WP1: Tools Interoperability and Service Registry

WP leaders: Søren Brunak (DK) and Alfonso Valencia (ES)

The cornerstone of the platform is the ELIXIR Tools and Data Services Registry, a discovery portal for a wide range of key bioinformatics resources. 

The registry is curated through a series of community-driven hackathons, knowledge exchange workshops and cross-domain strategy workshops.

All activities, including intensive user support and community benchmarking, are focused on delivering impact for end-users across academia, health organisations, and industry.

WP2: Benchmarking

WP leaders: Alfonso Valencia (ES) and Søren Brunak (DK)

The focus of the Benchmarking work package is on assessing bioinformatics methods in terms of quantitative performance and user friendliness. The partners at the participating Nodes will:

  • Organise and support relations to biology and medicine communities already running benchmarking exercises
  • Develop and maintain a generic infrastructure for benchmarking exercises in different subareas
  • Develop the technology to perform online, uninterrupted methods assessment in key areas of bioinformatics
  • Develop and implement data warehouse infrastructures to store benchmarking results and make them accessible to developers for subsequent transfer to the ELIXIR registry
  • Develop the procedures to create standards for benchmarking in different areas
  • Organise workshops, hackathons and jamborees for different user communities


ELIXIR-SI Resource Hackathon

ELIXIR-SI Resource Hackathon took place in Ljubljana, Slovenia on 8 April 2016 at the University of Ljubljana, Faculty of Computer and Information Science. A half-day event was aimed at the member of the Slovenian ELIXIR node to add their resources to the ELIXIR Tools & Data Service Registry (https://bio.tools) and to create a national catalogue of life science tools and data services. The hackathon participants added six tools to the Registry immediately at the hackathon, additional 19 resources were identified and will be registered in the near future. Read more on the ELIXIR SI website.

Second ELIXIR Resource Hackathon : DebianMed

The second in the series of “ELIXIR Resource Hackathon” brought together 16 developers from bio.tools, EDAM, Debian Med, Common Workflow Language, and the Global Microbial Identifiers initiative. The group focused on integration of bio.tools with Debian Med; a group dedicated to maintaining software packages of medical and biological interest within the larger volunteer framework that is the Debian Linux distribution.

Delegates enjoyed four days of hacking and curation, laying the ground for tagging of Debian packages using EDAM and sharing content with bio.tools. The workshop also outlined a tentative technical architecture for benchmarking the scientific performance of tools, involving a broad collaboration of community and infrastructure projects. The delegates thank the organisers for their support, and look forward to future events!

de.NBI - ELIXIR Codefest in Freiburg

The Tool platform organised a workshop on 19-20 January 2016 in collaboration with the German Network for Bioinformatics Infrastructure (de,NBI). Hosted by the Robert Bosch College in Freiburg, Germany, the event brought together 27 scientists and developers from de.NBI Service Centers, the Danish, French and Norwegian ELIXIR nodes, and the EDAM ontology.

Full with discussions, hacking and curation, the two days workshop centered around description of German services and use of the bio.tools registry.

In a cooperative atmosphere, the delegates registered their services with support from the bio.tools experts. There was a vivid exchange of ideas on how to further enhance the functions and usability of the registry, the bio.tools software schema, EDAM, and the ReGaTE tool for registration of Galaxy instances.

The technical leads - Björn Grüning and Jon Ison - would like to thank all the participants for their hard work and open approach, and look forward to more de.NBI / ELIXIR events in the future.

Read more on the de.NBI website