eScience Lab

University of Manchester to lead BioFAIR's first national Methods Commons

Thu, 02 Jul 2026 09:00:00 +0000

The University of Manchester will play a leading role in delivering new national infrastructure for UK life sciences.

The University and the Earlham Institute have been appointed by BioFAIR to lead a new consortium to establish the Methods Commons, the first spoke of the £34 million BioFAIR programme.

The Methods Commons will provide researchers with national-scale capabilities for the discovery, execution, sharing and reuse of the computational workflows, tools and notebooks that underpin modern data-driven life sciences.

Led by Professor Carole Goble at The University of Manchester, the consortium will develop services designed to improve the reproducibility, reliability and reuse of computational methods across UK bioscience.

The Methods Commons will deliver eight core capabilities for UK life sciences researchers, including Galaxy and Nextflow workflow execution, support for containerised bespoke workflows on HPC, a national workflow registry with a community-endorsement mechanism, a “workflow observatory” providing trust and quality assurance, a shared Jupyter notebook environment, and API standards for ingesting input data and sharing workflow results.

Tony Burdett, BioFAIR Director, said: “The Methods Commons tackles one of the longest-standing problems in computational bioscience — reproducibility and reuse of methods that produce the results to be included in publications as research outputs. We had a strong field of applicants, and the appointed consortium combines real delivery track record with deep roots in the UK and international workflow communities. Establishing the Methods Commons is a major milestone for BioFAIR as it’s the first spoke in our federated BioCommons and the point at which the services needed by our users really start to take shape.”

The consortium — which includes support from Nextflow, Seqera — was selected following a competitive two-stage process that opened with an Expression of Interest call in December 2025, followed by invited full proposals reviewed by an independent expert panel. BioFAIR is investing up to £4 million over an initial two-year period, with the expectation that the partnership will extend to deliver the full programme of work through to June 2029 and beyond.

Carole Goble, Methods Commons Project Lead, said: “We’re proud to be establishing the Methods Commons as part of BioFAIR. Computational workflows are how modern bioscience gets done, and giving UK researchers a trusted, national-scale set of services to find, run and share them — without having to reinvent the plumbing each time — is overdue. We’re looking forward to working with the BioFAIR Hub, the Fellows and Pathfinder Projects to make sure what we build is shaped by real user needs from day one.”

The Methods Commons will adopt an incremental, user-driven delivery model, with early value delivered to exemplar communities — including the first cohort of BioFAIR Pathfinder Projects — before scaling to national reach. It will operate alongside the forthcoming Data Commons, People Commons, Knowledge Hub and BioFAIR Portal in a hub-and-spokes federated infrastructure coordinated from the BioFAIR Hub at the Earlham Institute.

Image: Digital Molecular Structure Concept. credit BlackJack3D

ELIXIR community gathers in Lyon for All Hands 2026

Mon, 22 Jun 2026 09:00:00 +0000

The twelfth annual gathering of the ELIXIR community was hosted by ELIXIR France at the Lyon Convention Centre on the banks of the Rhone. Between 8–10 June, ELIXIR All Hands 2026 brought together more than 380 in-person attendees and over 60 online participants, including several international guests.

Across three days, participants came together to share progress, discuss challenges and look ahead to the second half of the current Programme. Sessions reflected the breadth of ELIXIR’s work across life science data, from sensitive and high-value datasets to biodiversity, human data, training, tools and infrastructure services.

Highlights of major contributions from the eScience Lab

The second day opened with a plenary, chaired by ELIXIR-UK Joint Head of Node, Carole Goble, about infrastructure enabling science. This first session invited perspectives from across European research spanning a number of key initiatives including BioFAIR, with a presentation titled “Establishing a national Bioscience Commons - applying old lessons and learning new ones”.
Several workshops and mini syposia were delivered and coordinated in part by Munazah Andrabi, Nick Juty, Phil Reed and Shoaib Sufi, spanning important community topics including FAIR assessment, data stewardship, interoperability, and training.
Seven posters were presented, including:

eScience Lab presents at ISCB-UK 2026 in Cambridge, UK

Fri, 24 Apr 2026 16:33:00 +0000

The first ISCB-UK 2026 conference (International Society for Computational Biology UK) was hosted at the University of Cambridge, UK on 21-22 April 2026. The UK has a large diverse bioinformatics and computational community; the meeting brought this community together to share cutting-edge science, foster collaborations, and build networks.

eScience Lab members Munazah Andrabi and Phil Reed presented the following talks and posters:

FAIRDOM-SEEK
- Platform for FAIR data and research asset management
- fairdomseek.org
RDMkit
- Research Data Management Toolkit for Life Scientists
- rdmkit.elixir-europe.org
RO-Crate
- Capturing FAIR research outputs in bioinformatics and beyond
- researchobject.org/ro-crate
mTeSS-X
- A federated, FAIR-aligned platform for distributed management and exchange of training resources
- elixirtess.github.io/mTeSS-X
RSQKit
- Research Software Quality Toolkit (RSQKit) lists curated best practices, tools and resources for improving the quality of research software
- everse.software/RSQKit
Bioschemas
- Applications of Bioschemas in FAIR, AI and knowledge representation
- bioschemas.org
WorkflowHub
- A FAIR registry for workflows
- workflowhub.org

See all the eScience Lab ISCB-UK 2026 posters and presentations on Zenodo.

Knowledge exchange at the FAIRDOM Collaboration Fest Online

Mon, 02 Feb 2026 08:30:00 +0000

In March 2026, we hosted the first FAIRDOM Collaboration Fest (CoFest) online. Users, developers, leaders and advocates from nine institutions in six countries created an opportunity to collaborate, discuss and progress a range of matters and features which will be of benefit to the wider FAIRDOM-SEEK community. We also welcomed those interested in learning more about FAIRDOM-SEEK and how it could benefit their work.

The mini CoFest format allowed us to discuss and plan upcoming work, without needing to commit any code immediately. We presented two topics, covering a range of concepts and teams.

A summary of FAIRDOM-SEEK features released in the last 12 months, thanks in part to your contributions at the FAIRDOM Mini Hackathon in February 2025.
Topic 1: Knowledge Graph and Linked Data. A discussion about querying the public knowledge graph of a FAIRDOM-SEEEK instance, through writing SPARQL queries, using Triple Stores and Extended Metadata.
Topic 2: Visualization and LLM Enabling. A presentation about how Neo4J, visualization tools, and Large Language Models (LLM) have been combined in NextSEEK to vastly reduce the time bioinformaticians spend filling out GEO forms.

To read a report of the event, please visit Knowledge exchange at FAIRDOM CoFest 2026.

Collaborations at the 4th BioHackathon Germany

Mon, 26 Jan 2026 00:00:00 +0000

The 4th BioHackathon Germany took place from 1-5 December 2025 in Walsrode, Germany, organised by de.NBI and ELIXIR Germany. Life scientists, data managers, software developers and project leaders attended the hybrid event to work together on open source code, standards and infrastructure to advance research data practices and tools.

Improving RO-Crate support in federated storage systems

One of the hackathon projects was titled Enhancing FAIR (Meta-)Data Practices in Life Science by Improving RO-Crates Support in Federated Storage Systems. It was led by Sebastian Beyvers and Jannis Schlegel (University of Giessen).

During their participation in the Biohackathon Germany 2025, their working group engaged in extensive discussions focused on the practical and technical challenges of integrating RO-Crates in federated storage systems for life science data. The group produced many outputs including extensions to ro-crate-py Python library and ro-crate-rs Rust library, an RO-Crate indexing tool, and the RO-Crate Explorer application to parse, visualise and traverse RO-Crates.

Read more on the RO-Crate blog

Making FAIRer access to training registries and learning paths across domains

The hackathon project titled On the path to machine-actionable training materials was led by Nick Juty (University of Manchester) and Petra Steiner (Technical University of Darmstadt). The lead author of the project report was Phil Reed (University of Manchester).

The project operated across three interrelated streams: metadata interoperability, material analysis, and the definition and representation of learning paths in a machine readable manner.

Content federation was demonstrated via the mTeSS-X platform, enabling cross-instance exchange and preparing for future integration with the EOSC federation. To enhance interoperability, relevant ontologies and crosswalks were curated between established metadata models, specifically MoDALIA and Schema.org/Bioschemas. These mappings were implemented within the open-source OERbservatory Python package, providing a facility for exchanging data between platforms such as DALIA and TeSS.
For material analysis, Large Language Models (LLMs) were utilised and vectorisation techniques were explored to calculate similarity, allowing for the identification of related materials and the potential for future deduplication of records across registries.
To address the lack of machine-actionable trajectories across related or sequential materials, new Bioschemas profiles were proposed, specifically for learning paths. This model was validated using SPARQL queries on knowledge graphs derived from real-world examples like the Galaxy Training Network.

Such advancements provide a foundation for automated path generation and improved discoverability within training catalogues, and serves as a use case and strategy with broader applicability beyond those materials.

Read more in the project report in BioHackrXiv (doi:10.37044/osf.io/un6cd_v1)

Project leadership and management at ELIXIR BioHackathon Europe 2025

Tue, 18 Nov 2025 00:00:00 +0000

In November 2025, the eScience Lab returned to the annual ELIXIR BioHackathon Europe event, this time on the outskirts of Berlin, Germamy. Colleagues joined the over 300 participants from the life sciences research community to address crucial challenges in bioinformatics.

Three featured projects were supported by the eScience Lab:

New ELIXIR RIRs: Transparent and Automated Evaluation for a FAIRer Future – led by Munazah Andrabi et al. Through an inclusive and transparent framework, Project 20 developed an improved set of criteria, ensuring that ELIXIR Recommended Interoperability Resources (RIRs) can be easily discovered, assessed, and used by researchers and service providers.
Towards a Robust Validation Service for Data and Metadata in ARC RO-Crates – led by Eli Chadwick et al. The overall goal of Project 28 was to provide a powerful, holistic validation mechanism for ARC RO-Crates, enhancing their reliability, trustworthiness, and FAIRness. Stuart Owen and Finn Bacall also helped to improve FAIRDOM-SEEK’s support of ISA RO-Crate metadata (a format that ARCs build upon). doi:10.37044/osf.io/zah28_v1
Mining the potential of knowledge graphs for metadata on training – joined by Phil Reed and Finn Bacall. In project 18, we created a queryable knowledge graph derived from training metadata in the Bioschemas format available from platforms including TeSS and glittr.org. doi:10.37044/osf.io/gv2ac_v1

The University of Manchester delegates taking a lakeside break at ELIXIR BioHackathon Europe 2025

To read more about the impact of BioHackathon participation over the last 7 years, please read this news article from ELIXIR Europe:

Accelerating open science – the impact of BioHackathon Europe

ELIXIR-UK All Hands 2025: AI, data and community

Mon, 17 Nov 2025 12:00:00 +0000

Last month, over 70 members and collaborators of the ELIXIR-UK, from 31 organisations met in Exeter for the annual All Hands meeting, a two-day event focused on connection, reflection and community building.

The meeting brought together researchers, data stewards and infrastructure leads from across the UK to share progress, exchange ideas and discuss priorities for the year ahead. Sessions covered topics ranging from national funding and sustainability to the practical use of AI in research.

Highlights of major contributions from the eScience Lab

The meeting opened with a welcome from Joint Head of Node, Carole Goble, who reflected on the Node’s growth and priorities for the coming year.
On the second day, Munazah Andrabi led a World Café dedicated to AI, where participants discussed bias, skills, data access, productivity and the future of research careers in an AI-driven research landscape.

ELIXIR joins forces to strengthen life science capacity within the European Open Science Cloud

Fri, 31 Oct 2025 13:00:00 +0000

The ELIXIR Consortium, Euro-BioImaging, Instruct-ERIC and EMBL have joined forces to establish the EOSC Life Sciences Connect Node – a candidate European Open Science Cloud (EOSC) node dedicated to improving access to data, tools and workflows across the life sciences.

Following an open call in summer, the Life Science Connect Node was selected as part of the first wave of candidate EOSC nodes. The Node aims to strengthen open science capacity across domains by connecting resources, aligning standards, and supporting FAIR and ethically compliant data sharing.

A series of use cases will showcase the Node’s capabilities, from cross-domain image analysis to federated data storage in structural biology and multi-domain workflows through Galaxy. Together, these examples will highlight how the EOSC Federation can enhance research efficiency and interoperability across Europe.

UK partners involved in ELIXIR will contribute expertise, among others, in data stewardship, workflow interoperability and capacity building through their participation in the broader ELIXIR consortium.

“By working together, within the framework of EOSC, we can make an even greater collective contribution to open science”, said Peter Maccallum, Coordinator of the EOSC Life Sciences Connect Node.

Read the full announcement on the ELIXIR Europe website.

Source: ELIXIR-UK

FONDA Fall 2025 Retreat

Fri, 31 Oct 2025 12:00:00 +0000

FONDA’s members met from 7th to 9th October 2025 in Potsdam for their Fall Retreat. In addition to subproject progress reports, each PhD student presented a poster regarding their thesis topic, and they had two marvelous keynote talks by Carole Goble and Sarah Cohen-Boulakia.

FONDA is Foundations of Workflows for Large-Scale Scientific Data Analysis, based at DFG Collaborative Research Center at Humboldt-Universität in Berlin, Germany. FONDA investigates methods for increasing productivity in the development, execution, and maintenance of Data Analysis Workflows for large scientific data sets.

Source

Job Opportunity: Senior Research Software Engineer (SAE-030028)

Mon, 27 Oct 2025 00:00:00 +0000

Join the eScience Lab at the University of Manchester and help shape the future of climate data sharing and use in Europe! We’re seeking a talented Senior Research Software Engineer to lead FAIR, ontology-driven approaches to climate data integration within the European Open Science Cloud (EOSC).

You’ll work at the cutting edge of reproducible research, semantic interoperability, and privacy-preserving data tracking—collaborating with climate scientists, technologists, and software engineers across Europe. From developing and contributing to knowledge graphs and FAIRification templates to driving open science practices and community consensus, this is a high-impact, team-driven role with global reach.

If you’re passionate about improving how climate data is handled and shared and making research more open and interoperable, we’d love to hear from you.

Climate-Adapt4EOSC

ClimateAdapt4EOSC, Advancing climate adaptation through open science and data integration in the European Open Science Cloud (EOSC), is a Horizon Europe funded project that specifically empowers researchers across multiple disciplines to tackle climate change more effectively by providing an advanced, EOSC-centred collaborative research environment. This environment integrates existing EOSC data and services while introducing new datasets and innovative features, such as FAIRification and Mapping and Entity Matching capabilities.

The project will create a climate change adaptation ontology and an EOSC Climate-Adapt Knowledge Graph, enabling enhanced findability, accessibility, tracking, and life cycle management of diverse research outputs. By fostering interoperability and innovation, the project will significantly strengthen the capacity of European scientific communities to address climate change.

Manchester’s role leverages their expertise in reproducibility, interoperability, provenance and their leadership in FAIR and reflects their involvement in various EOSC related projections and initiatives (e.g. the EOSC Opportunity Areas) to aid integration into the broader EOSC ecosystem.

About the role

The postholder will lead on strategy, research and development of FAIR, ontology driven approaches to climate data and their adoption, evaluation and communication within and beyond the boundaries of the project. This is a highly collaborative and consensus driven role and involves working with research software engineers, climate experts and technology experts in the Manchester team and partners across the project.

The postholder will be working closely with, and be line managed by the Manchester Principal Investigator Dr Stian Soiland-Reyes and be part of the eScience Lab team based in the Department of Computer Science at the University of Manchester.

The role holder will work with other research software engineers associated with the eScience Lab who have a climate background, they will work with project partners and their use cases and collaborate alongside lab experts and developers in FAIR and Research Objects. This co-working extends to colleagues at partner sites and collaborators in the UK, Europe and worldwide.

For full details and to apply, please visit the University of Manchester Job Posting and its supporting documents.