ELIXIR
ELIXIR is an intergovernmental organisation that brings together life science resources from across Europe. These resources include databases, software tools, training materials, cloud storage and supercomputers.
The goal of ELIXIR is to coordinate these resources so that they form a single infrastructure. This infrastructure makes it easier for scientists to find and share data, exchange expertise, and agree on best practices. Ultimately, it will help them gain new insights into how living organisms work.
TeSS is an example of an ELIXIR resource. TeSS is online training portal that gathers life science training materials and training courses from across Europe, and allows you to search it in one website. This makes it easier for scientists to find the training they need, and gives the training courses wider publicity.
ELIXIR includes 22 members and one Observer, bringing together over 220 research organisations. It was founded in December 2013 and began implementing its first scientific programme in 2014. It is currently implementing its second five-year scientific programme.
Web page: https://elixir-europe.org/
Funding details: Related items
Teams: IBISBA Workflows, GalaxyProject SARS-CoV-2, BioBB Building Blocks, Common Workflow Language (CWL) community, BioExcel Best Practice Guides, Specimen Data Refinery, FAIR Computational Workflows, Vertebrate Genomes Pipelines in Galaxy, TRE-FX, EuroScienceGateway, Biodiversity Genomics Europe (general), BY-COVID Baseline Use Case: SARS-CoV-2 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection, BY-COVID (general), BioDT additional pipelines, BioDT Use Case 4.1.1.1 Biodiversity dynamics, BioDT Use Case 4.1.2.2 DNA detected biodiversity, poorly known habitats, BioDT Use Case 4.1.2.1 Crop wild relatives and genetic resources for food security, BioDT Use Case 4.1.3.1 Invasive species, BioDT Use Case 4.1.3.2 Endangered species, BioDT Use Case 4.1.4.1 Disease outbreaks, BioDT Use Case 4.1.4.2 Pollinators, BioDT Use Case 4.1.1.2 Ecosystem services
Organizations: The University of Manchester
https://orcid.org/0000-0001-9842-9718
Presentations and events associated with work in FAIR Guiding Principles for Computational Workflows.
Space: ELIXIR
Public web page: https://workflows.community/groups/fair/
A team that gathers the workflow and workflow-related training activities related to ELIXIR, run by ELIXIR or affiliated to ELIXIR; its Hub, Nodes, platforms and communities
Space: ELIXIR
Public web page: https://elixir-europe.org
Abstract
Authors: Michael J. Roach, N. Tessa Pierce-Ward, Radoslaw Suchecki, Vijini Mallawaarachchi, Bhavya Papudeshi, Scott A. Handley, C. Titus Brown, Nathan S. Watson-Haigh, Robert A. Edwards
Date Published: 15th Dec 2022
Publication Type: Journal
Abstract (Expand)
Authors: Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble
Date Published: 24th Mar 2022
Publication Type: Journal
Abstract (Expand)
Authors: Alex Hardisty, Paul Brack, Carole Goble, Laurence Livermore, Ben Scott, Quentin Groom, Stuart Owen, Stian Soiland-Reyes
Date Published: 7th Mar 2022
Publication Type: Journal
Abstract (Expand)
Authors: Rafael Ferreira da Silva, Henri Casanova, Kyle Chard, Ilkay Altintas, Rosa M Badia, Bartosz Balis, Taina Coleman, Frederik Coppens, Frank Di Natale, Bjoern Enders, Thomas Fahringer, Rosa Filgueira, Grigori Fursin, Daniel Garijo, Carole Goble, Dorran Howell, Shantenu Jha, Daniel S. Katz, Daniel Laney, Ulf Leser, Maciej Malawski, Kshitij Mehta, Loic Pottier, Jonathan Ozik, J. Luc Peterson, Lavanya Ramakrishnan, Stian Soiland-Reyes, Douglas Thain, Matthew Wolf
Date Published: 1st Nov 2021
Publication Type: Journal
Abstract (Expand)
Authors: Anna-Lena Lamprecht, Magnus Palmblad, Jon Ison, Veit Schwämmle, Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin, Paul Groth, Hans Ienasescu, Pratik Jagtap, Matúš Kalaš, Vedran Kasalica, Alireza Khanteymoori, Tobias Kuhn, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft
Date Published: 2021
Publication Type: Journal
Abstract (Expand)
Authors: Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Date Published: 2020
Publication Type: Journal
Presented at Swedish eResearch Centre meeting, 13 may 2022
Creator: Carole Goble
Submitter: Carole Goble
External LinkKeynote JOBIM 2021 (French Bioinformatics Conference)
FAIR Computational Workflows https://jobim2021.sciencesconf.org/ 8 July 2021
Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for ...
Creator: Carole Goble
Submitter: Carole Goble
EOSC-Life FAIR hackathon 2021 Session 3: Workflow & Tools FAIRification
Creators: Carole Goble, Stuart Owen, Simone Leo, Finn Bacall, Stian Soiland-Reyes, Douglas Lowe
Submitter: Carole Goble
So, you want to build a pan-national digital space for bioscience data and methods? That works with a bunch of pre-existing data repositories and processing platforms? So you can share FAIR workflows and move them between services? Package them up with data and other stuff (or just package up data for that matter)? How? WorkflowHub (https://workflowhub.eu) and RO-Crate Research Objects (https://www.researchobject.org/ro-crate) that’s how! A step towards FAIR Digital Objects gets a workout. Keynote ...
Creator: Carole Goble
Submitter: Carole Goble
Keynote presented at WORKS 2021 https://works-workshop.org/
16th Workshop on Workflows in Support of Large-Scale Science November 15, 2021 Held in conjunction with SC21: The International Conference for High Performance Computing, Networking, Storage and Analysis
Creator: Carole Goble
Submitter: Carole Goble
Keynote at German Conference on Bioinformatics 2021 https://gcb2021.de/ FAIR Computational Workflows Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the ...
Creator: Carole Goble
Submitter: Carole Goble
invited presentation at https://researchsoft.github.io/FAIReScience/, FAIReScience 2021 online workshop virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)
20th Sept 2021
Creator: Carole Goble
Submitter: Carole Goble
Keynote Presented at the ICTeSSH 2021 Conference to Social Science and Humanities. ICTeSSH 2021, 30th June 2021
https://ictessh.uns.ac.rs/ In data intensive science multi-step tool-chains are widely used to help scientists manage, analyze, and share increasing volumes of complex data. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the exchange of processing know-how, and ...
Creator: Carole Goble
Submitter: Carole Goble
EOSC-Life 3rd Open Call Biohackathon induction workshop
Start Date: 16th Dec 2021
End Date: 16th Dec 2021
Event Website: https://docs.google.com/document/d/1Ks7mf7xVLdnP4vLWj0zcJ2dvOXWtQyAu/edit
Country: Not specified
City: Virtual
Reproducibility is a cornerstone of good scientific practice. Thanks to funding provided by ELIXIR Training Platform Task 2, we have brought together the biggest names in bioinformatics workflow management for a 3 day practical workshop. We have presentations from the development teams of CWL, Snakemake, Nextflow, nf-core and more. If you want to learn more about the workflow management concepts that will be addressed in this workshop, check out these articles:
Workflow systems turn raw data into ...
Start Date: 29th Nov 2021
End Date: 1st Dec 2021
Event Website: https://elixir-workflow-workshop.github.io/2021/
Country: 
Germany
City: Virtual
virtually co-located with the 17th IEEE International Conference on eScience (eScience 2021)
This discussion-focused workshop examines how the FAIR (Findable, Accessible, Interoperable, Reusable) principles are and can be applied to eScience research objects beyond data. Invited speakers will present the idea of FAIR and its application to objects such as software, workflows, machine learning models, and executable notebooks, and where FAIR is going. Invited talks will be followed by a panel ...
Start Date: 20th Sep 2021
End Date: 20th Sep 2021
Event Website: https://researchsoft.github.io/FAIReScience/
Country: Not specified
City: Virtual
The public and the press already expect to assess the trustworthiness of research relevant to pressing social and public health issues in terms of transparency. While widely recognized as a critical component of research reproducibility in principle, the promise of making research fully transparent—and scientific claims easier to evaluate—via reliable provenance has yet to be realized in full. In particular, it is still far from routine for researchers in the natural, social, and data sciences ...
Start Date: 22nd Jul 2021
End Date: 22nd Jul 2021
Event Website: https://iitdbgroup.github.io/ProvenanceWeek2021/t7.html
Country: 
United States
City: Virtual
The FAIR Principles have two aspects: They were written specifically for research data and they also claim to be general for all research objects. In practice, this means that while the high-level concepts (findable, accessible, interoperable, and reusable) are generally applicable, the details of the wording, their context, and how they are applied is not. Different groups have been studying how the FAIR principles could be applied to other types of research objects, such as research software, ...
Start Date: 22nd Jun 2021
End Date: 22nd Jun 2021
Event Website: https://www.go-fair.org/events/fair-festival-2021/
Country: Not specified
City: Virtual
Date: Friday 11 June 2021, 10.00 CEST
Chairs: Carole Goble, Stian Soiland-Reyes, Salvador Capella-Gutiérrez, José María Fernández González and Frederik Coppens
In Life Sciences, experimental laboratory procedures usually have a lifespan since their first inception, wide adoption along the years, and later being superseded by others. The same applies to the analysis of the generated experimental data. Workflow Lifecycle represents the different states of workflows during their “life”. This workshop ...
Start Date: 11th Jun 2021
End Date: 11th Jun 2021
Event Website: https://docs.google.com/document/d/1AOE9jLO5EbUFu9NTe0B-z_jx8eQGIMSySkMLRMYvXO0/edit#heading=h.podt37y5jukq
Country: Not specified
City: Virtual
Scientific workflows capture precise descriptions of the steps and data dependencies needed to carry out computational experiments in many areas of Science, ranging from Astrophysics to Bioinformatics or Geosciences. In order to promote long-term usability and uptake by the scientific community, workflows (as well as the tools that integrate them) should become findable, accessible, understandable, reusable, and citable so that author’s credit is attributed fairly and accurately.
The work on ...
Start Date: 30th Nov 2020
End Date: 30th Nov 2020
Event Website: https://conference.codata.org/FAIRconvergence2020/sessions/218/
Country: Not specified
City: Virtual
In the age of computational science, researchers in the life sciences – just as in other domains – regularly face the need of composing several individual software tools into pipelines or workflows that perform the specific data analysis processes that they need in their research. For over 20 years now, dedicated scientific workflow management systems have been supporting scientists in this task, and they continue to gain popularity. In fact, recent years have seen significant progress in the ...
Start Date: 7th Mar 2020
End Date: 13th Mar 2020
Event Website: https://www.lorentzcenter.nl/automated-workflow-composition-in-the-life-sciences.html
Country: 
Netherlands
City: Leiden
The results of the mentimeter for the FAIR workflows section of the EOSC-Life 3rd Open Call projects pre-hackathon induction
Creators: Carole Goble, Stian Soiland-Reyes, Stuart Owen, Finn Bacall, Simone Leo, Douglas Lowe
Submitter: Carole Goble
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