Research efficiency services

Name Description ELIXIR Node
ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Estonia, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Spain
ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR France, ELIXIR Germany, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI

This study aims to coordinate the provision and operation of a standards-compliant container orchestration platform. This will allow execution of containerised software tools and workflow workloads supporting public and sensitive data across ELIXIR Nodes. The study will enable containers to be deployed and operated at scale and across cloud systems through the container orchestration platform in standardised formats which will:

  • Focus on developing a standards (e.g. GA4GH) compliant, interoperable container orchestration platform
  • Comprise scientific software and workflows from ELIXIR Tools platform ecosystem e.g. Bio.tools, Biocontainers, and OpenEBench
  • Connect with existing relevant ELIXIR communities e.g. HGTD, Proteomics, Marine, Galaxy
  • Provide an easy-to-use and transparent way of automating service deployment, orchestration, and configuration through the platform that can support the ELIXIR use cases and communities.

This Task coordinates ELIXIR Compute Platform’s (ECP) expertise and resources to leverage the technology development in other funded projects in order to provide high-level, community-driven orchestration of containers across ELIXIR Nodes. This will allow standardised, containerised and community-driven software applications to be hosted on ELIXIR Nodes and ELIXIR cloud infrastructures. The target is to provide a high-level abstraction layer to the underlying integrated technological components provided by Tasks 1, 2 and 3.

WP4.1: Coordinate an ELIXIR container platform to allow execution of containerised software workflow loads developed with the ELIXIR Tools platform ecosystem

Lead: Susheel Varma (EMBL-EBI)

This task will coordinate the provision of a standards compatible platform that can be offered to users to execute and manage the lifecycle of their containers on cloud platforms. These will be made available from ELIXIR Nodes and later on European e-Infrastructures. This platform will be offered to end-users (application developers in this example) through standards compliant APIs deployed in front of the individual cloud providers.

WP4.2: Access to sensitive datasets with containers

Lead: Shubham Kapoor (ELIXIR FI)

This task will provide analysis pipelines as a service using containers that are able to process sensitive data using the ELIXIR security guidelines.

 EMBL-EBI, ELIXIR Finland, ELIXIR Switzerland, ELIXIR Luxembourg, ELIXIR Czech Republic, ELIXIR Italy, ELIXIR UK, ELIXIR Sweden, ELIXIR Germany, ELIXIR Belgium, ELIXIR France, ELIXIR Denmark, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia
ELIXIR Belgium, ELIXIR Czech Republic, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Netherlands, ELIXIR Spain, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Belgium
ELIXIR Belgium, ELIXIR Cyprus, ELIXIR Czech Republic, ELIXIR Denmark, ELIXIR Finland, ELIXIR France, ELIXIR Germany, ELIXIR Greece, ELIXIR Hungary, ELIXIR Israel, ELIXIR Italy, ELIXIR Netherlands, ELIXIR Norway, ELIXIR Portugal, ELIXIR Slovenia, ELIXIR Spain, ELIXIR Sweden, ELIXIR Switzerland, ELIXIR UK, EMBL-EBI
ELIXIR Netherlands
ELIXIR Norway
ELIXIR Belgium, ELIXIR Germany, ELIXIR Luxembourg, ELIXIR Netherlands, ELIXIR Portugal, ELIXIR Spain, ELIXIR Sweden, ELIXIR UK
EMBL-EBI
ELIXIR Finland
ELIXIR Spain
ELIXIR UK
ELIXIR UK
ELIXIR UK
ELIXIR Czech Republic, ELIXIR Finland, ELIXIR Hungary
EMBL-EBI
ELIXIR Switzerland
ELIXIR France
ELIXIR Germany
EMBL-EBI
ELIXIR Belgium, ELIXIR Germany
ELIXIR Belgium, ELIXIR Norway, ELIXIR Portugal
ELIXIR Finland, ELIXIR Germany, ELIXIR Norway, ELIXIR Spain, ELIXIR Sweden
ELIXIR Spain

This Implementation Study will allow the newly created Single-Cell Omics Community to tackle some of the main challenges identified and achieve the Community's short-term goals described in the white paper.

SCONE will address the need for scalable training by training more trainers and by providing easy access to up-to-date training resources, including lecture videos.

Efficient benchmarking of analysis tools will be achieved by providing curated benchmarking datasets. To effectively address shortfalls in current data/metadata standard paradigms, SCONE will monitor emerging technologies and organise workshops on standard and FAIR data management practices in use across the entire single-cell omics community, with involvement of key stakeholders including those providing standards, tools and data hosting solutions.

The ELIXIR Compute Platform will be kept up to date with the computing requirements of SCO researchers by active information exchange including a workshop.

Events and news

 ELIXIR Finland, ELIXIR Sweden, ELIXIR Germany, ELIXIR Italy, ELIXIR Switzerland, EMBL-EBI, ELIXIR Slovenia, ELIXIR Netherlands, ELIXIR UK, ELIXIR Belgium, ELIXIR Greece, ELIXIR Portugal, ELIXIR Ireland, ELIXIR Israel, ELIXIR Norway, ELIXIR Spain, ELIXIR France, ELIXIR Czech Republic, ELIXIR Luxembourg

This Implementation Study will allow the newly created Single-Cell Omics Community to tackle some of the main challenges identified and achieve the Community's short-term goals described in the white paper.

SCONE will address the need for scalable training by training more trainers and by providing easy access to up-to-date training resources, including lecture videos.

Efficient benchmarking of analysis tools will be achieved by providing curated benchmarking datasets. To effectively address shortfalls in current data/metadata standard paradigms, SCONE will monitor emerging technologies and organise workshops on standard and FAIR data management practices in use across the entire single-cell omics community, with involvement of key stakeholders including those providing standards, tools and data hosting solutions.

The ELIXIR Compute Platform will be kept up to date with the computing requirements of SCO researchers by active information exchange including a workshop.

Events and news

 ELIXIR Finland, ELIXIR Sweden, ELIXIR Germany, ELIXIR Italy, ELIXIR Switzerland, EMBL-EBI, ELIXIR Slovenia, ELIXIR Netherlands, ELIXIR UK, ELIXIR Belgium, ELIXIR Greece, ELIXIR Portugal, ELIXIR Ireland, ELIXIR Israel, ELIXIR Norway, ELIXIR Spain, ELIXIR France, ELIXIR Czech Republic, ELIXIR Luxembourg
ELIXIR Switzerland
ELIXIR Switzerland
ELIXIR Czech Republic, ELIXIR Netherlands