ELIXIR Implementation Study

Exploration work about the use of Beacons for proteomics data

While the existing Beacon network permits the discovery of genomic variants, the expression of these variants on the functional level depends on a wide range of factors. Adding information on variants on the proteome level will help to filter and to prioritize variants of functional relevance. The presence of genomic variants on the proteome level implies that clinical proteomics data is highly likely to be identifiable and thus specially protected under the EU GDPR guidelines.

The goals of this study are to 1) develop rules and best-practice guidelines for dealing with this type of data and align these efforts with the genomics community, 2) generate a list of potential use cases, 3) assemble a prototypical cloud-enabled pipeline for the extraction of proteomic variants, and 4) build a prototype Beacon implementation that integrates the extracted protein-level variants using existing local analysis pipelines in ELIXIR Belgium and ELIXIR Germany, and use it as a “proof of concept” to integrate proteomics data into the Beacon network.

The study is a joint effort of EMBL-EBI (Juan Antonio Vizcaíno), ELIXIR Belgium (Lennart Martens) and ELIXIR Germany (Oliver Kohlbacher).

1/11/2018 - 30/9/2019

Standardizing the fluxomics workflows

This Metabolomics Community-led study focusses on the standardization of fluxomics workflows. The study is led by ELIXIR Greece and ELIXIR Spain and supported by EMBL-EBI and 11 other national ELIXIR Nodes, among which ELIXIR Belgium (Bart Ghesquire).

The study aims at 1) establishing standards for isotopic labelling data deposition, a major fluxomics input, and accordingly extending Metabolights -  the reference database for quantitative metabolomics datasets, 2) establishing interoperability among largely-used fluxomic tools, building upon the PhenoMeNal fluxomic tool inventory, 3) extending BioSchemas to metabolic reactions and their dynamics, using the metabolic reaction database Rhea for metabolic model reconstruction, 4) containerizing the fluxomic workflow for use in cloud-based environment, and 5) standardizing the fluxomics training.

1/6/2019 - 31/5/2021

Interoperability Services for the Cloud

FAIRification for large-scale life sciences research requires FAIRification of all aspects: data, tools, training and hardware infrastructure. Cloud computing has emerged a key infrastructure that calls for interoperability of software to facilitate data retrieval and processes that are dispersed across multiple sites. The European Open Science Cloud (EOSC) programme is established in realisation of the large-scale cloud-based data integration. The ELIXIR Interoperability platform mission aligns with the EOSC terms of standardised best practices of implementation, and support of interoperability tools in the cloud.

This study will establish the need for cloud deployed instances of individual Recommended Interoperability Resources (RIRs) through consultation with ELIXIR Communities and established use cases. Cost benefit analyses will be performed for each RIR and the landscape and extent of the current cloud-enabled interoperability resources will be evaluated.

This project is part of the ELIXIR Interoperability platform tasks for the 2019-2023 Scientific programme. The study is a joint effort of EMBL-EBI (Helen Parkinson), ELIXIR Belgium (Frederik Coppens) and ELIXIR Norway (Sveinung Gundersen).

1/6/2019 - 31/12/2021

Packaging, containerisation & deployment

Software containers are a key element in the frame of Open Science & Open Source which is strongly supported and advocated by ELIXIR. Software containers guarantee data provenance when described as part of scientific workflows and are an important element towards reproducibility. This study is divided into three work-packages that complement each other:

  • WP1: Maintain and improve biocontainers infrastructure
  • WP2: Developing an integrated “Tools platform Ecosystem”
  • WP3: Fostering and evolving community participation and community workflows,

and aims to provide containerised tools and state-of-the-art benchmarked workflows available in Galaxy for scientific communities. This implies integrating data repositories, tools and training material. The provided workflows and tools will be curated to a high standard, rendered FAIR, and follow agreed standards within ELIXIR and by initiatives like GA4GH and EOSC.

This project is part of the ELIXIR Tools platform tasks for the 2019-2023 Scientific programme. Eight ELIXIR Nodes are involved: ELIXIR Spain (Salvador Capella, Josep Gelpi), ELIXIR Germany (Bjorn Gruning), EMBL-EBI (Yasset Perz-Riverol), ELIXIR Belgium (Frederik Coppens), ELIXIR Denmark (Piotr Chmura, Jon Ison), ELIXIR France (Herve Menager, Olivier Sallou), ELIXIR Italy (Giacomo Tartari) and ELIXIR Norway (Matus Kalas, Abdulrahman Azab, Kjetil Klepper, Kjell Petersen).  

1/6/2019 - 31/12/2021

FONDUE: FAIRification of plant genotyping data and its linking to phenotyping using ELIXIR platforms

Recent progress in sequencing technologies has produced several large scale data sets for crops. The insights gained by this data have been published in high profile scientific articles, but the underlying raw genotype data and the associated sample and population metadata have not been routinely submitted to appropriate archives. The aim of this implementation study is to provide this wealth of data according to FAIR principles ensuring an interoperable link with the phenotypic data that is stored in distributed institutional repositories which is crucial for accelerated crop breeding. A sustainable toolbox will be created to submit data to the ELIXIR deposition database “European Variation Archive” (EVA) and to enrich the data with interoperable metadata regarding plant data standards like “Multi-Crop Passport Descriptor” (MCPD) and “Minimal Information About a Plant Phenotyping Experiment (MIAPPE).

The study is a joint effort of ELIXIR France (Cyril Pommier, Anne-Francoise Adam-Blondon, Nacer Mohellibi, Manuel Ruiz), ELIXIR Germany (Uwe Scholz, Heidrun Gundlach, Klaus F.X. Mayer), ELIXIR the Netherlands (Richard Finkers), ELIXIR Belgium (Frederik Coppens, Bert Droesbeke) and EMBL-EBI (Cristina Yenyxe, Gonzalez Garcia, Melanie Courtot, Bruno Contreras-Moreira, Marc Rosello).

1/6/2019 - 31/5/2021

Deploying reproducible containers and workflows across cloud environments

This Strategic Implementation study around Container Orchestration aims to coordinate the ELIXIR Platforms (Compute & Tools) expertise within the Nodes, related projects and resources to establish ELIXIR-wide standards, protocols and processes for the orchestration of containerised applications provided by ELIXIR Communities.

The study will be approached in  4 workpackages: WP1) Leveraging EOSC-Life workflows infrastructure, WP2) ELIXIR infrastructure for orchestrating containers and workflows, WP3) Coordinating ELIXIR data discovery and transfer services, WP4) Community-led use cases. ELIXIR Belgium co-leads WP 3 and contributes to WP2.

Thirteen ELIXIR nodes and the ELIXIR Hub are involved in this study: Spain, Finland, Germany, France, Denmark, Belgium (Frederik Coppens), Sweden, Italy, Czech, the Netherlands, UK, Switzerland, EMBL-EBI.

1/6/2019 - 31/5/2021

Expanding the Galaxy: (meeting) the needs of ELIXIR Communities

As data analysis is common place in life sciences, we need to establish scalable ways to develop and share analysis workflows and train researchers to make use of them. The latter entails an end-to-end approach from access to data over selection and proper usage of the appropriate workflow and deploying this on available (cloud) resources.

As the ELIXIR Communities bring together domain experts, this is an ideal way to identify and develop standard workflows for commonly used analysis in specific domains. Since summer 2016, the Galaxy training network has been collecting and further developing training material for analysis and administration of Galaxy in a collaborative way (https://training.galaxyproject.org).

This project has three main goals: 1) Expand the portfolio of Community workflows including training material to describe them, 2) Facilitate access to data in Core Data Resources and Deposition Databases, 3) Improve the user experience of the Galaxy platform.

The study is a joint effort of ELIXIR France (Gildas le Gorguille, Erwan Corre), ELIXIR UK (Ralf Weber, Philippe Rocca-Serra, Christine Orengo), ELIXIR-NL (Michael Van Vliet, Saskia Hiltemann, Leon Mei, Peter Horvatovich, Anton Feenstra), ELIXIR Germany (Bjorn Gruning, Berenice Batut, Christophe Steinbeck, Oliver Kolhbacher), ELIXIR Spain (Salvador Capella, Oswaldo Trelles), ELIXIR Portugal (Daniel Faria, Ricardo Leite, Ana Portugal Melo), ELIXIR Norway (Erik Hjerde, Nils-Peder Willassen), EMBL-EBI (Henning Hermjakob), ELIXIR Greece (Irene Liampa), ELIXIR Italy (Marco Tangaro, Manuela Helmer-Citterich), ELIXIR Czech (Martin Hubalek), ELIXIR Belgium (Frederik Coppens).

1/6/2019 - 31/5/2021

Learning paths

With the growing number of life-science training resources currently available through TeSS, it can often be a struggle to choose which may be the most relevant to learning needs or an appropriate match to existing skills and competency level.

Guidance is therefore needed to help users to identify which competencies they need to acquire, which training resources will allow them to acquire such competencies and which learning path they should follow in order to move from their existing competency level to a higher one.

Therefore, the aims of this implementation study are to: 1) identify competency frameworks that are relevant to the ELIXIR user community, in order to derive a set of core competencies and a curriculum for bioinformatics and data science, 2) map ELIXIR training resources to such competencies and expose this information through TeSS, and 3) build learning paths for selected use cases, and make them available in TeSS, to help guide users in moving from one competency level to another by following such learning paths.

The study is a joint effort of ELIXIR UK (Gabriella Rustici, Terri Attwood, Niall Beard), ELIXIR-NL (Celia Van Gelder), ELIXIR France (Victoria Dominguez del Angel), ELIXIR Luxemburg (Roland Krause), ELIXIR Estonia (Hedi Peterson), ELIXIR Switzerland (Patricia Palagi), EMBL-EBI (Cath Brooksbank, Sarah Morgan), ELIXIR Italy (Allegra Via), ELIXIR Finland (Eija Korpelainen), ELIXIR Belgium (Alexander Botzki).

The study will also interact with ELIXIR Industry (develop learning path(s) that specifically address the needs of industry users), global players in bioinformatics (BioExcel, CORBEL, BD2K, H3ABionet, GOBLET) and data-science (CODATA-RDA, EDISON, Software/Data Carpentry) training, and the Bioschemas project (improve the metadata that are exposed through the Bioschemas specifications for training materials).

1/6/2018 - 30/12/2019

Beacon and Beacon Network as a Service

This study builds on the Beacon-2016 and Beacon-2017 ELIXIR implementation studies. Current Beacon-2018 study aims to evolve the ELIXIR Beacons into a GA4GH Driver project with full alignment to GA4GH Technical Work Streams and consolidate and establish a fully costed process of “lighting a Beacon” for any ELIXIR node. Moreover, this study has the ambition to deliver Beacon/Beacon Network as an established ELIXIR infrastructure service. In addition to the goals above, improvements to the Beacon APIs and security will also be a core focus within this implementation study. A further priority for 2018 is to increase strategic partnering with national data owners to enable data flow to the Beacon service.

By end 2019, a Beacon Reference Implementation with an updated v2.0 that supports enhanced metadata response types and query interfaces will be available. The project will also develop and deploy the Beacon Network to address more (‘real world’) use cases. This will ensure that the Beacon, Registry and Network APIs evolve and expand to address clinical and clinical research user needs.

Ten ELIXIR nodes are involved in this study: Spain (Jordi Rambla), Finland (Ilkka Lappalainen, Tommi Nyrönen), Switzerland (Michael Baudis), EMBL-EBI (Dylan Spalding), Sweden (Niclas Jareborg), Belgium (Yves Moreau), France (Macha Nikolski), the Netherlands (Morris Swertz), Italy (David Horner), ELIXIR Hub (Serena Scollen, Susheel Varma).  

1/1/2018 - 31/12/2018

ELIXIR integration from a User perspective

The goal of this study is to provide the life-scientist a powerful tool to find and use ELIXIR resources - across the spectrum - based on intuitive graphical diagrams of the most prevalent scientific workflows.  

Currently, a scientist can use TeSS to find training events and materials and then, in a separate search, use bio.tools to find relevant tools, and BioSharing to find standards and databases. Linking TeSS and bio.tools to ELIXIR’s computer resources via common workflow diagrams would enable end-users to discover and learn about the prevalent bioinformatics workflows. This study will link TeSS and bio.tools via most prevalent bioinformatics workflows and will lay the foundation to incorporate other ELIXIR platforms in a later stage, thereby providing an even more useful service for the researcher.

Eight ELIXIR nodes are involved in this study: Belgium (Frederik Coppens, lead), UK (Terri Attwood), Estland (Hedi Peterson), Denmark (Jon Ison), Swiss (Heinz Stockinger), EMBL-EBI (Sarah Morgan), Norway (Matus Kalas), France (Hervé Menager).

1/10/2017 - 30/9/2018