| Summary: | The improved understanding of complex interactions of marine ecosystem components makes the use of fully coupled hydrodynamic, biogeochemical and individual based models more and more relevant. At the same time, the increasing complexity of the models and diverse user backgrounds calls for improved user friendliness and flexibility of the model systems. We present FlexSem, a versatile and user-friendly framework for 3D hydrodynamic, biogeochemical, individual based and sediment transport modelling. The purpose of the framework is to enable natural scientists to conduct advanced 3D simulations in the marine environment, including any relevant processes. This is made possible by providing a precompiled portable framework, which still enables the user to pick any combination of models and provide user defined equation systems to be solved during the simulation. We here present the ideas behind the framework design, the implementation and documentation of the numerical solution to the Navier-Stokes equations in the hydrodynamic module, the surface heat budget model, the pelagic and benthic equation solvers and the Lagrangian movement of the agents in the agent based model. Five examples of different applications of the system are shown: 1) Hydrodynamics in the Disko Bay in west Greenland, 2) A biogeochemical pelagic and benthic model in the inner Danish waters, 3) A generic mussel farm model featuring offline physics, food levels and mussel eco-physiology, 4) Sediment transport in Clarion-Clipperton zone at the bottom of the Pacific and 5) Hydrodynamics coupled with an agent based model around Zanzibar in Tanzania. Hence we demonstrate that the model can be set up for any area with enough forcing data and used to solve a wide range of applications.
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