ELIXIR Implementation Study

Making container services integratable, sustainable and widely used

The aim of this new strategic implementation study (SIS) is to build on the current progress made through the ongoing implementation study, enabling the adoption and deployment of protocols and services by the broader ELIXIR community at scale.

The first SIS Containers study (2019-2021) has successfully convened and established a growing ELIXIR wide consensus on high-level community-driven service needs and related standards including:

  • Software containers registry service (Biocontainers, GA4GH TRS )
  • WorkflowHub registry service (GA4GH TRS)
  • Key Preferred workflows management systems (Galaxy, GA4GH WES).
  • Task orchestration services (e.g. the Pulsar Network, GA4GH TES) 
  • Data repository service (GA4GH DRS)

The ongoing study also engaged with 5 communities/use cases to ensure the standards being developed were able to be adopted by the different use cases and highlight potential bottlenecks and risks to adoption. Hence as stated, the aim of this new study is to build on the current progress and ensure adoption and deployment of these protocols and services by the broader ELIXIR community at scale and to establish plans for sustainability.

The work is divided across four work-packages:

  •  WP1 focuses on fostering community and user engagement across ELIXIR through the initiation of two open-calls for self-funded use-cases. 
  • WP2 focuses on support for users from ELIXIR Communities and Focus Groups by organising documentation of supported ELIXIR services so aiding in the identification and application of use cases. 
  • WP3 focuses on technical support for providers to roll out production services in alignment with ELIXIR and EOSC standards. 
  • WP4 will specifically address the services which will be needed to ensure the sustainability of the service portfolio assembled in this study.

The present study is participated in by thirteen ELIXIR Nodes: ELIXIR Belgium (Frederik Coppens, Ignacio Eguinoa, Bert Droesbeke), ELIXIR Switzerland, ELIXIR Czech, ELIXIR Germany, ELIXIR Denmark, EMBL-EBI, ELIXIR Spain, ELIXIR Italy, ELIXIR Finland, ELIXIR France, ELIXIR Greece, ELIXIR The Netherlands, and ELIXIR UK.


1/6/2021 - 31/5/2023

Infrastructure Service roadmap: Tools Platform Ecosystem

The ELIXIR Tools Platform Ecosystem, initiated by the ELIXIR Tools Platform, is a diverse and open initiative focused on the metadata exchange across registries and repositories. Its goal is to facilitate coordination among them, enhance interoperability, reduce mismatching information, promote good practices for resources enabling community curation and contribute towards the sustainability of each of its components over time. Hence, this project seeks to sustain and support this “Ecosystem” through three complimentary work packages:

  • WP1 - Governance model, community engagement, and project management: aims to act as a proxy for the different processes to facilitate the formal engagement of services and platforms, as well as foster community engagement through the adoption of community-agreed standards to enhance sustainability over time.
  • WP2 - Development of the Tools Ecosystem: further automate and consolidate the emerging Tools Ecosystem infrastructure. 
  • WP3 - Inclusion of new services in the Ecosystem: handle the inclusion of external resources (e.g. Galaxy, Bioconda, GitHub) and demonstrate the added value of this infrastructure.

This study features the participation of the ELIXIR Hub and ten ELIXIR Nodes: ELIXIR France, ELIXIR Norway, ELIXIR Germany, ELIXIR Denmark, ELIXIR Spain, EMBL-EBI, ELIXIR UK, ELIXIR Belgium (Frederik Coppens), ELIXIR Estonia, ELIXIR Italy.


1/6/2021 - 31/12/2023

Impact evaluation at Node-level - getting it done

Building on the knowledge and experience gained during the piloting of the RI-PATHS approach, an ELIXIR-funded Staff Exchange project, and related work done elsewhere in ELIXIR, this project aims to increase capacity in impact evaluation across a set of national ELIXIR Nodes.

With support from the ELIXIR Hub, activities will be undertaken in coordination with relevant work being done as part of the ELIXIR-CONVERGE project, and will include a specialised training event with hands-on learning complemented by knowledge-exchange. The application of the new skills and knowledge will be implemented by the Nodes themselves, focused on their chosen case studies. A case study is an activity or set of activities, carried out or planned by a Node, and whose impact will be evaluated during the project.

Results of the case studies will be disseminated so that lessons-learned and associated good practices benefit more widely across ELIXIR, and beyond. The main intended outcome from this project is an increased capacity at Node level to demonstrate and communicate its public value to funders and other key stakeholders, thereby contributing to long-term sustainability of Node-led activities. In parallel to this, it is anticipated that this project will work to reinforce the ‘community of practice’ that is emerging, across ELIXIR, around impact evaluation. To achieve these objectives, the project features three work packages:

  • WP1: Gaining new knowledge and skills through training and knowledge-exchange
  • WP2: Undertaking performance and impact evaluation at Node-level
  • WP3: Dissemination of case study results, good practices and lessons-learned

The project is a joint venture participated in by the ELIXIR Hub and fifteen ELIXIR Nodes: ELIXIR Portugal, ELIXIR Norway, ELIXIR Belgium (Kim De Ruyck), ELIXIR Italy, ELIXIR Greece, ELIXIR The Netherlands, ELIXIR Switzerland, ELIXIR UK, ELIXIR France, ELIXIR Czech, ELIXIR Finland, EMBL-EBI, ELIXIR Spain, ELIXIR Israel, and ELIXIR Germany.


1/6/2021 - 31/5/2023

Building on PDBe-KB to chart and characterize the conformational landscape of native proteins

This implementation study will create infrastructure to chart the experimentally sampled conformational diversity of native proteins by exploiting data from the PDB, augmented with results of state-of-the-art computational tools. By integrating resources and tools, workflows will be developed to:

  • compare and cluster different conformations adopted by homologs of the same protein and
  • identify protein regions with different flexibility properties. 

Pipelines will be created to characterize conformational ensembles in terms of:

  • the types of motions described (thermal fluctuations; collective motions) and
  • their functional relevance, using sequence information and functional annotations.

These data will be integrated into the PDBe Knowledge Base and presented in the aggregated views (PDBe is an ELIXIR-Core-Data-Resource), which are freely available to the scientific community. Applications of these new capabilities will be explored in a joint gap analysis with the IDP and Proteomics Communities, including joint meetings, in order to identify future implementations that best serve ELIXIR goals.

This study features the participation of nine ELIXIR Nodes: ELIXIR Norway, ELIXIR France, ELIXIR Spain, ELIXIR UK, EMBL-EBI, ELIXIR Belgium (Wim Vranken, Shoshana Wodak), ELIXIR Denmark, ELIXIR Hungary, and ELIXIR Italy.

 


1/6/2021 - 31/5/2023

Improving IDP tools interoperability and integration into ELIXIR

The increasingly well-documented role of intrinsic disorder in protein behavior and function requires infrastructure improvements to enable enhanced researcher access to related tools and data. A key existing infrastructure is MobiDB, which provides sequence-based predictions for the entire set of UniProtKB proteins from a number of different prediction tools. In addition, current prediction competitions involving disorder are CAID, for pinpointing the regions of proteins likely to be disordered, and a subcompetition of CAFA, where the predicted function of disorder in proteins is assessed. The current project connects and consolidates these infrastructures and investigates how they can best connect to other ELIXIR communities, by addressing the following points across four work packages:

  • Improved accessibility for tools that define where disorder is likely to appear in proteins (WP1).
  • Better integration of disorder with CAFA, including protein region definitions, so improving the connection between function and disorder (WP2).
  • Exploration of emerging disorder definitions and data for future prediction challenges (WP3).
  • A gap analysis study to connect to tools and data from the 3D-Bioinfo and Proteomics communities (WP4).

This study includes participation of the Galaxy community and the Interoperability, Tools and Training platforms, with participation from seven ELIXIR Nodes: ELIXIR Italy, ELIXIR Belgium (Wim Vranken, Lennart Martens, Shoshana Wodak, Frederik Coppens), ELIXIR Hungary, ELIXIR Spain, ELIXIR Greece, ELIXIR Germany.


1/6/2021 - 31/5/2023

Increasing the translational value of public proteomics datasets: Automatic metadata-driven reanalysis in cloud infrastructures

Following previous work by the ELIXIR Proteomics Community, PRIDE public proteomics datasets, as well as some open proteomics data analysis pipelines are starting to become available.This follow-on ELIXIR implementation study will use previous results as the base to develop a set of open and user-friendly analysis pipelines, which will be applied to  assess the possibilities for performing  more automated re-analyses using the metadata SDRF-encoded annotations of public datasets. Additionally, common ideas in this context and in others overlapping topics of interest will be explored e.g. in a joint gap analysis performed between the ELIXIR Proteomics and the Intrinsically Disordered Proteins (IDP) and 3D-BioInfo ELIXIR Communities, to further serve the overall ELIXIR goals.

This study therefore intends to provide a use case, which will motivate users to perform SDRF-annotations of public datasets. By developing and providing the community with data processing and analysis pipelines as well as by helping to standardise data management and annotation, two goals of the proteomics community will be addressed through the studies four work packages:

  • WP1: Metadata provision and processing
  • WP2: Workflow adaptation and development
  • WP3: Automating workflows for cloud environments
  • WP4: Intercommunity ‘gap analysis’ between the IDP, 3D-Bioinfo and  Proteomics Communities

This is a joint study between EMBL-EBI, ELIXIR Denmark, ELIXIR Belgium (Lennart Martens), ELIXIR Czech, ELIXIR Germany, ELIXIR France, ELIXIR Finland, ELIXIR Hungary, ELIXIR Italy, ELIXIR The Netherlands, and ELIXIR Sweden.


1/6/2021 - 31/5/2023

Strengthen data management in Galaxy

This project focuses on the enhancement of Galaxy's data management features to provide additional provenance information and improve the integration of Galaxy in the existing data management ecosystem. Existing technologies and services in ELIXIR will be supported and ongoing international projects (ELIXIR-CONVERGE, the COVID-19 Data Portal, EOSC-Life, etc.) will be complemented while building on national initiatives (German NFDI, ELIXIR Belgium strategy, UK BioFAIR, etc.).

The project objectives include: making the Galaxy Data Libraries more scalable; further improvement of the reusability features of the platform by metadata enrichment; and extending the Galaxy metadata system to enable the export of analysis records together with their provenance to relevant ELIXIR Core Data Resources and registries (e.g. WorkflowHub). A strong emphasis will be on the integration of EGA, FAIRtracks, and the GA4GH Beacon network into Galaxy to support analyses of human sensitive data.

Through the improvement of these data management features, this study aims to tackle concrete current worldwide needs, like the ones related to COVID-19 (meta-)analyses.

This study is a joint effort of ELIXIR Belgium (Frederik Coppens, Ignacio Eguinoa), ELIXIR Switzerland, ELIXIR Czech, ELIXIR Germany, ELIXIR Spain, ELIXIR France, ELIXIR Israel, ELIXIR Italy, ELIXIR The Netherlands, ELIXIR Norway, ELIXIR Slovenia, and ELIXIR UK.


1/6/2021 - 31/5/2023

Increasing Plant data findability and reuse beyond ELIXIR

Though the Plant Sciences Community has already implemented some critical elements of its roadmap, the project plan for this community implementation study features three key objectives, with each objective addressed in a corresponding work package:

  • Firstly, the promotion and finalizing of plant services and tools through ELIXIR service bundles. The first work-package of the study aims at increasing practicability of tools dedicated to studies in plant sciences and promoting their outreach. 
  • Secondly, the specification of a European Plant Data Portal that brings together all aggregation and deposition databases related to plants thereby ensuring FAIR data findability and reuse (WP2).
  • Lastly, the improvement of tools for services bundles and submission pipelines (WP3). Gathering and formatting of data and metadata increasingly relies on community driven tools such as FAIRDOM/Seek, COPO and ISA-Tools. Through aligned validation profiles and API use, their interoperability will be improved thereby easing submission to ELIXIR Databases and exchange across tools or repositories.

Ten ELIXIR Nodes are involved in this study: ELIXIR France, ELIXIR Belgium (Frederik Coppens, Flora D’Anna, Bert Droesbeke, Michiel Van Bel), ELIXIR Germany, ELIXIR France, ELIXIR Greece, ELIXIR Italy, ELIXIR The Netherlands, ELIXIR Portugal, ELIXIR Slovenia, and ELIXIR UK. 


1/6/2021 - 31/5/2023

Standardizing Intrinsically Disordered Proteins (IDPs) data

With intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) now recognised as major determinants in cellular regulation, the ELIXIR IDP community white paper presents a roadmap for e-infrastructure developments in the field of IDP research within the ELIXIR framework.

The goal of these developments is to drive the creation of tools and resources to support the characterisation of IDPs. The roadmap is the result of a workshop titled “An intrinsically disordered protein user community proposal for ELIXIR” held at the University of Padua. This workshop, and further consultation with the members of the wider IDP community, identified the key priority areas including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software.

This implementation study will focus on two identified priority areas for the ELIXIR IDP community: the development of formats for standardised data transfer and the creation of a central hub for data dissemination. These advances will simplify access to the output of IDP research and facilitate the integration of IDP data into the ELIXIR Core Data Resources.

These desired outcomes are set to be achieved through the implementation of four work packages:

  • WP1 - IDPcentral implementation: consolidate IDP resources through a single portal to improve accessibility for the wider biological community.
  • WP2 - Standards and interoperability: concentrates on completing the Minimum Information About Disorder Experiments (MIADE) standard, the HUPO-PSI intrinsic disorder (HUPO-PSI-ID) TAB format and the HUPO-PSI-ID XML interchange format and integrating the controlled vocabularies developed in WP3.
  • WP3 - Curation quality control: improve the efficiency and accuracy of curation, and the quality of the IDP ontology (IDPO).
  • WP4 - Training and dissemination: communicate the progress and output of the study through participation at the 2021 ELIXIR BioHackathon and organising a strategic workshop focused on IDPcentral, the IDP ontology and MIADE. Training material for the wider biological communities describing the best practices for IDP analyses will be developed and additional training capacity will be built. 

The implementation study is a collaboration between EMBL-EBI, EMBL Heidelberg, ELIXIR Italy, ELIXIR Hungary, ELIXIR Belgium (Wim Vranken), ELIXIR Germany, ELIXIR Czech, ELIXIR Spain, and ELIXIR Switzerland.


1/1/2021 - 31/12/2022

3D-Bioinfo Community Implementation study

The structural Bioinformatics Community (3D-BioInfo) has the mission to better integrate protein structure-based data and tools across Europe, and to improve standardisation through better ontologies and agreed benchmarking. The ties with the structural biology research communities in Europe will be strengthened and dedicated training and outreach efforts will be taken. Four major topics form the basis of this study:

  • WP1: Infrastructure for FAIR structural and functional annotations
  • WP2: Standards and workflows for annotating and characterising biologically meaningful 3D structures of macromolecular assemblies
  • WP3: Biomacromolecule-ligand interactions
  • WP4: Tools to build and analyse Nucleic Acid structures: interoperability and FAIR data

Fourteen ELIXIR Nodes are involved in this study: ELIXIR UK, ELIXIR Czech, EMBL-EBI, ELIXIR Belgium (Shoshana Wodak, Wim Vranken), ELIXIR Swiss, ELIXIR Spain, ELIXIR the Netherlands, ELIXIR France, ELIXIR Israel, ELIXIR Germany, ELIXIR Denmark, ELIXIR Italy, ELIXIR Sweden, and ELIXIR Slovenia.


1/6/2020 - 31/5/2022