BFM Report Series - Manuals

N.1 Vichi M., Lovato T., Butenschön M., Tedesco L., Lazzari P., Cossarini G., Masina S., Pinardi N., Solidoro C., Zavatarelli M. (2020). The Biogeochemical Flux Model (BFM): Equation Description and User Manual. BFM version 5.2. BFM Report series N. 1, Release 1.2, June 2020, Bologna, Italy,, pp. 104 (pdf)

N.2 Lovato T., Vichi M., Butenschön M. (2020). Coupling BFM with Ocean models: the NEMO model v3.6 (Nucleus for the European Modelling of the Ocean). BFM Report series N. 2, Release 1.1, June 2020, Bologna, Italy,, pp. 31 (pdf)

N.3 Zavatarelli M., Pinardi N., Mussap G., Lovato T., Amadio C., Butenschön M., Vichi M. (2020). Coupling BFM with Ocean models: the 1D Princeton Ocean Model. BFM Report series N. 3, Release 1.0, June 2020, Bologna, Italy,, pp. 58 (pdf)

Scientific Bibliography (BibTex)


Fransner, F., Gustafsson, E., Tedesco, L., Vichi, M., Hordoir, R., Roquet, F.,Spilling, K., Kuznetsov, I., Eilola, K., Mörth, C.-M., Humborg, C., Nycander, J. (2018). Non‐Redfieldian Dynamics Explain Seasonal pCO2 Drawdown in the Gulf of Bothnia. Journal of Geophysical Research: Oceans, 123(1), 166-188.


Mussap, G., & Zavatarelli, M. (2017). A numerical study of the benthic–pelagic coupling in a shallow shelf sea (Gulf of Trieste). Regional Studies in Marine Science, 9, 24-34.

Cossarini, G., Querin, S., Solidoro, C., Sannino, G., Lazzari, P., Di Biagio, V., & Bolzon, G. (2017). Development of BFMCOUPLER (v1. 0), the coupling scheme that links the MITgcm and BFM models for ocean biogeochemistry simulations. Geoscientific Model Development, 10(4), 1423.

Tedesco, L., Miettunen, E., An, B. W., Haapala, J., & Kaartokallio, H. (2017). Long-term mesoscale variability of modelled sea-ice primary production in the northern Baltic Sea. Elem Sci Anth, 5.

Thomas, D. N., Kaartokallio, H., Tedesco, L., Majaneva, M., Piiparinen, J., Eronen-Rasimus, E., Rintala, J.-M., Kuosa, H., Blomster, J., Vainio, J., Granskog, M. A. (2017). Life associated with Baltic Sea ice. In Biological oceanography of the Baltic Sea (pp. 333-357). Springer, Dordrecht.


Epicoco, I., Mocavero, S., Macchia, F., Vichi, M., Lovato, T., Masina, S., Aloisio, G. (2016). Performance and results of the high-resolution biogeochemical model PELAGOS025 v1. 0 within NEMO v3. 4. Geoscientific Model Development, 9, 2115-2128.

Lazzari, P., Solidoro, C., Salon, S., & Bolzon, G. (2016). Spatial variability of phosphate and nitrate in the Mediterranean Sea: A modeling approach. Deep Sea Research Part I: Oceanographic Research Papers, 108, 39-52.

Visinelli, L., Masina, S., Vichi, M., Storto, A., Lovato, T. (2016). Impacts of data assimilation on the global ocean carbonate system. Journal of Marine Systems, 158, 106-119.

Tedesco, L., Piroddi, C., Kämäri, M., & Lynam, C. (2016). Capabilities of Baltic Sea models to assess environmental status for marine biodiversity. Marine Policy, 70, 1-12.

Tagliabue, A., Aumont, O., DeAth, R., Dunne, J. P., Dutkiewicz, S., Galbraith, E., Misumi, K., Moore, J.K., Ridgwell, A., Sherman, E., Stock, C., Vichi, M., Völker, C., Yool, A. (2016). How well do global ocean biogeochemistry models simulate dissolved iron distributions?. Global Biogeochemical Cycles, 30(2), 149-174.


McKiver, W. J., Vichi, M., Lovato, T., Storto, A., & Masina, S. (2015). Impact of increased grid resolution on global marine biogeochemistry. Journal of Marine Systems, 147, 153-168.

Canu, D. M., Ghermandi, A., Nunes, P. A., Lazzari, P., Cossarini, G., Solidoro, C. (2015). Estimating the value of carbon sequestration ecosystem services in the Mediterranean Sea: An ecological economics approach. Global Environmental Change, 32, 87-95.

Cossarini, G., Lazzari, P., Solidoro, C. (2015). Spatiotemporal variability of alkalinity in the Mediterranean Sea. Biogeosciences, 12(6), 1647-1658.

Piroddi, C., Teixeira, H., Lynam, C. P., Smith, C., Alvarez, M. C., Mazik, K., Andonegi, E., Churilova, T., Tedesco, L., Chust, G. (2015). Using ecological models to assess ecosystem status in support of the European Marine Strategy Framework Directive. Ecological indicators, 58, 175-191.

Eilola, K., Almroth-Rosell, E., Edman, M., Eremina, T., Larsen, J., Janas, U., Razinkovas-Basiukas, A., Timmermann, K., Tedesco, L., Voloshchuk, E. (2015). Model set-up at COCOA study sites. SMHI.


Tedesco, L., & Vichi, M. (2014). Sea ice biogeochemistry: A guide for modellers. PloS one, 9(2), e89217.

Lazzari, P., Mattia, G., Solidoro, C., Salon, S., Crise, A., Zavatarelli, M., Oddo, P., Vichi, M. The impacts of climate change and environmental management policies on the trophic regimes in the Mediterranean Sea: Scenario analyses. Journal of Marine Systems 135 (2014): 137-149.

Lamon, L., Rizzi, J., Bonaduce, A., Dubois, C., Lazzari, P., Ghenim, L., Gana, S., Somot, S., Li, L., Melaku Canu, D., Solidoro, C., Pinardi, N., Marcomini, A. (2014). An ensemble of models for identifying climate change scenarios in the Gulf of Gabes, Tunisia. Reg Environ Change, DOI 10.1007/s10113-013-0430-x.


Ruggio, R., Vichi, M., Paparella, F., & Masina, S. (2013). Climatic trends of the equatorial undercurrent: A backup mechanism for sustaining the equatorial Pacific production. Journal of Marine Systems, 121, 11-23.

Cagnazzo, C., Manzini, E., Fogli, P. G., Vichi, M., & Davini, P. (2013). Role of stratospheric dynamics in the ozone–carbon connection in the Southern Hemisphere. Climate dynamics, 41(11-12), 3039-3054.

Vichi, M., Navarra, A., Fogli, P. G. (2013). Adjustment of the natural ocean carbon cycle to negative emission rates. Climatic Change, 118(1), 105-118. DOI: 10.1007/s10584-012-0677-0. [Download]

Mattia, G., M. Zavatarelli, M. Vichi, and P. Oddo (2013), The Eastern Mediterranean Sea biogeochemical dynamics in the 1990s: A numerical study, J. Geophys. Res. Oceans, 118, 2231–2248, doi:10.1002/jgrc.20160.

Fraysse M, Pinazo C, Faure VM, Fuchs R, Lazzari P, Raimbault P, Pairaud I (2013) Development of a 3D Coupled Physical-Biogeochemical Model for the Marseille Coastal Area (NW Mediterranean Sea): What Complexity Is Required in the Coastal Zone? PLoS ONE 8(12): e80012. doi:10.1371/journal.pone.0080012


Alessandri, A., Fogli, P. G., Vichi, M., and Zeng, N. (2012) Strengthening of the hydrological cycle in future scenarios: atmospheric energy and water balance perspective, Earth Syst. Dynam., 3, 199-212, doi:10.5194/esd-3-199-2012

Patara, L., M. Vichi, and S. Masina, 2012, Impacts of natural and anthropogenic climate variations on north pacific plankton in an earth system model, Ecol. Model., 244, 132–147, 10.1016/j.ecolmodel.2012.06.012.

Butenschön, M., Zavatarelli, M., 2012. A comparison of different version of the SEEK filter for assimilation of biogeochemical data in numerical models of marine ecosystem dynamics. Ocean Modelling, 4–55, 37–54, 10.1016/j.ocemod.2012.06.003.

Butenschön, M., Zavatarelli, M., Vichi, M., 2012. Sensitivity of a marine coupled physical biogeochemical model to time resolution, integration scheme and time splitting method. Ocean Modelling, 52–53, 36–53, doi:10.1016/j.ocemod.2012.04.008.

Lazzari, P., Solidoro, C., Ibello, V., Salon, S., Teruzzi, A., Béranger, K., Colella, S., Crise, A: Seasonal and inter-annual variability of plankton chlorophyll and primary production in the Mediterranean Sea: a modelling approach.Biogeosciences, 9, 217-233, doi:10.5194/bg-9-217-2012, 2012.

Patara, L., Vichi, M., Masina, S., Fogli, P. G. and Manzini, E. (2012) Global response to solar radiation absorbed by phytoplankton in a coupled climate model. Climate Dynamics . doi:10.1007/s00382-012-1300-9.

Tedesco, L., Vichi, M., and Thomas, D. N., 2012. Process studies on the ecological coupling between sea ice algae and phytoplankton. Ecological Modelling, 226, 120-138. doi:10.1016/j.ecolmodel.2011.11.011

Cheptsov, A., Koller, B., Adami, D., Davoli, F., Mueller, S., Meyer, N., Lazzari, P., Salon, S., Watzl, J., Schiffers, M., Kranzlmueller, D., 2012. e-Infrastructure for Remote Instrumentation, Computer Standards & Interfaces. doi:10.1016/j.csi.2011.10.012


Berline, L., Stemmann, L., Vichi, M., Lombard, F., and Gorsky, G., 2011. Impact of appendicularians on detritus and export fluxes: a model approach at DyFAMed site. Journal of Plankton Research, 33, 855-872, doi:10.1093/plankt/fbq163

Patara, L., Visbeck, M., Masina, S., Krahmann, G., and Vichi, M., 2011. Marine biogeochemical responses to the North Atlantic Oscillation in a coupled climate model. Journal of Geophysical Research, 116. doi:10.1029/2010JC006785

Teruzzi, A., Salon, S., Bolzon, G., Lazzari, P., Ficarelli, F., Solidoro, C., Crise, A., 2011. Operational forecasts of the biogeochemical state of Mediterranean Sea. Mercator Ocean Quarterly Newsletter, 40, 15-25.

Vichi, M., Manzini, E., Fogli, P., Alessandri, A., Patara, L., Scoccimarro, E., Masina, S., and Navarra, A., 2011. Global and regional ocean carbon uptake and climate change: sensitivity to a substantial mitigation scenario. Climate Dynamics, 37, 1929–1947, doi:10.1007/s00382-011-1079-0

Vichi, M., Allen, J., Masina, S., & Hardman‐Mountford, N. J. (2011). The emergence of ocean biogeochemical provinces: A quantitative assessment and a diagnostic for model evaluation. Global Biogeochemical Cycles, 25(2).


Lazzari, P., Teruzzi, A., Salon, S., Campagna, S., Calonaci, C., Colella, S., Tonani, M., Crise, A., 2010. Pre-operational short-term forecasts for the Mediterranean Sea biogeochemistry, Ocean Sciences, 6, 25-39. doi:10.5194/os-6-25-2010.

Macias, D., Ramirez-Romero, E., and Garcia, C. M., 2010. Effect of nutrient input frequency on the structure and dynamics of the marine pelagic community: A modeling approach. Journal of Marine Research, 68, 119-151. doi:10.1357/002224010793078979

Saba, V.S., Friedrichs, M.A.M., Carr, M-E., Antoine, D., Armstrong, R.A., Asanuma, I., Aumont, O., Bates, N.R., Behrenfeld, M.J., Bennington, V., Bopp, L., Bruggeman, J., Buitenhuis, E.T., Church, M.J., Ciotti, A.M., Doney, S.C., Dowell, M., Dunne, J., Dutkiewicz, S., Gregg, W., Hoepffner, N., Hyde, K.J.W., Ishizaka, J., Kameda, T., Karl, D.M., Lima, I., Lomas, M.W., Marra, J., McKinley, G.A., Mélin, F., Moore, J.K., Morel, A., O’Reilly, J., Salihoglu, B., Scardi, M., Smyth, T.J., Tang, S., Tjiputra, J., Uitz, J., Vichi, M., Waters, K., Westberry, T.K., Yool, A. 2010. Challenges of modeling depth-integrated marine primary productivity over multiple decades: A case study at BATS and HOT. Global Biogeochemical Cycles, 24, GB3020, doi:10.1029/2009GB003655

Tedesco, L., Vichi, M., Haapala, J., and Stipa, T., 2010. A dynamic Biologically-Active Layer for numerical studies of the sea ice ecosystem. Ocean Modelling, 35, 89–104. doi:10.1016/j.ocemod.2010.06.008


Cheptsov, A., Dichev, K., Keller, R., Lazzari, P., Salon, S., 2009. Porting the OPATM-BFM Application to a Grid e-Infrastructure- Optimization of Communication and I/O patterns. Computational Methods in Science and Technology, 15(1), 9-19.

Vichi, M. and Masina, S., 2009. Skill assessment of the PELAGOS global ocean biogeochemistry model over the period 1980-2000. Biogeosciences, 6, 2333–2353.

Vichi, M., Coluccelli, A., Ravaioli, M., Giglio, F., Langone, L., Azzaro, M., Azzaro, F., La Ferla, R., Catalano, G., and Cozzi, S., 2009. Modelling approach to the assessment of biogenic fluxes at a selected Ross Sea site, Antarctica. Ocean Sci. Discuss., 6, 1477–1512. doi:


Vichi, M., Masina, S., and Nencioli, F., 2008. A process-oriented model study of equatorial Pacific phytoplankton: The role of iron supply and tropical instability waves. Progress in Oceanography, 78, 147-162.


Carniel, S., Vichi, M., Sclavo, M., 2007. Sensitivity of a coupled physical–biological model to turbulence: high-frequency simulations in a northern Adriatic station. Chemistry and Ecology, 23, 157-175.

Polimene, L., Pinardi, N., Zavatarelli, M., Allen, J., I., Giani, M., Vichi, M., 2007. A numerical simulation study of dissolved Organic Carbon accumulation in the northern Adriatic Sea. Journal of Geophysical Research. doi: 10129/200JC003529.

Vichi, M., Masina, S., and Navarra, A., 2007. A generalized model of pelagic biogeochemistry for the global ocean ecosystem. Part II: numerical simulations. Journal of Marine Systems, 64, 110-134.

Vichi, M., Pinardi, N., and Masina, S., 2007. A generalized model of pelagic biogeochemistry for the global ocean ecosystem. Part I: theory. Journal of Marine Systems, 64, 89-109.


Polimene, L., Pinardi , N., Zavatarelli, M., Colella, S., 2006. The Adriatic Sea ecosystem seasonal cycle: validation of a three dimensional numerical model. Journal of Geophysical Research. doi: 10129/2005JC003260.


Vichi, M., Ruardij, P., and Baretta, J. W., 2004. Link or sink: a modelling interpretation of the open Baltic biogeochemistry. Biogeosciences, 1, 79-100.


Vichi, M., May, W., and Navarra, A., 2003. Response of a complex ecosystem model of the northern Adriatic Sea to a regional climate change scenario. Climate Research, 24, 141-159.

Vichi, M., Oddo, P., Zavatarelli, M., Coluccelli, A., Coppini, G., Celio, M., Fonda Umani, S., and Pinardi, N., 2003. Calibration and validation of a one-dimensional complex marine biogeochemical fluxes model in different areas of the northern Adriatic shelf. Annales Geophysicae, 21, 413-436.