The Tools Platform helps communities find, register and benchmark software tools. These tools help researchers access, analyse and integrate biological data, and so drive scientific discovery across the life sciences.
We maintain information standards for these tools, and produce, adopt and promote best practices for their development. We also:
- connect tools and data services
- link tools to training materials
- make it easy to download, deploy, and benchmark tools for performance
- put tools in the context of the common workflows in bioinformatics, including container technologies and Galaxy.
We are integrating and cross-linking the core products of the Platform (bio.tools, BioContainers and OpenEBench) to other ELIXIR resources, such as the training resource TeSS.
tools
tools
tools
tools
workflows
Services offered
- bio.tools: search the registry of software tools and data resources for life sciences.
- BioContainers: browse the list of software you can run on any operating system.
- OpenEBench: browse tools for benchmarking and monitoring software.
- UseGalaxy.eu: analyse your data with more than 2500 tools, visualisations and 200 reference genomes.
- Workflowhub.eu: a registry for describing, sharing and publishing scientific computational workflows.
How the Platform is organised
The Platform's work during 2024-2026 is split into five Work Packages (WPs):
WP1: Platform management and coordination
Goal: To provide the project management and coordination of the Tools Platform.
Activities:
- Setting up regular Platform meetings, both online and face-to-face.
- Monitoring and reporting the Platform's progress.
- Ensuring bi-directional communication about the Platform activities with other ELIXIR Platforms and Communities.
- Representing the Platform in EOSC, EuroHPC and the ELIXIR::GA4GH strategic partnership.
- Disseminating the activities of the Tools Platform.
Leads: Salva Capella-Gutierrez (BSC, Spain), Björn Grüning (University of Freiburg, Germany), Hervé Ménager (Institut Pasteur, France)
WP2: The ELIXIR Research Software Ecosystem (RSEc)
Goal: To further develop the ELIXIR Research Software Ecosystem (RSEc) to enable the federated access and curation of research software reference metadata.
Activities:
- Designing a software metadata editor for the ecosystem.
- Defining the next generation of the bio.tools search UI and backend.
- Engaging with publishers, funders and international organisations (e.g. EOSC and RDA) to promote good practices in publishing software metadata.
- Expanding our efforts beyond traditional scientific software to include machine learning models.
Leads: Hervé Ménager (Institut Pasteur, France), Magnus Palmblad (Leiden University Medical Center, Netherlands), Veit Schwämmle (University of Southern Denmark, Denmark), Radka Svobodová, Adrián Rošinec, Tomáš Raček (Masaryk University, Czech Republic)
WP3: Software management, stewardship and standards
Goal: To develop and promote guidelines, standards, and knowledge sharing to make research software FAIR.
Activities
- Developing best practices in research software building, including Machine Learning and web applications.
- Refining the current metadata schemas for machine-actionable Software Management Plans (SMPs).
- Aligning existing indicators for research software quality to services, tools and frameworks within the Tools Platform ecosystem.
- Continuing to expand the TeSS collection of training courses, learning pathways and training materials about software development best practices.
- Promoting the use of the EDAM ontology across ELIXIR Communities ELIXIR services, and ensuring it meets their needs.
Leads: Matúš Kalaš (University of Bergen, Norway), Eva Martin del Pico (BSC, Spain)
WP4: Defining a roadmap towards reproducible and distributed analysis using benchmarking
Goal: To promote scientific benchmarking efforts driven by research communities, and enable the distribution and deployment of software across heterogeneous computational systems.
Activities
- Defining standards for benchmarking datasets across emerging communities.
- Facilitating benchmarking through containerisation.
Leads: Mateo Boudet (IRISA, France), Pier Luigi Martelli (University of Bologna, Italy)
WP5: Democratised access to reusable complex workflows
Goal: To improve the reproducibility of scientific analysis workflows and the recognition of relevant service providers and researchers.
Activities
- Promoting best practices for workflows, and the contribution of FAIR workflows into WorkflowHub.
- Assessing the environmental impact of Galaxy and bioinformatics, and increasing the awareness of the environmental impact of research.
- Optimising the flexible upscaling of FAIR workflows.
Leads: Rafael Andrade Buono (VIB, Belgium), Stian Soiland-Reyes (University of Manchester, UK), Nicola Soranzo (Earlham Institute, UK), Björn Grüning (University of Freiburg, Germany)
Commissioned Services
The Compute Platform has also completed a number of short-term projects called Commissioned Services. For details of these projects, see the Commissioned Services page.
Leadership
(ELIXIR Spain)
Platform Lead
(ELIXIR Germany)
Platform Lead
(ELIXIR France)
Platform Lead
(ELIXIR Hub)
Platform Coordinator
Mihail Anton
(ELIXIR Hub)
Platform Liaison
Find out more
- Contact tools-exco@elixir-europe.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.
- Ison J, Ienasescu H, Chmura P, et al. The bio.tools registry of software tools and data resources for the life sciences. Genome Biol. 2019;20(1):164. Published 2019 Aug 12. doi:10.1186/s13059-019-1772-6
- Altenhoff AM, Garrayo-Ventas J, Cosentino S, et al. The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 2020;48(W1):W538-W545. doi:10.1093/nar/gkaa308