From BioHackathon to Nature Methods: SpaceHack Success Story

What started as the SpaceHack 2.0 initiative at the BioHackathon Germany 2023 has now resulted in a publication in Nature Methods. Led by Naveed Ishaque, the project developed new approaches for benchmarking clustering methods in spatial transcriptomics – demonstrating how BioHackathon collaborations can grow into sustainable, high-impact research.

And the story continues: SpaceHack 5.0 is already planned for this year’s BioHackathon Germany.

→ Nature Methods publication | Research Briefing | SpackHack project

Playing to Learn: Gamification Insights from BioHackathon Germany 2025

Life science training often involves dense technical specifications and complex data formats, creating challenges for engagement and retention. At the 4th BioHackathon Germany, trainers and developers from BioInfra.Prot and CAU explored how gamification can make bioinformatics education more engaging without compromising scientific content.

The team evaluated 20 digital tools and developed the “Ten Simple Rules for Gamification in Bioinformatics and Life Sciences Education”. Two pilot implementations – interactive R tutorials using swirl and browser-based quizzes on FAIR Research Data Management – demonstrated how gamification can turn abstract computational concepts into more interactive and collaborative learning experiences.

The results and practical recommendations are now available as a preprint.

Building the next-generation de.NBI Service Catalogue

The development of the new de.NBI Service Catalogue is progressing rapidly. By the end of Seüptember 2026,: 130+ services have been approved, 30 are currently going through the onboarding pipeline. The descriptions of the services have have been unified and updated, naming the key benefits of the individual application. The catalogue is now mirrored on the de.NBI website, so that the website always shows the current catalogue content. Thanks to a streamllined workflow, entries can be updated easily giving users a searchable and up-to-date overview of the groing de,NBI service portfolio.  

de.NBI Summer School 2026 – Bioinformatics for Proteomics

From 7–11 September, early-career researchers and scientists gathered at Ruhr University Bochum for five intensive days of bioinformatics for mass spectrometry-based proteomics in the frame of the de.NBI Summer School 2026 - Bioinformatics for Proteomics.

The programme covered the complete bottom-up proteomics workflow, from raw data formats and peptide identification to protein inference and DDA/DIA quantification. Hands-on sessions introduced tools including pyOpenMS, msAmanda and Proteobench, complemented by insights into machine learning, single-cell proteomics, immunopeptidomics and metaproteomics.

Many thanks to the organisers at BioInfra.Prot and Ruhr University Bochum, the international team of trainers, and all participants for making the Summer School a success!

Help shape the de.NBI Good Practice Guide for KPI Collection

As part of the development of the "de.NBI KPI Compass", the Service and Service Monitoring Working Group is collecting practical approaches to measuring service reach, usage and impact. Network members who have developed useful tools, workflows or solutions for KPI collection are invited to contribute their experience to a new Good Practice Guide.

Interested in contributing? This email address is being protected from spambots. You need JavaScript enabled to view it., our Service Coordinator.

Record interest in the 5th BioHackathon Germany

  News from ELIXIR

ELIXIR Director Tim Hubbard steps down
Former ELIXIR Director, Tim Hubbard Interim ELIXIR Director and Head of External Relations, Andrew Smith Tim Hubbard stepped down as ELIXIR Director on 31 August 2026. From 1 September, Andy Smith, Head of External Relations, is serving as Interim Director while the recruitment of a new Director continues.

de.NBI (ELIXIR Germany) would like to thank Tim for his strong commitment to ELIXIR and for his valuable support of the German Node. We greatly appreciated the collaboration and wish him all the best for the future. Read the announcement.

ELIXIR Equity, Diversity and Inclusion Focus Group
A new ELIXIR Equity, Diversity and Inclusion (EDI) Focus Group has been launched to strengthen inclusive, equitable and sustainable participation across the ELIXIR network.

Martinique Frentrup (ELIXIR-DE) co-leads the Focus Group together with Laura Chabot (ELIXIR-FR) and Jilly Cheshire (ELIXIR Hub). The group will bring together existing EDI activities and good practices, identify barriers to participation, and develop shared guidance on topics including psychological safety, accessibility, inclusive communication and support for newcomers.

The kick-off meeting will take place on 30 September, 13:00–14:00. Interested community members can join the mailing list via the EDI Focus Group website.

FAIR Pathogen Data: From Research Data Management Basics and Standards to ENA Submission
On 10–11 November, ELIXIR-PT, ELIXIR-ES, ELIXIR-NO and ELIXIR-DE will jointly host an online workshop on Research Data Management for non-human pathogen data.

Designed for researchers, data stewards and bioinformaticians, the two-half-day workshop covers the data life cycle from ENA metadata standards to hands-on submissions via the Webin system. Participants will also pilot a draft harmonised metadata template in interactive breakout sessions.

More information and registration

News from de.NBI and ELIXIR-DE Office

Welcome Florian Sprengel 
Florian has joined the Administration Office in Bielefeld on 1 August 2026. He will coordinate the de.NBI Industrial Forum and be active in service coordination. He is succeeding Nils-Christian Lübke. We are looking forward to a successful collaboration! 

  News on the de.NBI Cloud

The de.NBI Cloud User Symposium brings together users and experts for scientific and technical exchange, networking, and the presentation of research and solutions enabled by cloud infrastructure.
Participants are invited to contribute their own work to the programme. The call for abstracts is open until 30 September 2026, and registration for the symposium is open until 16 October 2026. 

More information, abstract submission and registration. 

Current figures on the de.NBI Cloud:

Three new user testimonials highlight the broad range of research enabled by the de.NBI Cloud – from genome-resolved soil ecology and microbial diversity in Pacific coral reef sediments to deep learning approaches for modelling genetic perturbations.

The projects demonstrate how scalable computing resources, large-memory systems, GPU infrastructure and storage support researchers in processing large datasets, comparing bioinformatics tools and running computationally demanding analyses.

Read the new testimonials and discover how researchers are using the de.NBI Cloud for their work.

News on de.NBI Services

• Galaxy: Release 26.1 introduces WES support, Galaxy Notebooks and new AI agent infrastructure. A new European Galaxy website has also launched, featuring de.NBI in the Galaxy Hall of Fame.
• SILVA: The new SILVA 144 SSU release is now available.
• Trimmomatic: Version 0.41 has been released with Java 25 support, simplified invocation and extensive performance improvements. Development is already underway for v0.42 with long-read trimming for ONT and PacBio data and v0.43 with UMI detection and correction.
• COPASI: New releases COPASI 4.47.
• FAIRDOM-SEEK: Release 1.18.1 is now available.
• LipidXplorer & LipidSpace: LipidXplorer 1.5 and LipidSpace 1.2.x have been released, with LipidSpace now also supporting ARM-based Macs.
• BIIGLE: BIIGLE has expanded its annotation functionality, including LabelBOT support for videos and improvements to the Magic SAM tool. 
• Platon: Platon 1.8 has also been released with updated dependencies and tools.
• PanBARLEX: PanBARLEX has been extended with epigenetic data and a new dynamic synteny browser.

Recent Publications by de.NBI partners

• Zhu Z, Bernhart SH, ..., Hoffmann S. metilene: identifying DMRs across multiple conditions with auto-classification. Nature Communications. 2026 Jul 04. https://doi.org/10.1038/s41467-026-74931-y
• Fährrolfes R, Sieg J, Flachsenberg F, Rarey M. PegaPlus─Interactive Machine Learning by Human Observation for Efficient Clustering and Analysis of Structure-Activity Data. Journal of Chemical Information and Modeling. 2026 Jul 13. https://doi.org/10.1021/acs.jcim.6c00524
• Schmitt P, Hönig K, ..., Akalin A, Blankenstein T. Oncogene inactivation-induced senescence facilitates tumor relapse. Nature Communications. 2026 Jul 15. https://doi.org/10.1038/s41467-026-75021-9
• Pribus SJ, Osredek I, ..., Korbel JO, Ernst A. Multiomic profiling links L1 retrotransposition to genomic instability and ecDNA in bladder cancer. Nature Communications. 2026 Jul 16. https://doi.org/10.1038/s41467-026-75399-6
• Siegert JAJ, Kelber F, ..., Meiler J. Rapid and energy-efficient ultra-large library screening for drug discovery on a SpiNNaker2 neuromorphic chip. Communications Chemistry. 2026 Jul 21. https://doi.org/10.1038/s42004-026-02122-3
• Schulte-Mattler J, Reinert K. RSHash: a fast and space-efficient hash table for k-mers. Bioinformatics. 2026 Aug 01. https://doi.org/10.1093/bioinformatics/btag440
• Iorio F, Garnett MJ, ..., Boutros M, Wessels L. The PRECISE European initiative for cancer-vulnerability mapping and prediction. Nature Genetics. 2026 Aug 01. https://doi.org/10.1038/s41588-026-02658-z
• Meyer-Bender M, Vöhringer H, ..., Huber W. Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data. Nature Methods. 2026 Aug 01. https://doi.org/10.1038/s41592-026-03155-1
• Schäfer PSL, Zimmermann L, ..., Saez-Rodriguez J. ParTIpy: a scalable framework for archetypal analysis and Pareto task inference. Molecular Systems Biology. 2026 Aug 01. https://doi.org/10.1038/s44320-026-00209-6
• Ramírez-Rafael JA, Korchmaros A, ..., Stadler PF, Hernández-Rosales M. REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories. PLoS Computational Biology. 2026 Aug 01. https://doi.org/10.1371/journal.pcbi.1013017
• Schmidt C, Franken J, ..., Saez-Rodriguez J. Integrated metabolomics data analysis to generate mechanistic hypotheses with MetaProViz. Molecular Systems Biology. 2026 Aug 17. https://doi.org/10.1038/s44320-026-00231-8
• Capraz T, Vöhringer H, ..., Huber W. Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data. Nature Communications. 2026 Aug 20. https://doi.org/10.1038/s41467-026-74694-6
• Sun J, Biharie K, ..., Eils R, Ishaque N. Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering. Nature Methods. 2026 Sep 01. https://doi.org/10.1038/s41592-026-03194-8
• Oleksyk TK, Isakova LH, ..., Huber W, Kondrashov FA. Training as infrastructure for biological data science in wartime Ukraine. Nature Genetics. 2026 Sep 01. https://doi.org/10.1038/s41588-026-02702-y
• Saez-Rodriguez J, Schäfer PSL, Kalavros N, Stolovitzky G. Benchmarking biomedical foundation models. Nature Methods. 2026 Sep 01. https://doi.org/10.1038/s41592-026-03182-y
• Kostrykin L, Massei R, ..., Serrano-Solano B. Bioimage management and analysis in Galaxy: Tools, workflows, training, and community practices. Journal of Microscopy. 2026 Sep 08. https://doi.org/10.1111/jmi.70165
• Gruber AJ, Olsen AV, ..., Brors B, Weischenfeldt J. Integrated signatures define mutational processes in prostate cancer. Nature. 2026 Sep 09. https://doi.org/10.1038/s41586-026-10468-w
• Schlegel J, Beyvers S, ..., Goesmann A, Förster F. Pithos - a scalable and secure data container for FAIR-compliant research data management in life sciences. Journal of Integrative Bioinformatics. 2026 Dec 01. https://doi.org/10.1515/jib-2025-0051
• Quadros E, Reimer LC, Koblitz J. The DSMZ Digital Diversity Annotation Hub: a pipeline for database expansion via text mining and human curation. Journal of Integrative Bioinformatics. 2026 Dec 01. https://doi.org/10.1515/jib-2025-0058
• Ebeling M, Lange M, Weise S, Scholz U. Advancing cross-domain integration and semantic technologies: proceedings of the 19th international symposium on integrative bioinformatics. Journal of Integrative Bioinformatics. 2026 Dec 01. https://doi.org/10.1515/jib-2026-0019
• Dörpholz H, Simon R, Usadel B, Kranz A. Integrating cross-omics research through FAIR Digital Objects with DataPLANT. Journal of Integrative Bioinformatics. 2026 Dec 01. https://doi.org/10.1515/jib-2025-0056

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The de.NBI Quarterly Newsletter is a service of de.NBI - German Network for Bioinformatics Infrastructure for members, partners and interested public. All photos are copyright of the de.NBI administration office unless marked otherwise.