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.
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:
1. Tools and services registry
Goal: To deliver bio.tools, a discovery portal for bioinformatics software information.
Leader: Jon Ison (ELIXIR Denmark)
- 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)
- 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)
- BioContainers: The group is working with the bioinformatics community to develop BioContainers. Biocontainers allow you to bundle up software into a 'container'. Containers make it easy to share bioinformatics analysis and training software, and make it easier to collaborate with others in developing the software. You are welcome to browse the list of containers, follow discussions on the Biocontainers Gitter, and contribute on Github.
- Collaborating with and supporting other related efforts like BioConda, and is aiming to do the same with other ELIXIR-related efforts like BioShadock.
- Architecture for Software Containers at ELIXIR and its use by EXCELERATE Use Case Communities: an Implementation Study with the goal of providing a stable infrastructure for unifying software containers solutions within ELIXIR.
- See also the webinar on Bioconda and Biocontainers (March 2017).
4. Workflows and workbenches
Goal: Ensure the integration of the bio.tools registry with integrated environments (Galaxy, Taverna, etc).
Leader: Hervé Menager (ELIXIR France)
- 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)
- Engaging with the bioinformatics community to facilitate the adoption of best-practices.
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)
- 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.
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)
- See the Galaxy Community page.
The Tools Platform is involved in a number of short-term, technical projects called Commissioned Services. These are currently:
- Packaging, containerisation and deployment
- Performance benchmarking and technical monitoring
- Registry of bioinformatics tool information and identifiers
- Software Best Practices
- Reuse, extension, scaling of scientific workflows
- Data Validation
- Metabolite Identification
For completed studies see the Commissioned Services page.
Find out more
- Contact tools-exco[at]elixir-europe[dot]org if you'd like to know more about the Platform's work.
- The Platform is involved in outreach through workshops and international conferences. See 'Related events' below or the Events section for upcoming events.
- View the list of Tools services offered by ELIXIR Nodes.
- Integrating ELIXIR Italy into ELIXIR activities: an Implementation Study the Tools Platform is involved in, which aims to reinforce collaboration between ELIXIR Italy and the rest of ELIXIR.
- Doppelt-Azeroual, O., Mareuil, F., Deveaud, Kalaš, M., Soranzo, N., van den Beek, M., Grüning, B., Ison, J. and Ménager, H. (2017). ReGaTE: Registration of Galaxy Tools in Elixir GigaScience, doi:10.1093/gigascience/gix022