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TITAN comprises a well-grounded stack of Big Data technologies including Apache Kafka for inter-component communication, Apache Avro for data serialisation and Apache Spark for data analytics. Furthermore, DRAMA framework is the underlying workflow orchestrator engine used by TITAN.
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This online and interactive environment provides access to all data of the European Tracking Network. The VRE includes a database for storage and integration of acoustic telemetry data and a number of analytical tools for analysing the data using R that are: - the LifeWatch Data Explorer for fish telemetry, a RShiny GUI for data exploration; - an RStudio IDE that allows the user to develop and run R scripts online on the available telemetry data; - an Rpackage that incorporates specific functions to start a smooth analysis of telemetry data.
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The LifeWatch Italy national node has realised the Alien and Invasive Species Virtual Research Environment (Alien Species VRE) for supporting researchers to address basic and applied studies on ecosystem vulnerability to alien species arrival. The Alien Species VRE allows to: - access and download harmonised data on the national distribution of species of fauna and flora belonging to different habitats (marine, fresh and transitional waters, and terrestrial) published through the LifeWatch Italy Data Portal and distributed by the LifeWatch ERIC Metadata Catalogue; - upload their own datasets structured according to the LifeWatch Italy Data Schema in order to execute the service included in the VRE.
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MedOBIS is the Regional OBIS Node for the Mediterranean Sea. It is hosted by the Institute of Marine Biology, Biotechnology and Aquaculture https://imbbc.hcmr.gr/ (IMBBC), Hellenic Centre for Marine Research, HCMR https://www.hcmr.gr/en/ , Heraklion (Crete). Launched in 2003, it has already been operational in 2005 as a Tier 3 Node of EurOBIS and covered the Eastern Mediterranean and the Black Sea. Under the European projects EMODNET and LifeWatchGreece (started in 2013), it became a Tier 2 node and extended to all Mediterranean Sea. MedOBIS provides access to data from a wide range of sources and time periods, including new and historical data sets. MedOBIS actively contributes to global scientific efforts for FAIR and OPEN data. The MedOBIS vLab consists of the MedOBIS IPT (Integrated Publishing Toolkit- http://ipt.medobis.eu/), which is available for sharing data and metadata, and Medobis viewer as a geodata tool, developed by open layers for visualization. MedOBIS can accept any data files from its data sources or data providers, and it publishes these data on its Integrated Publishing Toolkit (IPT), which is harvested by central OBIS. The Integrated Publishing Toolkit (IPT) is developed and maintained by the Global Biodiversity Information Facility (GBIF). For more information check here: https://obis.org/manual/contribute/ MedOBIS currently (2021) hosts 54 datasets, covering the period 1844 to 2017, with over 77,000 occurrence records accompanied with taxonomical, trait, geographical and environmental information. Login is required to access the vLab; while the IPT is open to any user.
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The MicroCTvlab is a service which was created in order to present and disseminate micro-CT (micro-computed tomography) datasets through the framework of the LifeWatchGreece project. This service offers virtual galleries and online tools for the 3D manipulation of the micro-CT datasets. The creation and dissemination of these "cyber-specimens" aim to contribute to a massive digitization of biological collections. The Micro-CT is a web application compatible with all major web browsers. So far, 24 micro-CT datasets have been published, representing a selection of biological and biomedical samples scanned with different parameters. On the main page, scans are presented as a preview of images accompanied by the title of the dataset. When any of these micro-CT datasets is selected by the user, the dataset details are displayed in four tabs, featuring: a) an overview page; b) an interactive tool for manipulating the 3D representation; c) a preview video and d) metadata for the dataset. A Micro-CT Rest API is also available for getting and creating new content.
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This vLab comprises of two online coupled models, which are parameterised and initialised for the specific conditions at a few specifically identified areas for which the required datasets exist. In an attempt to make the tool user friendly a graphic user interface (GUI) developed in the course of previous projects will be used. The GUI allows the user to view model results dynamically through any internet browser. Model results will be stored at the HCMR servers and the user will be able to select the area, scenario, and parameter required, which will then be returned as results in the form of plots. All model parameters and options will be available to the user online. The ultimate operation, therefore, of this vLab will be to allow the user to submit a request for the model to run under a different scenario than those already available.
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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.
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The Bird Movement Modelling virtual lab was developed by SURFsara Computing & Networking Services and the Institute for Biodiversity and Ecosystem Dynamics of the University of Amsterdam. It is an e-Science infrastructure designed for users of the UvA Bird Tracking System (UvA-BiTS), a bio-logging system which includes hardware, software and a supporting data infrastructure. The VL-BMM can be used by project partners to control the tracking system, access data log files, access processed data from a centralized PostgreSQL database, explore or analyze measurements of the UvA-BiTS. The VL-BMM also includes a website where the public view and interact with the most recently downloaded data from select projects.
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The LifeWatch Italy national node has realised the Phytoplankton Virtual Research Environment (Phyto VRE) for supporting researchers to address basic and applied studies on phytoplankton ecology at a level of resolution going from individual cells to whole assemblages. The Phyto VRE enables researchers to: - produce harmonised data on taxonomy and morphological traits by using the Atlas of Phytoplankton, Atlas of Shapes and Phytoplankton Traits Thesaurus; - access, download, and select LifeWatch Italy datasets (published through the LifeWatch Italy Data Portal and distributed by the LifeWatch ERIC Metadata Catalogue) or upload their own datasets structured according to the Phyto template based on the LifeWatch Italy Data Schema in order to execute the services included in the VRE; - faciliatate the computation of morphological and demographic traits (such as hidden dimension, biovolume, surface area, surface-volume ratio, cell carbon content, etc.) and investigate their distribution patterns at different levels of data aggregation (i.e. spatial, temporal, taxonomic) by means of services, which automate a set of operations written in the R language.
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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.