10^th Anniversary of de.NBI

On the occasion of this year's de.NBI & ELIXIR Germany All Hands Meeting 2025, 19-21 November in Berlin we were honoured to celebrate the 10^th anniversary of de.NBI, which started its work 2015.

Thanks to the outstanding engagement of all network partners - and especially our first coordinator, Alfred Pühler, between 2015 and 2021 – we secured long‑term funding from 2022 onwards after a seven‑year period of BMFTR project support. Today de.NBI stands as a reliable, highly effective bioinformatics infrastructure that delivers versatile services and computing capabilities to hundreds of thousands of users each year. We play a vital role in Germany’s life‑sciences sector and are one of the leading nodes of ELIXIR.

The All Hands Meeting 2025 had 137 participants, 41 of which were new in the network or at an AHM. Three of our new associated partners took the opportunity to present their work and meet with longstanding network partners. In the presenation programm we exhanged highlights on new developments as well as the service  and training activities of the service centers. The convention started with meetings of the working groups trianing, service and service monitoring, and cloud and concluded with the 10. CCU meeting.   

de.NBI & ELIXIR-DE meets GHGA webinar series started

Summary of the 6^th Annual Meeting of the de.NBI Industrial Forum

The 6^th Annual Meeting of the de.NBI Industrial Forum entitled “Converge of AI, Data Science, and Biological Data: Current Frontiers in Life Science” took place virtually on 27 November 2025. This year’s event linked current academic research and industrial use cases and presented themes from pharmaceutical research and development (R&D), biomedical artificial intelligence (AI), plant bioinformatics, federated learning, to analysis and application of omics data. Presentations from the de.NBI & ELIXIR-DE network covered computational analysis of plant biosynthetic pathways (Boas Pucker, University of Bonn), machine learning in proteomics (Karin Schork, Ruhr University Bochum), and epistemically transparent agentic AI (Sebastian Lobentanzer, Helmholtz Munich). Presentations from de.NBI Industrial Forum Members shared insights on "Applications of Large Languge Models (LLMs) in pharmaceutical R&D" (Astrid Rheinländer, Bayer AG), "Analysis and usage of metabolomics data" (Philip Wenig, Lablicate GmbH), and "Federated-learning approaches in drug discovery" (Robin Röhm, Apheris AI). 
The de.NBI & ELIXIR-DE administration office would like to thank all speakers for their presentations and the audience for their interest. Further information on the programme and the book of abstracts can be found here.  

4^th Biohackathon Germany

The BioHackathon Germany has firmly established itself as a premier event for the German life sciences and bioinformatics communities, promoting interdisciplinary collaboration and creative problem-solving. The 2025 edition, held at the Anders Hotel in Kassel from 1-5 December, was a remarkable success, with over 175 participants attending in person or remotely. “Hackers” teamed up on 11 diverse projects, tackling a broad array of challenges in bioinformatics and life sciences and advancing essential tools for the field. See the list of projects here. Highlights of the social program included a lively pub quiz and board game night, a fun evening at Colosseum Bowling and the legendary “After-Hack-Party.”

Looking ahead, the BioHackathon Germany 2026 will continue its mission to address significant scientific and technical challenges, drive innovation, and strengthen networks within the community. The project application phase will begin in mid-April 2026. Stay tuned for your chance to join the next chapter of this vibrant and innovative hackathon series!

  News from ELIXIR

24^th ELIXIR Board Meeting in Berlin

We were honoured to welcome board delegates from across the ELIXIR Nodes, as well as Katharina Peter, Andreas Klein, and Dr  Nicola Scholz from BMFTR, who emphasised the crucial role of bioinformatics research infrastructures in enabling a strong and innovative research ecosystem. During the social programme at the Museum für Naturkunde - surrounded by dinosaurs - Andreas Klein and Katharina Peter perfectly the essence of the meeting in their welcome remarks: “Research infrastructures can be many things - but never dinosaurs. Flexible, connected, and future-ready.”
During the German Node session, Prof Dr Oliver Kohlbacher and Prof Dr Alexander Sczyrba presented the strengths and opportunities of the German Node, highlighting our contributions in bioinformatics services, cloud computing, and training, and reminding us that investing in people is central to driving progress. 

We are also delighted to share that Prof. Dr. Alexander Goesmann from JLU Giessen has been re-elected as Chairman of the ELIXIR Board for 2026-27. We thank him sincerely for his dedication and look forward to the important work ahead under his chairmanship!

ELIXIR People & Node Tier Workshop

16 December 2025 | 10:00-16:30 CET. To support the development of the 2027-28 ELIXIR People and Node Tier Commissioned Services, all ELIXIR members are invited to join an online workshop on 16 December. The event will bring together colleagues from across the ELIXIR community to enable broad participation. In small, topic-focused groups, participants will contribute to defining the Activity Areas for the next programme cycle through a bottom-up, community-driven approach. Here you can find the draft agenda and the registration link.

New ELIXIR implementation studies 2026-2027 granted

Eight new ELIXIR-funded projects, worth a total of €705,000 and aimed at strengthening open science and supporting FAIR practices in the life sciences, have been selected to start in 2026. Out of these ELIXIR Germany is participating in three studies:

• Building FAIR metadata standards for non-human pathogen genomic and phenotypic data>
  • Participant: D. Wibberg, (Admin. Office, FZ Jülich) will take the lead on the training aspect, providing a hands-on workshop, developing guidance materials, and delivering community support to enable adoption of these new standards
• Creation of a virtual assistant guiding plant researchers in making their datasets FAIR compliant>
  • Particpant: D. Arend, M. Feser (IPK Gatersleben), S. Beier (FZ Jülich, IBG-4)

• FAIR annotation workflows for PDBe-KB via community-driven Nextflow development and training
  • Participant M. Rarey (U Hamburg) 

BioHackathon Europe 2025 - Strong Participation from ELIXIR Germany 

News from de.NBI and ELIXIR-DE Office

  News on the de.NBI Cloud

• • The de.NBI Cloud is part of work package 1 of the EOSC United project with Galaxy Europe (Freiburg University), SimpleVM and ELIXIR OnCloud (FZJ, Bielefeld) to demonstrate integration with the EOSC EU node for scientific use cases.
  • The de.NBI Cloud Working Group has met as part of the de.NBI & ELIXIR-DE All Hands Meeting 2025 in Berlin and has finalized the Position paper on cooperation between NFDI and de.NBI & ELIXIR-DE (published on Zenodo: Nov 30, 2025).

• • Number of users: 4772 (4437), number of active projects: 696 (664), number of publications referencing the use of the de.NBI Cloud: 1840 (1504). This equals an increase of ~7% in users, ~4.8% in projects and ~22.3% in publications since August 2025.

• • 27-28 January 2026: EOSC Winter School 2026, Nice. de.NBI Cloud will participate as EOSC United and EOSC ENTRUST project partners, as well as through involvement in the EOSC Task Forces.

• • Phylogeography of Schistidium atrofuscum
  • Teaching Content Analysis with LLMs

News on Services

• STRING: Updated interaction datasets and improved scoring schemes.
• proGenomes: Expanded genomic clusters and refined functional annotations. New Publication: Fullam A, Letunic I, ..., Bork P, Mende DR. proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Research. 2025 Nov 20. https://doi.org/10.1093/nar/gkaf1208COPASI / basico: Performance and documentation improvements.
• SeqAn 3: Major new release with faster minimizer indexing and updated tutorials.
• SeqAn 2: Maintenance update ensuring long-term compatibility.
• FAIRDOM-SEEK v1.17.1: Enhanced FDS support & metadata interoperability.
  Zenodo record: https://zenodo.org/records/17360523
• OpenMS: New version plus new logo and refreshed website branding.
• Trimmomatic: New website, updated documentation, new logo.
• Helixer: Updated branding.
• SILVA: New website branding and updated dataset DOIs (04 Sep 2025). New Article: Chuvochina M, Gerken J, ..., Glöckner FO, Reimer LC. SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity. Nucleic Acids Research. 2025 Nov 18. https://doi.org/10.1093/nar/gkaf1247BRENDA Knowledge Graph: Updated ontology alignment and metadata integration.
• BRENDA: New Article: Hauenstein J, Jeske L, ..., Reimer LC, Bunk B. BRENDA in 2026: a Global Core Biodata Resource for functional enzyme and metabolic data within the DSMZ Digital Diversity. Nucleic Acids Research. 2025 Nov 06. https://doi.org/10.1093/nar/gkaf1113
• LPSN: Main reference article published (IJSEM). 
• DOI: https://doi.org/10.1099/ijsem.0.006943
• CloWM (BiGi Bielefeld): New service: Cloud-based Workflfow Manager for Nextflow workflows.
• sORFdb (BiGi Gießen): New service. Darta base for short open reading frames. 

Recent Publications by de.NBI partners

• Bossche TVD, Alexandrov T, ..., Wein SP. mzPeak: Designing a Scalable, Interoperable, and Future-Ready Mass Spectrometry Data Format. Journal of Proteome Research. 2025 Nov 07. https://doi.org/10.1021/acs.jproteome.5c00435
• Till A, Siddiqui RA, ..., Kohlbacher O. Germany's national genomDE strategy. Nature Medicine. 2025 Oct 15. https://doi.org/10.1038/s41591-025-03991-2
• Louail P, Brunius C, ..., Neumann S, Rainer J. in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem. Analytical Chemistry. 2025 Dec 08. https://doi.org/10.1021/acs.analchem.5c04338
• Neumann S, Meier R, ..., Schymanski EL. MassBank: an open and FAIR mass spectral data resource. Nucleic Acids Research. 2025 Nov 11. https://doi.org/10.1093/nar/gkaf1193
• Piro VC, Reinert K. ganon2: up-to-date and scalable metagenomics analysis. NAR Genomics and Bioinformatics. 2025 Sep 01. https://doi.org/10.1093/nargab/lqaf094
• Gogna A, Arend D, ..., Beier S, Reif JC. Order from entropy: big data from FAIR data cohorts in the digital age of plant breeding. Theoretical and Applied Genetics. 2025 Sep 24. https://doi.org/10.1007/s00122-025-05040-5
• Holst F, Bolger AM, ..., Usadel B, Denton AK. Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model. Nature Methods. 2025 Nov 24. https://doi.org/10.1038/s41592-025-02939-1
• Kuhn M, Schmidt TSB, ..., Bork P. Metalog: curated and harmonised contextual data for global metagenomics samples. Nucleic Acids Research. 2025 Oct 31. https://doi.org/10.1093/nar/gkaf1118
• Sandmann S, Hegselmann S, ..., Eils R, Varghese J. Benchmark evaluation of DeepSeek large language models in clinical decision-making. Nature Medicine. 2025 Aug 01. https://doi.org/10.1038/s41591-025-03727-2
• Lindenhofer D, Bauman JR, ..., Huber W, Steinmetz LM. Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing. Nature Methods. 2025 Oct 01. https://doi.org/10.1038/s41592-025-02805-0
• Lin Y, Breuer K, ..., Walter J, Lutsik P. Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard. Nucleic Acids Research. 2025 Oct 14. https://doi.org/10.1093/nar/gkaf970
• Larralde M, Zeller G, Carroll LM. PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity. NAR Genomics and Bioinformatics. 2025 Sep 01. https://doi.org/10.1093/nargab/lqaf095
• Uyar B, Savchyn T, ..., Akalin A. Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond. Nature Communications. 2025 Sep 12. https://doi.org/10.1038/s41467-025-63688-5
• Nasr E, Pechlivanis N, ..., Grüning B, Batut B. Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data. bioRxiv. 2025 Sep 16. https://doi.org/10.1101/2024.12.23.629682

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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.