ICES TCRE Virtual Research Environment

This VLab that supported the ICES Training Course in the R Environment (TCRENV) (Date: 29 February-4 March 2016, Location: Copenhagen, Denmark). The objective of the course was to provide participants with a solid foundation in efficient use of the R environment using various typical and familiar fisheries data sets (landings data, catch data, survey data and tagging data) as case examples. Emphasis was put on data munging and literate programming starting with 'raw' data (individual stations, individual fish measurements) and culminating with deliverance of publishable output produced from a single coded document file. This VRE provides access to processing as well as to data preparation and sharing facilities, including: an online R development environment (RStudio), data mining algorithms, a tabular data management application, GIS maps of environmental and biological data, access to biodiversity occurrence records and taxonomic data from major data providers (e.g. OBIS, GBIF, WoRMS, Catalog of Life), state-of-the-art stock assessment models and sharing tools (Workspace, Social Networking). In addition to the basic functionalities, as a workspace for sharing objects of interest, a social networking area for supporting the discussions among members and a user management facility for managing membership, this VRE is specifically equipped with the following capability: Tabular Data Management: a facility enabling users to import, curate and manage tabular data. This feature can support data managers during the whole life cycle of data management from data capture to publication and visualisation. It enables data managers to import and transform datasets (CSV, SDMX, JSON) into tabular resources (i.e. tabular data having proper types associated with columns eventually referring to code lists) and reference datasets (code lists) representing recognized value instances of the elements the dataset is about (e.g., species, zones, countries). This functionality guarantees that the tabular resources are compliant with the defined types and code lists. Besides the curation, the facility supports the analysis of the data by enabling a user to perform operations like grouping and filtering, producing charts and GIS maps (if the data have geographic features) and analysing the data via an R environment as well as via the data analytics facilities. Finally, the environment supports the publishing of tabular resources in the infrastructure by equipping them with rich metadata so that such resources can be used in other application contexts Data Analytics at Scale: a facility enabling users to benefit from the offering of the DataMiner service and interactively execute a large array of data analytics tasks on datasets. These algorithms range from data clustering and anomalies detection methods (e.g. DBScan and KMeans) to algorithms for manipulating datasets from the geospatial perspective (e.g. transform FAO Area Code in latitude and longitude) Species Data Discovery: facility enabling users to discover and manage species data products (occurrence data and taxonomic data) from a number of heterogeneous providers (including GBIF and speciesLink for occurrences data, and ASFIS, BrazilianFlora, CatalogueOfLife, IRMNG, IT IS, NCBI, WoRDSS, WoRMS for taxonomic data) in a seamless way. Once discovered, objects can be stored in the workspace for future uses Geospatial Data View: facility enabling users to discover and visualize GIS layers, e.g. species distribution maps, Sea Surface Temperature, that have been generated and/or published. This facility relies on the GeoExplorer portlet and makes it possible to effectively exploit the generated maps and perform comparisons and analysis of the diverse distributions by enabling maps overlay, transects production and values inspection

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Additional Info
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About VRE Expiration The VRE expiration date can either be extended or anticipated upon VRE Manager's request. Any of these requests will take one month to be carried out.
Access Policy Private
Acknowledgment Statement This work has received support from the BlueBRIDGE Project (European Union’s Horizon 2020 research and innovation programme, Grant agreement No 675680) and is operated by the D4Science Infrastructure (D4Science.org).
Public page https://bluebridge.d4science.org/web/ices_tcre
VRE Creation Date December 15, 2015
VRE Expiration Date February 28, 2020
system:type VirtualResearchEnvironment
Management Info
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Author Perciante Costantino
Maintainer Perciante Costantino
Version 1
Last Updated 16 April 2018, 10:28 (CEST)
Created 27 March 2018, 11:41 (CEST)