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Flanders Marine Institute (VLIZ)

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  • In the marine domain, LifeWatch provides data services for a large and broad user community dealing with a variety of data types. Activities include provision of data tools and services for taxonomic, ecological, omics, biogeographic, environmental and biological observation data. Tools for data archiving, access, quality control, standardization, harmonization, analysis and publication are integrated in a Marine Virtual Research Environment (Marine VRE). In this regard, the LifeWatch Marine VRE aspires to be the transparent gateway to access, analyze and develop marine data resources. The Marine VRE is built on three components: - Through the "Access" page, the user can retrieve marine biodiversity and ecosystem data. For all resources listed, a description of the data on offer is available and connecting web links are displayed. - Arriving at the "Analyze" page, one can find applications and tools for advanced calculations, modelling and data processing. Through these environments, state-of-the-art workflows and modelling approaches are shared and accessible to all. - Finally, the "Develop" page allows the user to access data services, as well as develop their own. Documented R scripts and tutorials, outputs from expert workshops and detailed methodological workflow of certain data products or scientific publications are only a few examples of how Marine VRE puts the sharing of data and expertise to practice. Now, a marine researcher can access a multitude of available data, find the appropriate tools for analysis, apply and develop existing expertise through data services. Facilitating a scientist's pursuit of knowledge, the LifeWatch Marine VRE contributes to high quality marine research.

  • The package lwdataexplorer retrieves biodiversity, environmental or genetic data from the projects supported by LifeWatch Belgium. These data are also available to explore and download through the LifeWatch Data Explorer: an R Shiny application that allows you to check and download data from your browser.

  • Benthos Ecosystem Quality Index (BEQI). BEQI is a biological index that is used to assess the state of the benthos of coastal and transitional waters for the Water Framework Directive. Taking into consideration the large intrinsic variability of estuarine and coastal systems and the importance of ecosystem functioning within a water body, Ysebaert & Herman (2003) advocate a multilevel scale-dependent approach for the classification of the quality elements in coastal and transitional waters. The proposed multilevel approach consists of three levels: (1) level 1 - Ecosystem level; (2) level 2 - Habitat level; (3) level 3 - Community (within habitat) level. Where suitable input and reference data is provided, the tool will calculate Ecosystem quality scores and produce a list of species that are responsible for observed deviations from the reference state.

  • A tool for Quality Controlling Darwin Core based datasets according to the EMODnet Biology guidelines. The tool performs a thorough QC on OBIS-env datasets and occurrence core datasets. It can use an IPT resource URL as input. Quality controlling a dataset is fundamental in order to ensure its appropriate usage. The EMODnetBiocheck R package is developed in the framework of the LifeWatch and EMODnet Biology projects, and managed by the EurOBIS (European Ocean Biodiversity Information System) Data Management Team at the Flanders Marine Institute (VLIZ). It helps users to Quality Control their (marine) biological datasets by performing a varied number of quality checks on both published and unpublished datasets. This R package also allows a thorough visual exploration of the dataset, while highlighting potential issues within the dataset. The R package can be used on: i) public IPT resources; ii) loaded data tables. The only requirement to use the R package is the existence of an Occurrence table in the dataset, although the analysis reaches its full potential using an IPT resource with OBIS-ENV data format (Core: "Event"; Extensions: "Occurrence" and "Extended Measurements or Facts").

  • One of the virtual laboratories developed by LifeWatch Belgium is the Belgian LifeWatch eLab. This online application allows users to standardise, analyse and visualise their data, making use of web services built on top of internal and external reference databases. The ultimate goal of LifeWatch is to set up a network for data exchange and data analysis through web services. Web services are systems that allow communication between two computers over the web, and allow the user to access the most recent and up-to-date information directly from within other applications. Within LifeWatch Belgium, several web services are available to standardise, analyse and visualise your data, and to extract additional data from several sources. The user can select several data services (taxonomic, geographic, thematic, etc.) and run them successively through a straightforward online user interface. You can also use the LifeWatch.be web services in a concatenated way, i.e. the output of one web service is the input for the next web service. Establishing such workflows helps solving (complicated) biological questions. Several use cases demonstrate the use of the LifeWatch web services. So as to facilitate the use of the LifeWatch web services, several applications and tools were documented in use cases and tutorials. These can be found on the links below, as well as on the specific websites of software packages and Github repositories. The Belgian LifeWatch E-Lab online application allows users to standardize, analyze and visualize their data, making use of web services built on top of internal and external reference databases. A user can select several data services (taxonomic, geographic, thematic, etc.) and run them successively through a straightforward user interface. As explained in the user guide, the LifeWatch.be web services can be used in a concatenated way, i.e. the output of one web service is the input for the next web service.

  • This interactive online tool gives access to all sensor data collected in the framework of the Flemish LifeWatch project, and provides an interface to explore and analyze these data. Several thematic portals have been set up as part of the Data Explorer: - Underway Data Explorer - Station Data Explorer - Zooplankton Data Explorer - GPS Bird Tracking Data Explorer - Fish Telemetry Data Explorer - Batcorder Data Explorer - CPOD (marine mammals) Data Explorer Within the RShiny LifeWatch Data Explorer, five general sections are available to explore, plot, visualize and download data. Some of the more recent data is temporarily under moratorium and therefore protected by password access. The LifeWatch Data Explorer is built using RShiny server, Leaflet, ggplot2, PLotly, Dygraph and DataTables. The system is able to query MSSQL, PostgreSQL, Geoserver (WFS) and MongoDB servers.

  • pyporcc is an open-source Python package developed to detect and classify harbour porpoise’s clicks in audio files using the PorCC algorithm and offering the possibility to create new clicks classifiers. It provides a framework to train different models such as Support Vector Machines, Linear Support Vector Machines, Random Forest and K-Nearest Neighbour that classify sound clips in Noise, and Low-Quality and High-Quality harbour porpoises’ clicks. The algorithm from PAMGuard to detect possible clicks clips is also implemented.

  • Acoustic monitoring is a powerful technique for learning about the ecology of bats. Bat recorders provide continuous registration of bat activity by recording echolocation calls of passing bats. Since the bat calls are highly reliable taxonomic features, the acquired data can be used to estimate diversity and relative abundance of the occurring species. The generated data provides a basis for ecological and behavioral research of the bat species occurring in our coastal and marine areas. BatSounds is an open source repository that contains scripts to work with BatCorder data and BatCorder devices. The repository contains two scripts that are useful to process and send the audio data retrieved by ecoObs Batcorders (https://ecoobs.com/): - Raw_to_wav is a python script that adds a header to raw audio files from the BatCorder so it can more easily be used by different softwares as a wav file. - beaglebone_batcorder is a bash-script to run on a Beaglebone Black minicomputer connected to a BatCorder. It copies the data from the BatCorder daily to its own SD card and sends it to an FTP server over Ethernet. It allows for remote data transfer and memory management of the BatCorder. LifeWatch Belgium has currently four ecoObs BatCorders installed. You can find more information here: https://lifewatch.be/en/sensor-network-bat-detection

  • The goal of MarineSPEED is to provide a benchmark data set for presence-only species distribution modeling (SDM) in order to facilitate reproducible and comparable SDM research. It contains species occurrences (coordinates) from a wide diversity of marine species and associated environmental data from Bio-ORACLE and MARSPEC. Some additional information about MarineSPEED can be found in the R Shiny viewer at https://rshiny.lifewatch.be/marinespeed/.

  • The Marine Regions team at VLIZ provides access to several data products in common GIS formats such as geopackage, shapefile, geojson or kml. Some of these are developed by the Marine Regions team. For example, the Maritime Boundaries which include all the provisions of the United Nations Convention on the Law of the Sea; or the sea areas delimited in the document "Limits of Oceans & Seas, Special Publication No. 23" published by the IHO in 1953. When possible, Marine Regions also offers access to these products following the specifications of the Open Geospatial Consortium (OGC), such as Web Feature Services (WFS), Web Map Services (WMS) or Catalogue Service for the Web (CSW). There is a wrapper in the R programming language for these services together with the Gazetteer webservices in the form of an R package: 'mregions', developed by the rOpenSci consortium and maintained by the Marine Regions team.