scholarly journals Using Gaming Technology to Explore and Visualize Management Impacts on Marine Ecosystems

2021 ◽  
Vol 8 ◽  
Author(s):  
Jeroen Steenbeek ◽  
Dalai Felinto ◽  
Mike Pan ◽  
Joe Buszowski ◽  
Villy Christensen
Keyword(s):  
Information Overload ◽  
Marine Ecosystem ◽  
Three Dimensional ◽  
Ecosystem Model ◽  
Ecosystem Modeling ◽  
Scientific Data ◽  
Scientific Software ◽  
Visualization Toolkit ◽  
Scientific Results ◽  
Ecosystem Changes

We have developed an approach that connects a complex and widely used scientific ecosystem modeling approach with a game engine for real-time communication and visualization of scientific results. The approach, OceanViz, focuses on communicating scientific data to non-scientific audiences to foster dialogue, offering experimental, immersive approaches to visualizing complex ecosystems whilst avoiding information overload. Within the context of ecosystem-based fisheries management, OceanViz can engage decision makers into the implicit operation of scientific software as an aid during the decision process, and it can be of direct use for public communication through appealing and informative visualizations. Beside a server-client architecture to centralize decision making around an ecosystem model, OceanViz includes an extensive visualization toolkit capable of accurately reflecting marine ecosystem changes through a simulated three-dimensional (3D) underwater environment. Here we outline the ideas and concepts that went into OceanViz, its implementation and its related challenges. We reflect on challenges to scientific visualization and communication as food-for-thought for the marine ecosystem modeling community and beyond.

scholarly journals Ecological ReGional Ocean Model with vertically resolved sediments (ERGOM SED 1.0): coupling benthic and pelagic biogeochemistry of the south-western Baltic Sea

2019 ◽  
Vol 12 (1) ◽  
pp. 275-320 ◽  
Author(s):  
Hagen Radtke ◽  
Marko Lipka ◽  
Dennis Bunke ◽  
Claudia Morys ◽  
Jana Woelfel ◽  
...  
Keyword(s):  
Baltic Sea ◽  
Marine Ecosystem ◽  
Nutrient Recycling ◽  
Three Dimensional ◽  
Ecosystem Model ◽  
Ocean Model ◽  
Ecosystem Models ◽  
Predictive Capacity ◽  
Sediment Types ◽  
Marine Ecosystem Model

Abstract. Sediments play an important role in organic matter mineralisation and nutrient recycling, especially in shallow marine systems. Marine ecosystem models, however, often only include a coarse representation of processes beneath the sea floor. While these parameterisations may give a reasonable description of the present ecosystem state, they lack predictive capacity for possible future changes, which can only be obtained from mechanistic modelling. This paper describes an integrated benthic–pelagic ecosystem model developed for the German Exclusive Economic Zone (EEZ) in the western Baltic Sea. The model is a hybrid of two existing models: the pelagic part of the marine ecosystem model ERGOM and an early diagenetic model by Reed et al. (2011). The latter one was extended to include the carbon cycle, a determination of precipitation and dissolution reactions which accounts for salinity differences, an explicit description of the adsorption of clay minerals, and an alternative pyrite formation pathway. We present a one-dimensional application of the model to seven sites with different sediment types. The model was calibrated with observed pore water profiles and validated with results of sediment composition, bioturbation rates and bentho-pelagic fluxes gathered by in situ incubations of sediments (benthic chambers). The model results generally give a reasonable fit to the observations, even if some deviations are observed, e.g. an overestimation of sulfide concentrations in the sandy sediments. We therefore consider it a good first step towards a three-dimensional representation of sedimentary processes in coupled pelagic–benthic ecosystem models of the Baltic Sea.

scholarly journals An Ensemble Kalman Filter with a complex marine ecosystem model: hindcasting phytoplankton in the Cretan Sea

2003 ◽  
Vol 21 (1) ◽  
pp. 399-411 ◽  
Author(s):  
J. I. Allen ◽  
M. Eknes ◽  
G. Evensen
Keyword(s):  
Data Assimilation ◽  
Marine Ecosystem ◽  
Three Dimensional ◽  
Ecosystem Model ◽  
Sequential Data ◽  
Model Errors ◽  
In Situ Data ◽  
Marine Ecosystem Model ◽  
Cretan Sea

Abstract. The purpose of this paper is to examine the use of a complex ecosystem model along with near real-time in situ data and a sequential data assimilation method for state estimation. The ecosystem model used is the European Regional Seas Ecosystem Model (ERSEM; Baretta et al., 1995) and the assimilation method chosen is the Ensemble Kalman Filer (EnKF). Previously, it has been shown that this method captures the nonlinear error evolution in time and is capable of both tracking the observations and providing realistic error estimates for the estimated state. This system has been used to assimilate long time series of in situ chlorophyll taken from a data buoy in the Cretan Sea. The assimilation of this data using the EnKF method results in a marked improvement in the ability of ERSEM to hindcast chlorophyll. The sensitivity of this system to the type of data used for assimilation, the frequency of assimilation, ensemble size and model errors is discussed. The predictability window of the EnKF appears to be at least 2 days. This is an indication that the methodology might be suitable for future operational data assimilation systems using more complex three-dimensional models. Key words. Oceanography: general (numerical modelling; ocean prediction) – Oceanography: biological and chemical (plankton)

scholarly journals A narrative overview of utilizing biomaterials to recapitulate the salient regenerative features of dental-derived mesenchymal stem cells

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Sevda Pouraghaei Sevari ◽  
Sahar Ansari ◽  
Alireza Moshaverinia
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Tissue Regeneration ◽  
3D Structure ◽  
Three Dimensional ◽  
Scientific Data ◽  
Clinical Practices ◽  
Human Teeth ◽  
Innovative Strategies ◽  
Local Recruitment

AbstractTissue engineering approaches have emerged recently to circumvent many limitations associated with current clinical practices. This elegant approach utilizes a natural/synthetic biomaterial with optimized physiomechanical properties to serve as a vehicle for delivery of exogenous stem cells and bioactive factors or induce local recruitment of endogenous cells for in situ tissue regeneration. Inspired by the natural microenvironment, biomaterials could act as a biomimetic three-dimensional (3D) structure to help the cells establish their natural interactions. Such a strategy should not only employ a biocompatible biomaterial to induce new tissue formation but also benefit from an easily accessible and abundant source of stem cells with potent tissue regenerative potential. The human teeth and oral cavity harbor various populations of mesenchymal stem cells (MSCs) with self-renewing and multilineage differentiation capabilities. In the current review article, we seek to highlight recent progress and future opportunities in dental MSC-mediated therapeutic strategies for tissue regeneration using two possible approaches, cell transplantation and cell homing. Altogether, this paper develops a general picture of current innovative strategies to employ dental-derived MSCs combined with biomaterials and bioactive factors for regenerating the lost or defective tissues and offers information regarding the available scientific data and possible applications.

scholarly journals The SoftWipe tool and benchmark for assessing coding standards adherence of scientific software

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adrian Zapletal ◽  
Dimitri Höhler ◽  
Carsten Sinz ◽  
Alexandros Stamatakis
Keyword(s):  
Open Source ◽  
Review Process ◽  
Selection Process ◽  
Software Selection ◽  
Scientific Software ◽  
Worst Case ◽  
Computational Tools ◽  
Research Areas ◽  
Coding Standards ◽  
Scientific Results

AbstractScientific software from all areas of scientific research is pivotal to obtaining novel insights. Yet the coding standards adherence of scientific software is rarely assessed, even though it might lead to incorrect scientific results in the worst case. Therefore, we have developed an open source tool and benchmark called , that provides a relative software coding standards adherence ranking of 48 computational tools from diverse research areas. can be used in the review process of software papers and to inform the scientific software selection process.

scholarly journals PhytoSFDM version 1.0.0: Phytoplankton Size and Functional Diversity Model

2016 ◽  
Vol 9 (11) ◽  
pp. 4071-4085 ◽  
Author(s):  
Esteban Acevedo-Trejos ◽  
Gunnar Brandt ◽  
S. Lan Smith ◽  
Agostino Merico
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
Marine Ecosystem ◽  
Three Dimensional ◽  
Functional Trait ◽  
Global Ocean ◽  
Total Biomass ◽  
Spatially Resolved ◽  
Phytoplankton Communities ◽  
Natural Complexity

Abstract. Biodiversity is one of the key mechanisms that facilitate the adaptive response of planktonic communities to a fluctuating environment. How to allow for such a flexible response in marine ecosystem models is, however, not entirely clear. One particular way is to resolve the natural complexity of phytoplankton communities by explicitly incorporating a large number of species or plankton functional types. Alternatively, models of aggregate community properties focus on macroecological quantities such as total biomass, mean trait, and trait variance (or functional trait diversity), thus reducing the observed natural complexity to a few mathematical expressions. We developed the PhytoSFDM modelling tool, which can resolve species discretely and can capture aggregate community properties. The tool also provides a set of methods for treating diversity under realistic oceanographic settings. This model is coded in Python and is distributed as open-source software. PhytoSFDM is implemented in a zero-dimensional physical scheme and can be applied to any location of the global ocean. We show that aggregate community models reduce computational complexity while preserving relevant macroecological features of phytoplankton communities. Compared to species-explicit models, aggregate models are more manageable in terms of number of equations and have faster computational times. Further developments of this tool should address the caveats associated with the assumptions of aggregate community models and about implementations into spatially resolved physical settings (one-dimensional and three-dimensional). With PhytoSFDM we embrace the idea of promoting open-source software and encourage scientists to build on this modelling tool to further improve our understanding of the role that biodiversity plays in shaping marine ecosystems.

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