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Research infrastructures have been established throughout Europe in order to create robust organizations that will facilitate and enhance research and innovation processes and will advance society with innovative products and services. The Hellenic Integrated Marine Observing, orecasting and Technology System (component of HIMIOFoTS RI) has been implemented in the framework of the National Roadmap for Research Infrastructures to form a large-scale infrastructure for the marine environment in Greece. It links together ocean observing and forecasting systems, coastal zone monitoring and management practices, as well as ocean engineering testing facilities. The overarching framework of the system supports the coordination of five organizations with expertise in the field of marine science and technology, the central management of research activities, and the common development of services and products. It comprises facilities and resources while it provides open access to research communities (academia, industry) to support the scientific advancements and innovation in their fields. The Hellenic Marine Observing, Forecasting and Technology System was further enhanced during its implementation through significant upgrades and developments in order to extend its observing capacity and the forecasting and technological abilities, while advancing the provided services and products. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.

This report describes the governance of the European HF radar network including: the landscape of the Ocean observation networks and infrastructures, the role and links between operators of observational systems and stakeholders, the role and activities of the EuroGOOS HF radar Task Team in building a sound community strategy, the roadmap of the community with current achievements and future work lines.

Ecosystem models are recognized as valuable tools to understand marine ecosystem dynamics and address management questions, requiring an integrated approach of physical and biotic processes. In the present study, a three-dimensional basin scale Mediterranean hydrodynamic/biogeochemical model, currently operational as part of the POSEIDON forecasting system, was extensively validated against available in-situ and satellite data. The generic POSEIDON ecosystem model skill was objectively assessed, in capturing the observed seasonal variability of the main chemical ecosystem components within the planktonic food web. A cluster K-means analysis was applied to obtain an objective `biogeography' of the Mediterranean Sea, allowing a more efficient validation of model outputs against observational data. The model presented a reasonable skill in reproducing the seasonal cycle and observed patterns of the Mediterranean inorganic nutrients and chlorophyll-a, characterized by a prominent west-to-east gradient and their increase in areas receiving lateral nutrient inputs. Despite some model deviations, validation results have demonstrated the capability of the model to represent the Mediterranean ecosystem, ranging from oligotrophic open ocean to mesotrophic conditions in productive coastal areas.

Microplastics (MPs) are a contaminant of growing concern due to their widespread distribution and Interactions with marine species, such as filter feeders. To Investigate the MPs accumulation In wild and cultured mussels, a dynamic energy budget (DEB) model was developed and validated with the available field data of Mytilus edulis (M. edulis, wild) from the North Sea and Mytilus galloprovincialis (M. galloprovincialis, cultured) from the northern Ionian Sea. Towards a generic DEB model, the site-specific model parameter, half-saturation coefficient (Xk), was applied as a power function of food density for the cultured mussel, while for the wild mussel It was calibrated to a constant value. The DEBaccumulation model simulated the uptake and excretion rate of MPs, taking Into account environmental characteristics (temperature and chlorophyll a). An accumulation of MPs equal to 0.53 particles per Individual (fresh tissue mass 1.9 g) and 0.91 particles per Individual (fresh tissue mass 3.3 g) was simulated for the wild and cultured mussel after 4 and 1 years respectively, In agreement with the field data. The Inverse experiments Investigating the depuration time of the wild and cultured mussel In a clean-from-MPs environment showed a 90% removal of MPs load after 2.5 and 12 d respectively. Furthermore, sensitivity tests on model parameters and forcing functions highlighted that besides MPs concentration, the accumulation Is highly dependent on temperature and chlorophyll a of the surrounding environment. For this reason, an empirical equation was found, directly relating the environmental concentration of MPs, with the seawater temperature, chlorophyll a, and the mussel's soft tissue MPs load. © Author(s) 2020. This work Is distributed under the Creative Commons Attribution 4.0 License.

A three-dimensional coupled hydrodynamic/biogeochemical numerical model, currently in operation as part of the POSEIDON forecasting system, was implemented in the Mediterranean Sea. The model was assessed regarding its efficacy in representing the main biogeochemical components and seasonal dynamics of the Mediterranean planktonic system. Model outputs were compared with available historical data in a proposed objective eco-regionalisation of the Mediterranean basin, based on productivity. The simulated production (primary, bacterial) and planktonic biomass (phytoplankton, zooplankton and bacteria), as well as particulate and dissolved organic carbon, were found consistent with observational estimates in different areas of the Mediterranean Sea, following large scale productivity gradients. Although some limitations of the model were identified, the observed variability of the phytoplanktonic community structure was reasonably well-reproduced, simulating a dominant microbial food web with an intermittent development of the classical food web. The generic POSEIDON ecosystem model skill assessment provides a benchmark for future model improvement, highlighting the need to expand the range of biological variables sampled for further model calibration and validation. © 2020 Elsevier Ltd

This publication is primarily aimed at stakeholders involved in ocean observing, spanning diverse roles from commissioning, managing, funding and coordinating, to developing, implementing, or advising on, ocean observation programmes. Such programmes will have strategic and policy drivers but their main purpose may vary from predominantly researchdriven scientific purposes to environmental monitoring for providing data and reporting to legally-binding regulations or directives. The main focus is on European capabilities but set in a global context with the various actors spanning a variety of geographical scales from national to regional and European. Key stakeholder organizations include environmental or other agencies; marine research institutions, their researchers and operators; international and regional ocean observing initiatives and programmes; national, regional and European policy makers and their advisors; national stations for observations; etc.). It will also be of interest to the wider marine and maritime research and policy community. The main aim of the publication is to increase the relevance of current (and future) European biological ocean observation capacity to strengthen global efforts towards our understanding of the ocean and enhance marine biodiversity conservation, for maintaining a healthy ocean for healthy societies. This document explains why biological ocean observations are needed to assess progress against national and international conservation targets, the Sustainable Development Goals (SDGs), the Blue Growth agenda and to contribute to key EU directives including the Marine Strategy Framework Directive (MSFD). To achieve this, the publication highlights the need of biological ocean observations to reflect clearly defined hypotheses about potential causes of change, including the combined impacts of local and global drivers, and to support the management of our impacts on the ocean. Additionally, it calls for flexible biological ocean observing programmes to capture the relevant drivers operating at multiple spatial scales, by networking and integration of ongoing monitoring programmes, methodological standardization and appropriate policies of data integration and dissemination. It then presents key variables, elements and information products to inform on the status and trends of marine biodiversity.

The Mediterranean community represented in this paper is the result of more than 30 years of EU and nationally funded coordination, which has led to key contributions in science concepts and operational initiatives. Together with the establishment of operational services, the community has coordinated with universities, research centers, research infrastructures and private companies to implement advanced multi-platform and integrated observing and forecasting systems that facilitate the advancement of operational services, scientific achievements and mission-oriented innovation. Thus, the community can respond to societal challenges and stakeholders needs, developing a variety of fit-for-purpose services such as the Copernicus Marine Service. The combination of state-of-the-art observations and forecasting provides new opportunities for downstream services in response to the needs of the heavily populated Mediterranean coastal areas and to climate change. The challenge over the next decade is to sustain ocean observations within the research community, to monitor the variability at small scales, e.g., the mesoscale/submesoscale, to resolve the sub-basin/seasonal and inter-annual variability in the circulation, and thus establish the decadal variability, understand and correct the model-associated biases and to enhance model-data integration and ensemble forecasting for uncertainty estimation. Better knowledge and understanding of the level of Mediterranean variability will enable a subsequent evaluation of the impacts and mitigation of the effect of human activities and climate change on the biodiversity and the ecosystem, which will support environmental assessments and decisions. Further challenges include extending the science-based added-value products into societal relevant downstream services and engaging with communities to build initiatives that will contribute to the 2030 Agenda and more specifically to SDG14 and the UN's Decade of Ocean Science for sustainable development, by this contributing to bridge the science-policy gap. The Mediterranean observing and forecasting capacity was built on the basis of community best practices in monitoring and modeling, and can serve as a basis for the development of an integrated global ocean observing system. © Copyright © 2019 Tintoré, Pinardi.

A dynamic energy budget (DEB) model was developed to investigate the growth and reproduction of cultured bivalve species raised under different environmental conditions (varying phytoplankton carbon biomass [Phyto-C], particulate organic carbon [POC] and temperature) and tuned against field data for Mytilus galloprovincialis from the Maliakos and Thermaikos Gulfs (Aegean Sea, Greece). Values of most DEB model parameters were adopted from the literature, while half saturation constant (Xk) and initial values of energy reserves (E) and reproductive buffer (R) were calibrated. Different values have been found for Xk in the 2 areas (Maliakos: Xk = 36 mg C m-3; Thermaikos: Xk = 28 mg C m-3), suggesting that Xk should be treated as a site-specific parameter. Food density (X) was adapted to include not only Phyto-C but also POC in the diet of M. galloprovincialis and only when Phyto-C density was low compared to POC density. Results showed a small contribution of POC during spring in the Maliakos Gulf and almost none at Thermaikos Gulf. The simulated mussel growth showed good agreement with field data. Sensitivity tests on the calibrated parameters (E, R and Xk) were performed to investigate model uncertainty. The standard deviation of simulations with perturbed parameter/initial values remained relatively small and appeared to increase as the modeled mussel grew, in agreement with observations. © The authors 2017.

The development and use of FerryBox systems as a cost-effective instrument for continuous observations of the marine environment has been well established since more than 15 years. The systems have evolved to maturity and are since widely used around the coastal ocean of Europe. The availability of newly developed sensors allows the extension of FerryBox measurements to more biogeochemical parameters which are of interest for the requirements of the Marine Strategy Framework Directive (MSFD). The FerryBox community initially formed from the partners of an EU funded FerryBox project provides mutual exchange of experience and is now organized within EuroGOOS as a so called FerryBox Task Team (www.ferrybox.org). Within the EU funded infrastructure projects JERICO and JERICO-NEXT the technical harmonization as well as the developing of best practise guides for FerryBox systems have been a step further to high quality environmental data products. Within JERICO-NEXT it has been decided to build up a common FerryBox database and data portal in order to make the FerryBox data more available and visible. Furthermore this database will be function as a close link to the Copernicus Marine Environmental Monitoring Services (CMEMS) and the EMODnet portal.

This handbook collects the “best practices” in all phases of the system covering the entire infrastructural chain of data acquisition. It includes recommendations on how to produce high quality data aiming towards common methodologies and protocols within the FixO3 network. The Fixed point Open Ocean Observatory network (FixO3) seeks to integrate European open ocean fixed point observatories and to improve access to these key installations for the broader community. This network integrates open ocean moorings, surface buoys and deep cable observatories included in the ERIC EMSO. Unpublished Current

A new approach for processing the remote sensing chlorophyll-α (Chl-α) before assimilating into an ecosystem model is applied in two contrasting, regarding productivity and nutrients availability, Mediterranean sites: the DYFAMED and POSEIDON E1-M3A fixed point open ocean observatories. The new approach derives optically weighted depth-distributed Chl-α profiles from satellite data based on the model simulated Chl-α vertical distribution and light attenuation coefficient. We use the 1D version of the operational ecological 3D POSEIDON model, based on the European Regional Seas Ecosystem Model (ERSEM). The required hydrodynamic properties are obtained (off-line) from the POSEIDON operational 3D hydrodynamic Mediterranean basin scale model. The data assimilation scheme is the singular evolutive interpolated Kalman (SEIK) filter, the ensemble variant of the singular evolutive extended Kalman (SEEK) filter. The performance of the proposed assimilation approach was evaluated against the Chl-α satellite data and the seasonal averages of available in situ data for nitrate, phosphate and Chl-α. An improvement of the model simulated near-surface and subsurface maximum Chl-α concentrations is obtained, especially at the DYFAMED site. Model nitrate is improved with assimilation, particularly with the new approach assimilating depth-distributed Chl-α, while model phosphate is slightly worse after assimilation. Additional sensitivity experiments were performed, showing a better performance of the new approach under different scenarios of model Chl-α deviation from pseudo-observations of surface Chl-α. © 2016 Elsevier B.V..

This document constitutes Deliverable 5.5 of the JERICO project. It is intended to furnish members of the JERICO community with a basic understanding of how to proceed when attempting to establish measurement uncertainty for marine temperature, salinity and chlorophyll-a sensors. The document presents descriptions of the three measurands from a metrological standpoint, and discusses the approaches that could be taken to prepare uncertainty budgets for relevant sensors with some suitable examples and useful advice. The estimation of the uncertainty associated with the results of a measurement is an objective way to numerically depict the trustworthiness of those results. It is, therefore, a crucial part of the measuring process. Any measured value can be considered complete only if accompanied by a relative estimate of uncertainty. However, the latter characteristic is rarely discussed in marine observing circles and in the marine data management community despite its intimate link to sensor performance, data quality and data usability issues. This disregard arises from ignorance concerning the rigor required of modern measuring activity and the complexity of the underlying metrological system supporting it. There is a pressing need to begin to address this state of affairs, and the present publication, intended as a guidance document for members of the JERICO community, is a first step. The document deals with outlining a possible approach to determining uncertainty for sensor measurements of seawater temperature, salinity and chlorophyll-a. The approach is based on the generally accepted methodology for uncertainty evaluations given in the BIPM (Bureau International des Poids et Mesures) publication “Evaluation of measurement data - Guide to the expression of uncertainty in measurement”, commonly referred to as the GUM (2008). In all three cases, the conceived blueprint for action is based on the following topical cornerstones: the specification of the measurand, the descriptions of the realized quantity and the relative reference value, and finally, the identification of the uncertainty components and the quantification of the uncertainty. The present document is intended to be used in conjunction with the GUM, which continues to remain the master reference document for the evaluation of uncertainty in measurement at this time. Published Refereed Current Standard Operating Procedure

The objective of the workshop was to address main issues of JERICO project: - TNA: overview and formal approval of the selected proposals after the 3rd call - The JERICO Label document: content and issues - The JERICO strategy for the future. The document reports hereafter the synthesis of the discussions.

International audience; This paper conducts a detailed survey on the use of FPGA-based reconfigurable computing platforms for a wide range of sequence and structural bioinformatics applications, with emphasis on performance and energy savings of the underlying architectures. Applications considered include sequence comparison, multiple sequence alignment, RNA and protein secondary structure prediction, gene prediction, and phylogenetic tree computation.

Considering the importance of observing systems and the substantial investment made until now, an important task of JERICO is to describe best practices in all phases of the system (pre-deployment test, maintenance, calibration etc); to adopt common methodologies and protocols and to move towards the harmonisation of equipment which will help in reducing maintenance and calibration costs. These efforts are described and analysed in depth in this deliverable. European Commission, Joint European Research Infrastructure network for Coastal Observatories (JERICO) Project, Grant Agreement n° 262584 Published Permission to deposit: Patrick Farcy, Coordinator JERICO Project (jerico@ifremer.fr) Refereed Current

This paper presents an in-depth look of how FPGA computing can offer substantial speedups in the execution of bioinformatics algorithms, with specific results achieved to date for a broad range of algorithms. Examples and case studies are presented for sequence comparison (BLAST, CAST), multiple sequence alignment (MAFFT, T-Coffee), RNA and protein secondary structure prediction (Zuker, Predator), gene prediction (Glimmer/GlimmerHMM) and phylogenetic tree computation (RAxML), running on mainstream FPGA technologies as well as high-end FPGA-based systems (Convey HC1, BeeCube). This work also presents technological and other obstacles that need to be overcome in order for FPGA computing to become a mainstream technology in Bioinformatics.

The EuroSITES project was funded within the EU framework 7 to aid the convergence of the efforts of the 11 European-wide deep ocean observatories which formed its core. A major output of the project was envisaged as the synergies of the 13 partners working together to create a network providing sets of data in near-real-time, and in delayed-mode, which have been collected and processed in such a way as to be accessible to the wider scientific community, and comparable across time and site. The common data policy agreed by all the partners at the start of the project, and the evolution of a EuroSITES quality control manual which includes all the observatories practices, have formed the framework within which each data management group has delivered datasets which now carry the EuroSITES 'brand' as well as all the originators details. As a focal point for the, currently, 12 sites the EuroSITES data managers have worked as the European partner within the international OceanSITES project, developing the OceanSITES distribution standard, and studying the options for attaching additional metadata to data sets. The influence of EuroSITES as the European champion for the distribution of data in OceanSITES format will be an enduring legacy. The EuroSITES website (www.eurosites.info) provides a highly visible, and user accessible platform for the distribution of near-real time data from the observatories, as it becomes available. The data from the diverse sites are displayed in a consistent manner and the web pages form a coherent 'shop window' where potential data users can source data sets useful to their research, as well as a visual means of monitoring the health of the observatories. The sister site (outreach.eurosites.info) has been developed in parallel to be accessible to non-scientists. Working together EuroSITES has been able to develop a single conversion software package taking MEDATLAS and ODV ascii files and outputting the OceanSITES format. The sharing of knowledge in this and other developments ensures that costly duplication of effort is minimised. During the 3 years of the project the data management groups have interacted to share best practice, and although each is still independent and serves its own National Data Centre, the EuroSITES data inventory now carries data from all 13 sites, distributed in the OceanSITES v1.2 format. This format is NetCDF based, and carries within the file metadata. This describes the data in a consistent manner which achieves the first step towards interoperablility. The future of the funding of EuroSITES after April 2011 is not yet clear, but the project has achieved a remarkable degree of harmonisation already, and the relationships between the data management groups will undoubtedly continue as the cost benefits of resource and knowledge sharing become ever more important in the scientific arena.