Fig 1.
The lego block coupling concept of IBMlib.
In a configuration, a physics module (light blue) is combined with a biology module (green) describing an individual organism together with a task (red) controlling the overall computational flow. The light blue physics modules refer to examples of physical/biogeochemical model with an interface to IBMlib: the HIROMB Baltic Model (HBM) [20–22], the ECOSystem MOdel (ECOSMO) [23, 24], the NORWegian ECOlogical Model (NORWECOM) [25, 26] and the Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS) [27, 28]. Modules “Test” refer to idealized hydrographical flows and data used for developing/validating/analyzing biological models.
Table 1.
Upper level biology interface in IBMlib.
The interface defines particle behavior, states and dynamics. The derived type state_attributes contains all the internal state variables pertaining to the complexity level organisms are described at.
Table 2.
Upper level physics interface.
The basic physical interface and current interface extensions in IBMlib. Interface extensions are for specialized cases and need not be implemented for standardized tasks.
Fig 2.
Module dependence hierarchy in IBMlib core.
Dependencies and the relation to provider modules (task, biology and physics). An IBMlib configuration is built from the bottom up. Provider modules for physics, biology and task are linked to the IBMlib core (yellow) at build time, forming an executable program.
Fig 3.
A particle in IBMlib is a plain composition of a generic spatial_attributes instance and a state_attributes instance, defined by the used biological module.
Table 3.
Benchmark of simulation for different number of particles released and different physical models applied. For the HIROMB Baltic Model (HBM) data set, see [20–22].
Fig 4.
Comparison of drift of herring larvae released in autumn 2000 in the North Sea.
Simulations using operational setups of different circulation models: HBM, NORWECOM and POLCOMS. (a) Average distance from spawning area after initial day-of-release of larval distribution (b) Snapshot of larval distributions 50 days after time of release. Black box indicates spawning area following [36].
Fig 5.
Influence of DVM active behavior.
Maps of the final distribution of cod larvae exhibiting DVM active behavior for the period 2004-2007- different colors indicate the total displacement (in km) of the larvae from the spawning origin.
Fig 6.
Plaice connectivity in Skagerrak/Kattegat.
(a) Normalized settlement intensity for plaice in Skagerrak/Kattegat of Denmark in 2013 with map resolution (∼ 10 km) corresponding to the underlying physical model HBM. Color intensity is settlement per spawning per area (b) Connectivity matrix on log10 scale for plaice larvae spawned in German Bight, Skagerrak, Kattegat settling in Skagerrak/Kattegat. Spawning area are columns, settling area are rows.
Fig 7.
a) Quiver plot of the average surface currents in the Black Sea on 01 Jan 2004, extracted from a BIMS-ECO data set by IBMlib. b) Micro zooplankton density in ICES statistical rectangle 36E5 covering 5°W to 4°W and 53.5°N to 54°N in the Irish Sea, averaged over the upper 10 meters through April 2004, extracted from a POLCOMS+ERSEM data set by IBMlib.
Fig 8.
Input data generation for spatial biological modelling.
a) Atlantis habitat polygons for the Baltic setup [57]. b) Time series of salinity for 3 vertical strata in 2005 for a selected habitat polygon (brown, indicated by connecting lines to two box corners).
Fig 9.
Local down grazing of zooplankton in the Dogger Bank area of the North Sea, simulated by IBMlib in the Eulerian configuration. Color intensity shows time-averaged zooplankton density on scale of the saturation level. Boxes are sandeel foraging habitats populated with a biomass at a level corresponding to regional stock assessment. The biological and physical setup are as in [58], except that the simulation is for 2009.
Fig 10.
Reconstruction of early life histories.
Reconstruction of environmental history for a single larva using hydrographic backtracking in IBMlib. (a) Density of back-tracked particle trajectories (blue coloring: darker shades indicate a higher density) released from the position of larval capture (red dot). The 50 and 200 m isobaths are shown for reference (light grey lines). Thick black lines denote the spatial regions associated with each herring spawning component in the North Sea. (b) Assignment of larvae to a spawning component: darker blues indicate a higher proportion of larvae. The known spawning periods of each component are indicated by the red boxes and the estimated contribution of each component to a haul is indicated at right—this larva is clearly of ‘Banks’ origin. (c) Temperature history of the larvae; median value (thick black line) and central 95% confidence region (thinner black lines). (d) Photoperiod (daylight hours per day) experienced by the larva.