We describe our experience of three-dimensional numerical simulation of thermohydrodynamic and biogeochemical processes in the White Sea in collaboration with several institutes of the Russian Academy of Sciences and foreign colleagues. The comprehensive model of the White Sea, called JASMINE, is based on the FEMAO model of the Arctic Ocean. It reproduces the dynamics of sea water and ice and includes, i. a., a pelagic biogeochemical submodel BFM, which is able to describe fluxes of matter between scalar fields corresponding to groups of organisms or organic and inorganic matter of various forms and fractions. Matter and energy exchange with bottom sediments and sea ice has also been modeled, and the model includes a sea-ice ecology block BFMSI. Besides, it is possible to simulate contamination transport for tracers of arbitrary origin. We relate the history of developing the model, tell how the spatial resolution was increased, describe the resolved and yet unresolved problems. The problem of boundary values is discussed, as well as the possibility of a cascade simulation, where coarser models of larger objects provide data for more precise regional models. As an example, we introduce the already implemented interaction between the INM RAS model of the Earth system and JASMINE on INM RAS cluster. We touch upon the systemic problem of the development of complex computing systems in the field of Earth sciences, i. e. the lack of documentation and community, and the fact that the project depends on the availability of a single person: the author of the model. A prototype of a data assimilation system for the model is described: it allows correcting the phase state according to observational data (such as station data). The possibilities of carrying out numerical experiments are demonstrated: the transfer of a passive tracer with a delta-shaped initial distribution, the response of the sea to climate change and, in particular, to variations in river runoff, and other applications of the model to achieve a better understanding of the processes in the White Sea.