29 record(s)
Type of resources
Contact for the resource
From 1 - 10 / 29
  • 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.

  • The Polychaetes Scratchpad site is dedicated to information (images, videos, publications, specimens, etc.) of marine bristle worms (Polychaeta). The site has started to be populated with content very recently and information is gradually being added. The classification used in this site does NOT reflect current taxonomic knowledge. It is currently being used for browsing content only, but will be cleaned up in the future. Developed by: The database is maintained by the Institute of Marine Biology, Biotechnology and Aquaculture of the Hellenic Centre for Marine Research (HCMR). It is supported by the Greek LifeWatch infrastructure. Scratchpads was developed by the Virtual Biodiversity Research and Access Network for Taxonomy (ViBRANT), a EU FP7 project. Technology or platform: The site is based on a virtual research environment called Scratchpads, which in turn is based on the content management software Drupal.

  • The objective of RAMS is to compile and manage an authoritative taxonomic list of species occurring in the Antarctic marine environment, for establishing a standard reference for marine biodiversity research, conservation and sustainable management. The taxonomic scope of RAMS covers Antarctic species from the three realms of the Southern Ocean: the sea floor (meio-, macro- and megazoobenthos; micro- and macrophytobenthos), the water column (phytoplankton, zooplankton, nekton) and the sea-ice. Developed by: The RAMS website and databases are developed and hosted by the Flanders Marine Institute (VLIZ). The RAMS content is managed by an Editorial Board comprising an Executive Committee and associate Taxonomic Editors. The RAMS Executive Committee plays an advising role in the development of RAMS and proposes Taxonomic Editors. It links with the SCAR-MarBIN International Steering Committee. To allow RAMS to be as exhaustive as possible, the role of the network of Taxonomic Editors is crucial. These Taxonomic Editors are world experts on the taxonomy of their relevant taxa and are in charge of the content and quality control of data for their specific group. Used data resources: A series of preliminary species lists of Antarctic marine invertebrates, mostly for macrobenthic groups, were compiled by Andrew Clarke and Nadine Johnston of the British Antarctic Survey (BAS), with funding from the UK Foreign & Commonwealth Office and British Antarctic Survey. These lists have been or are being checked and updated by taxonomic experts.

  • 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.

  • The purpose of MarineRegions is to create a standard, relational list of geographic names, coupled with information and maps of the geographic location of these features. Marine Regions is an integration of the VLIMAR Gazetteer and the VLIZ Maritime Boundaries Geodatabase (MARBOUND). The VLIMAR Gazetteer is a database with geographic, mainly marine names such as seas, sandbanks, seamounts, ridges, bays or even standard sampling stations used in marine research. The geographic cover of the VLIMAR gazetteer is global but initially focused on the Belgian Continental Shelf and the Scheldt Estuary and the Southern Bight of the North Sea. Gradually more regional and global geographic information was added to VLIMAR and combining this information with the Maritime Boundaries database, representing the Exclusive Economic Zone (EEZ) of the world, led to the creation of marineregions.org.​ In order to preserve the identity of the marine geographic objects from the database, and to name and locate the geographic resources on the web, MarineRegions promotes the Marine Regions Geographic IDentifier, or the MRGID. Developed by: MarineRegions is managed by the Flanders Marine Institute (VLIZ). Funding for the creation of the VLIMAR gazetteer was provided initially through the EU Network of Excellence MarBEF, but also other European initiative such as EMODNet and Lifewatch provide the necessary funding for the maintenance and management of MarineRegions. Used data resources: MarineRegions uses several sources: marine boundaries, ecological classifications, fishing zones, thematic gazetteers, regional gazetteers, global gazetteers and several others. Web services: MarineRegions provides numerous web services which allow the user to have direct access to the geographic data, maps and metadata from a GIS desktop or for online applications. Currently MarineRegions provides the OGC services WMS, WFS and CSW.

  • Scratchpads are an online virtual research environment for biodiversity scientists, allowing anyone to share their data and create their own research networks. Sites are hosted at the Natural History Museum London, and offered freely to any scientist that completes an online registration form. Sites can focus on specific taxonomic groups, or the biodiversity of a biogeographic region, or indeed any aspect of natural history. Scratchpads are also suitable for societies or for managing and presenting projects. Key features of Scratchpads include: tools to manage biological classifications, bibliography management, media (images, video and audio), rich taxon pages (with structured descriptions, specimen records, and distribution data), and character matrices. Scratchpads support various ways of communicating with site members and visitors such as blogs, forums, newsletters and a commenting system. Translations of the Scratchpads software are available via our localization server and site content can be created in multiple languages. Developed by: The Scratchpads Virtual Research Environment is developed and supported by the Natural History Museum, London. It has received funding from several European Union and UK funded projects including the EU-FP6 EDIT and FP7 ViBRANT projects (http://vbrant.eu/) as well as the NERC-funded eMonocot Project (http://about.e-monocot.org/). Used in tools: As of August 2015 there are almost 700 active research communities using Scratchpads. Examples of major projects using multiple Scratchpad sites include: eMonocot: A project to aggregate information on the taxonomy and distribution of monocot plants. Each major monocot family using a separate community Scratchpad and these data are centrally aggregated through the e-monocot portal. http://about.e-monocot.org/ Encyclopedia of Life (EOL): Scratchpads replace the EOL LifeDesk system which was one of the systems previously used to supply community contributions to Encyclopedia of Life. An example of an EOL contributing site is Antkey, a community resource for the identification of invasive, introduced and commonly intercepted ant species from across the globe. http://eol.org/ AVIS-IBIS: The Avian Information System (AVIS) is an extensive database information system about all birds of the Indian subcontinent in the series of web-based portals under IBIS to contribute plethora of information available on birds to science and conservation. http://avis.indianbiodiversity.org/ Flora of Thailand: The e-Flora of Thailand aims to provide a web-based flora as a decentralized platform where authors manage, share, and publish taxonomic data online. It will eventually bring together taxonomic data of all of Thailand’s 303 plant families, with keys, descriptions, uses, illustrations, maps, and high-quality photographs of the estimated total number of 10,624 species. http://floraofthailand.myspecies.info/ Technology or platform: Scratchpads are built on top of the Open Source CMS, Drupal. Drupal has been extended with over 150 custom modules developed by the Scratchpads development team, and over 100 contributed modules developed by the Drupal community. The majority (>700 of ~750) of the Scratchpads are hosted at the Natural History Museum, London (NHM). The current setup, which has been honed and improved since its initiation in 2007, uses a single load balancing server running Varnish, two application servers running Apache/PHP, two data servers running Percona (MySQL) and Memcache, and one search server running Apache Solr. This setup can be easily extended to increase capacity for more users or more Scratchpads. Sites are managed using Aegir, a Drupal specific tool for creating and managing Drupal websites.

  • 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. The ETN data management platform is an online web application to store, access and share aquatic telemetry data and metadata. The portal is open to all European users for data management of telemetry data in marine, estuarine and freshwater environments. ETN now contains data of 15 fish species. Currently ETN supports acoustic telemetry data, but aims to extend this to different telemetry techniques (e.g. PIT data-storage tags and satellite tags) to be able to monitor habitat use and migration patterns of a range of species in the aquatic environment. On a technical note, the portal requires the receiver and deployment metadata, as well as the transmitter tag and animal metadata before detection data can be uploaded. The uploaded data are subjected to quality control. Access is password protected and data moratorium rules are in place. The ETN data portal is developed by the Flanders Marine Institute (VLIZ) as part of the Flemish contribution to LifeWatch. New developments and additional features are added on a continuous basis. The web application is built using PHP (using the Symfony framework) for the back-end side and Bootstrap/jQuery/Datatables/… (among others) to facilitate the development of the front-end side.

  • 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.

  • 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.

  • 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.