Tools

To gain greater insights from life science data, scientists need software tools to access, study and compare the data. They need clear descriptions of the use, performance, and licensing of these tools, and they need to integrate the tools into robust scientific workflows.

The main objective of the ELIXIR Tools Platform is to improve the discovery, quality and sustainability of software resources.

Services offered

  • bio.tools: search the repository of software tools for life science.
  • Biocontainers: browse the list of software you can run on any operating system.
  • OpenEBench: browse tools for benchmarking and monitoring software.

What the Platform does

  • Helps life scientists find, deploy and benchmark software tools, including workflows.
  • Helps software providers and developers better describe and develop software tools and integrate them into workflows.

To achieve these goals the Platform is split into seven groups, each with their sub-goals:

1. Tools and services registry

Goal: To deliver bio.tools, a discovery portal for bioinformatics software information.

Leader: Jon Ison (ELIXIR Denmark)

Activities:

  • bio.tools: The group is developing bio.tools, a portal where you to search and access life science tools and services. It uses the EDAM ontology for precise tool descriptions, and the biotoolsSchema as a description model for the software. This makes it easier for people to find, understand and compare software tools.
  • ELIXIR integration from a user perspective (Implementation Study): bio.tools is working with the Training Platform to integrate bio.tools with TeSS, ELIXIR's training portal. This will enable people to discover software tools on bio.tools then easily find related courses on TeSS.

Get involved: Join the discussions and follow the progress of bio.tools on GitHub.

2. Scientific benchmark and technical monitoring

Goal: To provide an infrastructure to benchmark and monitor bioinformatics tools and services.

Leader: Salvador Capella-Gutierrez (ELIXIR Spain)

Activities:

  • OpenEbench: This is software that will provide guidance and software infrastructure for the benchmarking and technical monitoring of bioinformatics tools, web servers and workflows. The work is part of Work Package 2 of the ELIXIR-EXCELERATE project.
  • Working on a paper: 'Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking'. This will be published by the end of 2017.

3. Software deployment

Goal: To support community efforts on bioinformatics software deployment methods, in particular the BioContainers initiative.

Leader: Yasset Perez-Riverol (EMBL-EBI)

Activities:

4. Workflows and workbenches

Goal: Ensure the integration of the bio.tools registry with integrated environments (Galaxy, Taverna, etc).

Leader: Hervé Menager (ELIXIR France)

Activities:

  • Developing the link between discovery and execution so that you can easily locate bioinformatics tools provided as service by platforms like Galaxy.
  • Reusing the high quality meta data provided by bio.tools to guide the creation and maintenance of the workbench components (workbench enabler service).
  • Using the bio.tools, TeSS, and EDAM information to facilitate the navigation of available tools and services linked to reference bioinformatics analysis workflows.
  • See Ménager, Hervé et al. (2015) Using registries to integrate bioinformatics tools and services into workbench environments, In International Journal on Software Tools for Technology Transfer, 17,  p. 1-6. doi: 10.1007/s10009-015-0392-z 

5. Software development best practices

Goal: Implementation of agreed ELIXIR recommendations regarding Open Source Software principles.

Leader: Rafael Jimenez (ELIXIR Hub)

Activities:

  • Engaging with the bioinformatics community to facilitate the adoption of best-practices.

See also:

6. Tools interoperability

Goal: To engage service providers to define and work towards the adoption of best practices for tools and workflow description, standardised containment, and validation.

Leader: Josep Ll. Gelpi (ELIXIR Spain)

Activities:

  • Coordinate activities with the ELIXIR Interoperability Platform, by extending its use cases to the Tools Platform domain, including tools and workflows registration and annotation (bio.tools, EDAM).
  • Follow the coordination between the Tools Platform and FairSharing in relation to databases and use of standards.
  • Define an interoperability observatory in coordination with tools monitoring initiative.
Galaxy logo

7. Galaxy Working Group

Goal: To build an ELIXIR Galaxy community and contribute to the development of the Galaxy platform, to facilitate the integration and adoption of Galaxy by the ELIXIR Platforms, and to provide specific training for users, developers and system administrators.

Leaders: Frederik Coppens (ELIXIR Belgium), Björn Grüning (ELIXIR Germany)

Activities:

Leadership

Søren Brunak
Søren Brunak
(ELIXIR Denmark)
Platform Lead
Alfonso Valencia
Alfonso Valencia
(ELIXIR Spain)
Platform Lead
Salvador Capella
Salvador Capella
(ELIXIR Spain)
Platform Coordinator
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Jon Ison
(ELIXIR Denmark)
Platform Coordinator
Pascal Kahlem
Pascal Kahlem
(ELIXIR Hub)
Platform Coordinator

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