem Model (ERSEM) upgraded with a more detailed representation of the DOC-bacteria interactions and resolving different level of DOC lability/refractivity. The circulation model is the Adriatic Sea implementation of the Princeton Ocean Model. The analysis of simulations confirms the important role of the Po river nutrient input on the ecosystem dynamics and highlights the presence of a strong across-shelf trophic gradient that, affecting the Bacterial Growth Efficiency (BGE), could be a key factor for the DOC accumulation. The simulations show the importance of circulation features in modulating the exchanges between areas having different trophic structure such as the western coastal strip, strongly influenced by the Po river runoff, and the open sea areas in the centre of the northern Adriatic sub-basin. The DOC produced in the high energy system of the Po runoff coastal strip, characterized by high BGE, is transported toward the open areas, which is a more oligotrophic environment with lower BGE. In this area the DOC turnover time is strongly increased giving rise to the DOC accumulation.},
	Author = {Polimene, L. and Pinardi, N. and Zavatarelli, M. and Allen, J. I. and Giani, M. and Vichi, M.},
	Date = {2007/03/07},
	Date-Added = {2012-08-29 16:08:39 +0000},
	Date-Modified = {2016-11-17 10:03:51 +0000},
	Doi = {10.1029/2006JC003529},
	Isbn = {0148-0227},
	Journal = {J. Geophys. Res.},
	Keywords = {BFM; DOC; ecosystem model; Adriatic Sea; Marine systems; Carbon cycling; Ecosystems structure and dynamics},
	Month = {03},
	Number = {C3},
	Pages = {C03S20},
	Publisher = {AGU},
	Title = {A numerical simulation study of dissolved organic carbon accumulation in the northern Adriatic Sea},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1029/2006JC003529},
	Volume = {112},
	Year = {2007},
	Bdsk-Url-1 = {http://dx.doi.org/10.1029/2006JC003529}}

@article{tedesco10,
	Author = {Tedesco, L. and Vichi, M. and Haapala, J. and Stipa, T.},
	Date-Added = {2009-05-18 16:35:57 +0200},
	Date-Modified = {2012-08-29 14:13:56 +0000},
	Doi = {doi:10.1016/j.ocemod.2010.06.008},
	Journal = {Ocean Modelling},
	Keywords = {BFM},
	Pages = {89--104},
	Title = {A dynamic Biologically-Active Layer for numerical studies of the sea ice ecosystem},
	Volume = {35},
	Year = {2010},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.ocemod.2010.06.008}}

@article{tedesco12,
	Author = {Letizia Tedesco and Marcello Vichi and David N. Thomas},
	Date-Added = {2011-12-13 18:44:19 +0200},
	Date-Modified = {2012-08-29 14:14:04 +0000},
	Doi = {10.1016/j.ecolmodel.2011.11.011},
	Journal = em,
	Keywords = {BFM},
	Pages = {120--138},
	Title = {Process studies on the ecological coupling between sea ice algae and phytoplankton},
	Volume = {226},
	Year = {2012},
	Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.ecolmodel.2011.11.011}}

@article{vichi03,
	Author = {M. Vichi and P. Oddo and M. Zavatarelli and A. Coluccelli and G. Coppini and M. Celio and S. {Fonda Umani} and N. Pinardi},
	Date-Modified = {2012-08-29 14:08:54 +0000},
	Journal = ag,
	Keywords = {BFM},
	Pages = {413-436},
	Title = {Calibration and validation of a one-dimensional complex marine biogeochemical fluxes model in different areas of the northern {A}driatic shelf.},
	Volume = {21},
	Year = {2003}}

@article{vichi03cr,
	Author = {M. Vichi and W. May and A. Navarra},
	Date-Modified = {2012-08-29 14:09:09 +0000},
	Journal = {Climate Research},
	Keywords = {BFM},
	Pages = {141--159},
	Title = {Response of a complex ecosystem model of the northern {Adriatic} {Sea} to a regional climate change scenario},
	Volume = {24},
	Year = {2003}}

@article{vichi04,
	Author = {M. Vichi and P. Ruardij and J. W. Baretta},
	Date-Modified = {2012-08-29 14:09:24 +0000},
	Journal = {Biogeosciences},
	Keywords = {BFM},
	Pages = {79--100},
	Title = {Link or sink: a modelling interpretation of the open {Baltic} biogeochemistry},
	Volume = {1},
	Year = {2004}}

@article{vichi07_part1,
	Author = {M. Vichi and N. Pinardi and S. Masina},
	Date-Modified = {2012-08-29 14:09:35 +0000},
	Journal = jms,
	Keywords = {BFM},
	Pages = {89--109},
	Title = {A generalized model of pelagic biogeochemistry for the global ocean ecosystem. {P}art {I}: theory},
	Volume = {64},
	Year = {2007}}

@article{vichi07_part2,
	Author = {M. Vichi and S. Masina and A. Navarra},
	Date-Modified = {2012-08-29 14:09:44 +0000},
	Journal = jms,
	Keywords = {BFM},
	Pages = {110--134},
	Title = {A generalized model of pelagic biogeochemistry for the global ocean ecosystem. {P}art {II}: numerical simulations},
	Volume = {64},
	Year = {2007}}

@article{Vichi2008,
	Abstract = {The response of phytoplankton growth to iron supply and its modulation by large-scale circulation and tropical instability waves (TIWs) in the eastern equatorial Pacific has been investigated with an ocean biogeochemical model. This process study shows that iron can be efficiently advected from the New Guinea shelf through the Equatorial Undercurrent (EUC) to the eastern Pacific. The presence of a continental iron source is necessary for the maintenance of the observed subsurface iron maximum in the EUC core. In the eastern Pacific region, phytoplankton production is enhanced when additional iron is available in the EUC. Simulated phytoplankton variability is linked to TIWs activity, as revealed by a wavelet analysis of the total autotrophic carbon. The net local effect of the waves on phytoplankton can be either positive or negative depending on several factors. When the iron nutricline is sufficiently shallow to be reached by the wave vertical scale, the effect of the waves is to enhance iron availability in the euphotic zone leading to a net local increase of phytoplankton biomass. We therefore suggest that the local maxima of phytoplankton observed in moorings off the Equator in the eastern Pacific might be not only the result of concentration mechanisms, but also the result of an increase in local production sustained by advected iron.},
	Author = {Vichi, M. and Masina, S. and Nencioli, F.},
	Date = {2008},
	Date-Added = {2008-12-09 10:10:30 +0100},
	Date-Modified = {2016-11-17 10:06:15 +0000},
	Date1 = {August, 2008 %@ 00796611},
	Journal = po,
	Keywords = {Biogeochemical model; BFM; PELAGOS; Tropical instability waves; Iron; Equatorial pacific},
	Number = {2},
	Pages = {147-162},
	Publisher = {Elsevier Science},
	Title = {A process-oriented model study of equatorial Pacific phytoplankton: The role of iron supply and tropical instability waves},
	Volume = {78},
	W = {/cgi-bin/sciserv.pl?collection=journals&journal=00796611&issue=v78i0002&article=147_apmsoeisatiw},
	Year = {2008}}

@article{Vichi2009,
	Author = {Vichi, M. and Masina, S.},
	Date = {2009/11/02},
	Date-Added = {2009-11-07 15:52:58 +0100},
	Date-Modified = {2016-11-17 10:06:23 +0000},
	Isbn = {1726-4170},
	J1 = {BG},
	Journal = {Biogeosciences},
	Keywords = {BFM},
	Local-Url = {http://www.biogeosciences.net/6/2333/2009/bg-6-2333-2009.pdf},
	Month = {11},
	Number = {11},
	Pages = {2333--2353},
	Publisher = {Copernicus Publications},
	Title = {Skill assessment of the PELAGOS global ocean biogeochemistry model over the period 1980-2000},
	Ty = {JOUR},
	Url = {http://www.biogeosciences.net/6/2333/2009/},
	Volume = {6},
	Year = {2009},
	Bdsk-Url-1 = {http://www.biogeosciences.net/6/2333/2009/}}

@article{vichi09osd,
	Author = {Vichi, M. and Coluccelli, A. and Ravaioli, M. and Giglio, F. and Langone, L. and Azzaro, M. and Azzaro, F. and La Ferla, R. and Catalano, G. and Cozzi, S.},
	Date = {2009/07/08},
	Date-Added = {2009-09-21 10:40:58 +0200},
	Date-Modified = {2012-08-29 14:13:25 +0000},
	Doi = {http://www.ocean-sci-discuss.net/6/1477/2009/},
	Isbn = {1812-0806},
	J1 = {OSD},
	Journal = {Ocean Sci. Discuss.},
	Keywords = {BFM},
	Local-Url = {http://www.ocean-sci-discuss.net/6/1477/2009/osd-6-1477-2009.pdf},
	Month = {07},
	Number = {2},
	Pages = {1477--1512},
	Publisher = {Copernicus Publications},
	Title = {Modelling approach to the assessment of biogenic fluxes at a selected Ross Sea site, Antarctica},
	Ty = {JOUR},
	Url = {http://www.ocean-sci-discuss.net/6/1477/2009/},
	Volume = {6},
	Year = {2009},
	Bdsk-Url-1 = {http://www.ocean-sci-discuss.net/6/1477/2009/}}

@article{vichi11b,
	Author = {Vichi, Marcello and Manzini, Elisa and Fogli, Pier and Alessandri, Andrea and Patara, Lavinia and Scoccimarro, Enrico and Masina, Simona and Navarra, Antonio},
	Date = {2011/11/01/},
	Date-Added = {2012-01-02 17:06:15 +0100},
	Date-Modified = {2015-08-28 19:03:39 +0000},
	Day = {01},
	Doi = {10.1007/s00382-011-1079-0},
	Isbn = {0930-7575},
	Journal = cdyn,
	Keywords = {Earth and Environmental Science;BFM},
	Month = {11},
	Number = {9},
	Pages = {1929--1947},
	Publisher = {Springer Berlin / Heidelberg},
	Title = {Global and regional ocean carbon uptake and climate change: sensitivity to a substantial mitigation scenario},
	Ty = {JOUR},
	Url = {http://dx.doi.org/10.1007/s00382-011-1079-0},
	Volume = {37},
	Year = {2011},
	Bdsk-Url-1 = {http://dx.doi.org/10.1007/s00382-011-1079-0}}