eScience Lab

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.

Job Opportunity: Research Fellow in Health Informatics

Tue, 21 Oct 2025 00:00:00 +0000

Join the eScience Lab at The University of Manchester, where innovation meets impact in data-driven life science research. We are seeking a talented and motivated Research Fellow to lead work within the TREvolution project — an exciting DARE UK initiative focused on advancing Trusted Research Environments (TREs) for multi-site, AI-enabled health data analytics.

Working under the guidance of Dr Stian Soiland-Reyes and collaborating closely with Professor Carole Goble and interdisciplinary teams across the UK, you’ll drive forward metadata architecture and develop cutting-edge techniques using RO-Crate, natural language processing, and synthetic data. You’ll act as senior product owner for RO-Crate metadata across six early adopter teams, guiding technical development and shaping strategy.

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

Federation First: Making the £600 Million Health Data Research Service Work

Tue, 21 Oct 2025 00:00:00 +0000

In April 2025, the UK Government announced a landmark £600 million investment to establish a Health Data Research Service (HDRS) — a secure, single access point to NHS datasets in England. This initiative, backed by Wellcome and central to the Life Sciences Sector Plan, aims to address long-standing challenges in health data access for researchers.

But as DARE UK rightly points out, ambition alone won’t be truly transform healthcare, the HDRS must be built on a foundational principle: federation.

Federation: Connecting What Already Works

Health data in the UK resides in numerous Trusted Research Environments (TREs) and Secure Data Environments (SDEs) — each with robust privacy protections. Rather than centralising sensitive data into a new mega-repository, HDRS should build secure bridges between these existing environments.

This federated approach enables:

Remote analysis: Researchers send analysis code to run within local TREs/SDEs, returning only anonymised insights.
Guarded data convoys: De-identified data moves securely between environments under strict governance.
Hybrid models: Combining both methods for complex studies.

These mechanisms preserve data custodianship and public trust while unlocking the power of distributed datasets.

TREvolution: From Blueprint to Reality

DARE UK’s TREvolution project, funded by UKRI, is standardising operations across TREs/SDEs. It’s developing tools for federated analysis, semi-automated output checking, and shared standards for data formatting, access, and auditing.

Early adopter projects are already piloting these capabilities in over 10 live environments — including NHS sub-national SDEs, the national TRE in Wales, and the UK Data Service.

What’s Next for HDRS?

To succeed, HDRS must:

Embed federation from day one
Mandate interoperability via open standards
Scale up existing infrastructure
Prioritise public and patient involvement with transparency and accountability

This vision extends beyond health. As the UK explores a National Data Library (NDL), federation offers a model for cross-domain research infrastructure — spanning education, environment, social welfare, and more.

A Global Opportunity

Federation also positions the UK for international collaboration. The European Network of Trusted Research Environments (EOSC-ENTRUST) has already published a blueprint informed by DARE UK’s Federated Architecture.

As we build HDRS, the question isn’t just how — but who will help assemble it. The challenge is complex, but the opportunity to deliver public benefit is transformational.

eScience Lab in TREvolution

eScience Lab is a partner in TREvolution with a particular focus on FAIR (Findable, Accessible, Interoperable, Reusable) and transparent analysis of sensitive data and use of RO-Crate. In addition to working with the DARE UK early adopters, we are joining this with our effort on the federated analytics programme in Health Data Research UK, and the European architecture for trusted research environments in EOSC-ENTRUST.

This blog post is syndicated from DARE UK post by Westley Igbo https://dareuk.org.uk/news-and-events/the-600-million-question-how-to-make-the-health-data-research-service-work/