Tutorial on Hybrid Data Infrastructures: D4Science as a case studyBlue BRIDGE
An e-Infrastructure is a distributed network of service nodes, residing on multiple sites and managed by one or more organizations allowing scientists residing at distant places to collaborate. They may offer a multiplicity of facilities as-a-service, supporting data sharing and usage at different levels of abstraction. E-Infrastructures can have different implementations (Andronico et al 2011). A major distinction is between (i) Data e-Infrastructures, i.e. digital infrastructures promoting data sharing and consumption to a community of practice (e.g. MyOcean, Blanc 2008) and (ii) Computational e-Infrastructures, which support the processes required by a community of practice using GRID and Cloud computing facilities (e.g. Candela et al. 2013). A more recent type of e-Infrastructure is the Hybrid Data Infrastructure (HDI) (Candela et al. 2010), i.e. a Data and Computational e-Infrastructure that adopts a delivery model for data management, in which computing, storage, data and software are made available as-a-Service. HDIs support, for example, data transfer, data harmonization and data processing workflows. Hybrid Data e-Infrastructures have already been used in several European and international projects (e.g. i-Marine 2011; EuBrazil OpenBio 2011) and their exploitation is growing fast supporting new projects and initiatives, e.g. Parthenos, Ariadne, Descramble.
A particular HDI, named D4Science (Candela et al. 2009), has been used by communities of practice in the fields of biodiversity conservation, geothermal energy monitoring, fisheries management, and culture heritage. This e-Infrastructure hosts models and resources by several international organizations involved in these fields. Its capabilities help scientists to access and manage data, reuse data and models, obtain results in short time and share these results with other colleagues.
Workshop about research data archiving and open access publishing at the Rese...Dag Endresen
The Research Council of Norway (RCN) organizes a workshop on 1st November 2016 to collect experiences on research data archiving and open access data publishing. The Norwegian GBIF-node will present the GBIF framework including dataset DOIs and download DOIs.
See also:
GBIF.no (2016), http://www.gbif.no/news/2016/data-archiving-ncr.html
GBIF GB21 (2014), http://www.gbif.org/newsroom/news/gb21-science-symposium
GBIF GB21 Slides, http://www.gbif.org/resource/81918
Vimeo video (2014), https://vimeo.com/107148220#t=6m28s
Web service technologies, at CGIAR ICT-KM workshop in Rome (2005)Dag Endresen
Presentation of web services for the CGIAR ICT-KM training workshop on information interoperability, 13th June 2005, at IPGRI Rome Italy. Dag Endresen (Nordic Gene Bank).
Presented by Tony Mathys at a Current Issues and Applications of the Geospatial Technologies Lecture, Department of Geography and Environment, Aberdeen University, 24 February 2012
Tutorial on Hybrid Data Infrastructures: D4Science as a case studyBlue BRIDGE
An e-Infrastructure is a distributed network of service nodes, residing on multiple sites and managed by one or more organizations allowing scientists residing at distant places to collaborate. They may offer a multiplicity of facilities as-a-service, supporting data sharing and usage at different levels of abstraction. E-Infrastructures can have different implementations (Andronico et al 2011). A major distinction is between (i) Data e-Infrastructures, i.e. digital infrastructures promoting data sharing and consumption to a community of practice (e.g. MyOcean, Blanc 2008) and (ii) Computational e-Infrastructures, which support the processes required by a community of practice using GRID and Cloud computing facilities (e.g. Candela et al. 2013). A more recent type of e-Infrastructure is the Hybrid Data Infrastructure (HDI) (Candela et al. 2010), i.e. a Data and Computational e-Infrastructure that adopts a delivery model for data management, in which computing, storage, data and software are made available as-a-Service. HDIs support, for example, data transfer, data harmonization and data processing workflows. Hybrid Data e-Infrastructures have already been used in several European and international projects (e.g. i-Marine 2011; EuBrazil OpenBio 2011) and their exploitation is growing fast supporting new projects and initiatives, e.g. Parthenos, Ariadne, Descramble.
A particular HDI, named D4Science (Candela et al. 2009), has been used by communities of practice in the fields of biodiversity conservation, geothermal energy monitoring, fisheries management, and culture heritage. This e-Infrastructure hosts models and resources by several international organizations involved in these fields. Its capabilities help scientists to access and manage data, reuse data and models, obtain results in short time and share these results with other colleagues.
Workshop about research data archiving and open access publishing at the Rese...Dag Endresen
The Research Council of Norway (RCN) organizes a workshop on 1st November 2016 to collect experiences on research data archiving and open access data publishing. The Norwegian GBIF-node will present the GBIF framework including dataset DOIs and download DOIs.
See also:
GBIF.no (2016), http://www.gbif.no/news/2016/data-archiving-ncr.html
GBIF GB21 (2014), http://www.gbif.org/newsroom/news/gb21-science-symposium
GBIF GB21 Slides, http://www.gbif.org/resource/81918
Vimeo video (2014), https://vimeo.com/107148220#t=6m28s
Web service technologies, at CGIAR ICT-KM workshop in Rome (2005)Dag Endresen
Presentation of web services for the CGIAR ICT-KM training workshop on information interoperability, 13th June 2005, at IPGRI Rome Italy. Dag Endresen (Nordic Gene Bank).
Presented by Tony Mathys at a Current Issues and Applications of the Geospatial Technologies Lecture, Department of Geography and Environment, Aberdeen University, 24 February 2012
Global Biodiversity Information Facility - 2013Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF), GBIF-Norway and the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken) at the Norwegian Institute for Forestry and Landscape (Skog og Landskap) at Ås outside Oslo on the 17th October 2013. Seminar together with the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken).
Presentation slides from a lecture given at the University of the West of England (UWE) as part of the Advanced Information Systems module of the MSc in Library and Library Management, University of the West of England Frenchay Campus, Bristol, October 24th, 2006
ARCLib project presentation from Pasig 2016dp-blog-cz
Digital preservation project by a group of Czech Libraries, financed by the Ministery of Culture of Czech Republic applied research grant. First information.
EURISCO and GBIF IPT, at the Vavilov Institute in St Petersburg (27 April 2010)Dag Endresen
Visit to the NI Vavilov Institute for Plant Industry (VIR) in April 2010. Installation of the GBIF IPT toolkit for data publishing as a test upgrade for the EURISCO data infrastructure of European genebanks.
The BlueBRIDGE approach to collaborative researchBlue BRIDGE
Gianpaolo Coro, ISTI-CNR, at BlueBRIDGE workshop on "Data Management services to support stock assessement", held during the Annual ICES Science conference 2016
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 1Gianpaolo Coro
An e-Infrastructure is a distributed network of service nodes, residing on multiple sites and managed by one or more organizations. e-Infrastructures allow scientists residing at distant places to collaborate. They offer a multiplicity of facilities as-a-service, supporting data sharing and usage at different levels of abstraction, e.g. data transfer, data harmonization, data processing workflows etc. e-Infrastructures are gaining an important place in the field of biodiversity conservation. Their computational capabilities help scientists to reuse models, obtain results in shorter time and share these results with other colleagues. They are also used to access several and heterogeneous biodiversity catalogues.
In this course, the D4Science e-Infrastructure will be used to conduct experiments in the field of biodiversity conservation. D4Science hosts models and contributions by several international organizations involved in the biodiversity conservation field. The course will give students an overview of the models, the practices and the methods that large international organizations like FAO and UNESCO apply by means of D4Science. At the same time, the course will introduce students to the basic concepts under e-Infrastructures, Virtual Research Environments, data sharing and experiments reproducibility.
Global Biodiversity Information Facility - 2013Dag Endresen
Presentation of the Global Biodiversity Information Facility (GBIF), GBIF-Norway and the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken) at the Norwegian Institute for Forestry and Landscape (Skog og Landskap) at Ås outside Oslo on the 17th October 2013. Seminar together with the Norwegian Biodiversity Information Centre (NBIC, Artsdatabanken).
Presentation slides from a lecture given at the University of the West of England (UWE) as part of the Advanced Information Systems module of the MSc in Library and Library Management, University of the West of England Frenchay Campus, Bristol, October 24th, 2006
ARCLib project presentation from Pasig 2016dp-blog-cz
Digital preservation project by a group of Czech Libraries, financed by the Ministery of Culture of Czech Republic applied research grant. First information.
EURISCO and GBIF IPT, at the Vavilov Institute in St Petersburg (27 April 2010)Dag Endresen
Visit to the NI Vavilov Institute for Plant Industry (VIR) in April 2010. Installation of the GBIF IPT toolkit for data publishing as a test upgrade for the EURISCO data infrastructure of European genebanks.
The BlueBRIDGE approach to collaborative researchBlue BRIDGE
Gianpaolo Coro, ISTI-CNR, at BlueBRIDGE workshop on "Data Management services to support stock assessement", held during the Annual ICES Science conference 2016
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 1Gianpaolo Coro
An e-Infrastructure is a distributed network of service nodes, residing on multiple sites and managed by one or more organizations. e-Infrastructures allow scientists residing at distant places to collaborate. They offer a multiplicity of facilities as-a-service, supporting data sharing and usage at different levels of abstraction, e.g. data transfer, data harmonization, data processing workflows etc. e-Infrastructures are gaining an important place in the field of biodiversity conservation. Their computational capabilities help scientists to reuse models, obtain results in shorter time and share these results with other colleagues. They are also used to access several and heterogeneous biodiversity catalogues.
In this course, the D4Science e-Infrastructure will be used to conduct experiments in the field of biodiversity conservation. D4Science hosts models and contributions by several international organizations involved in the biodiversity conservation field. The course will give students an overview of the models, the practices and the methods that large international organizations like FAO and UNESCO apply by means of D4Science. At the same time, the course will introduce students to the basic concepts under e-Infrastructures, Virtual Research Environments, data sharing and experiments reproducibility.
USING E-INFRASTRUCTURES FOR BIODIVERSITY CONSERVATION - Module 3Gianpaolo Coro
An e-Infrastructure is a distributed network of service nodes, residing on multiple sites and managed by one or more organizations. e-Infrastructures allow scientists residing at distant places to collaborate. They offer a multiplicity of facilities as-a-service, supporting data sharing and usage at different levels of abstraction, e.g. data transfer, data harmonization, data processing workflows etc. e-Infrastructures are gaining an important place in the field of biodiversity conservation. Their computational capabilities help scientists to reuse models, obtain results in shorter time and share these results with other colleagues. They are also used to access several and heterogeneous biodiversity catalogues.
In this course, the D4Science e-Infrastructure will be used to conduct experiments in the field of biodiversity conservation. D4Science hosts models and contributions by several international organizations involved in the biodiversity conservation field. The course will give students an overview of the models, the practices and the methods that large international organizations like FAO and UNESCO apply by means of D4Science. At the same time, the course will introduce students to the basic concepts under e-Infrastructures, Virtual Research Environments, data sharing and experiments reproducibility.
GBIF BIFA mentoring, Day 5a Data management, July 2016Dag Endresen
GBIF BIFA mentoring in Los Banos, Philippines for the South-East Asian ASEAN Biodiversity Heritage Parks. With Dr. Yu-Huang Wang, Dr. Po-Jen Chiang, and Guan-Shuo Mai from TaiBIF the GBIF node of Taiwan (Chinese Tapei); and the Biodiversity Informatics team at ASEAN Centre For Biodiversity. http://www.gbif.no/events/2016/gbif-bifa-mentoring.html
Credits: EUDAT/OpenAire, December 2015 & May 2016, CC-BY-4.0
* http://www.slideshare.net/EUDAT/eudat-research-data-management
* http://www.slideshare.net/EUDAT/research-data-management-introduction-eudatopen-aire-webinar?ref=https://eudat.eu/events/webinar/research-data-management-an-introductory-webinar-from-openaire-and-eudat
* https://eudat.eu/events/webinar/research-data-management-an-introductory-webinar-from-openaire-and-eudat
* http://www.instantpresenter.com/WebConference/RecordingDefault.aspx?c_psrid=EB57D6888147
Text (personal views position statement) to accompany presentation on what research infrastructures really need for data, XLDB-Europe, 8-10th June 2011, Edinburgh
RDMkit, a Research Data Management Toolkit. Built by the Community for the ...Carole Goble
https://datascience.nih.gov/news/march-data-sharing-and-reuse-seminar 11 March 2022
Starting in 2023, the US National Institutes of Health (NIH) will require institutes and researchers receiving funding to include a Data Management Plan (DMP) in their grant applications, including the making their data publicly available. Similar mandates are already in place in Europe, for example a DMP is mandatory in Horizon Europe projects involving data.
Policy is one thing - practice is quite another. How do we provide the necessary information, guidance and advice for our bioscientists, researchers, data stewards and project managers? There are numerous repositories and standards. Which is best? What are the challenges at each step of the data lifecycle? How should different types of data? What tools are available? Research Data Management advice is often too general to be useful and specific information is fragmented and hard to find.
ELIXIR, the pan-national European Research Infrastructure for Life Science data, aims to enable research projects to operate “FAIR data first”. ELIXIR supports researchers across their whole RDM lifecycle, navigating the complexity of a data ecosystem that bridges from local cyberinfrastructures to pan-national archives and across bio-domains.
The ELIXIR RDMkit (https://rdmkit.elixir-europe.org (link is external)) is a toolkit built by the biosciences community, for the biosciences community to provide the RDM information they need. It is a framework for advice and best practice for RDM and acts as a hub of RDM information, with links to tool registries, training materials, standards, and databases, and to services that offer deeper knowledge for DMP planning and FAIR-ification practices.
Launched in March 2021, over 120 contributors have provided nearly 100 pages of content and links to more than 300 tools. Content covers the data lifecycle and specialized domains in biology, national considerations and examples of “tool assemblies” developed to support RDM. It has been accessed by over 123 countries, and the top of the access list is … the United States.
The RDMkit is already a recommended resource of the European Commission. The platform, editorial, and contributor methods helped build a specialized sister toolkit for infectious diseases as part of the recently launched BY-COVID project. The toolkit’s platform is the simplest we could manage - built on plain GitHub - and the whole development and contribution approach tailored to be as lightweight and sustainable as possible.
In this talk, Carole and Frederik will present the RDMkit; aims and context, content, community management, how folks can contribute, and our future plans and potential prospects for trans-Atlantic cooperation.
Data policy must be partnered with data practice. Our researchers need to be the best informed in order to meet these new data management and data sharing mandates.
De-centralized but global: Redesigning biodiversity data aggregation for impr...taxonbytes
Biodiversity data pose fundamental challenges for unification-based paradigms of data science. In particular, a hierarchical, backbone-driven approach to aggregating global biodiversity data tends to limit community engagement. Data quality, trust, fitness for use, and impact are similarly reduced. This presentation will outline an alternative, de-centralized design for aggregating biodiversity data globally. The design requires a coordinative approach to representing and reconciling evolving systematic perspectives, and further social but technologically mediated coordination between regionally and taxonomically constrained "communities of practice" (sensu Wenger, 2000, https://doi.org/10.1177/135050840072002). Important next steps in this direction include the development of use cases that quantify the benefits of a de-centralized biodiversity data aggregation - in terms of lowering costs to expert engagement, raising efficiency of curation, validating novel integration services, and improving reproducibility and provenance tracking across heterogenous data structures and portals.
Virtual Research Environments supporting tailor-made data management service...Blue BRIDGE
Presented by Pasquale Pagano of CNR at the BlueBRIDGE Workshop at SeaTech Week 2016 in Brest, France. http://www.bluebridge-vres.eu/events/join-bluebridge-10th-biennial-sea-tech-week-brest-france
"Open data repository for scientific data sharing with the southern countries" was the subject of the talk given by Jean-Chsritophe Desconnets, head of the IRD's Infrastructure and Digital Data Mission (MIDN), in Gabarone (Botswana) on 2018, november 8th during the International Data Week. It presents the IRD's data repository project that will open in 2019. This project is co-managed by MIDN, IT and IST Services.
Vince smith-delivering biodiversity knowledge in the information age-notextVince Smith
Smith, V.S. 2013. Delivering biodiversity knowledge in the information age. Hellenic Botanical Society, Thessaloniki, Greece, 3-6 Oct. 2013. [Delivered via video link through Google Hangouts]
Managing tuna fisheries data at a global scale: the Tuna Atlas VREBlue BRIDGE
On 18th January 2018, 3pm CET BlueBRIDGE will hosted the webinar: "Managing tuna fisheries data at a global scale: the Tuna Atlas VRE" that presented how, through the Tuna Atlas Virtual Research Environment (VRE), users can easily produce their own datasets of fisheries at regional, multi-regional or global scale and how they can share these datasets in ways that allow other users to access, process and visualise them efficiently.