Newsletter 41

📢 8^th de.NBI Cloud  & de.KCD User Meeting 

The annual user meeting will highlight topics of interest to the de.NBI Cloud user community. This year, we are teaming up with the Jülich Supercomputing Center, de.KCD, and BIH/Charité, offering a mixture of courses for trainers, beginners and advanced users as well as opportunities to engage with experts on diverse cloud computing topics. The de.NBI Cloud & de.KCD User Meeting supports the interaction with our growing community. Thus, we would like to hear from you about the specific needs of the scientific life sciences community, allowing us to shape the future of the de.NBI Cloud according to sophisticated and specialized use cases.

The de.NBI Cloud & de.KCD User Meeting will be held as an in person event in Berlin from 30 Sep – 2 Oct 2025. Please register here; registration will be open until 5 September 2025.

European Galaxy Days meeting in Autumn 2025 

The European Galaxy Days will take place from 1–3 October 2025 in Freiburg im Breisgau, Germany. The first two days will give an overview of the current state of the Galaxy framework and community with several talks, demonstrations, and Birds of a Feather sessions. As part of a CoFest, the third day will offer the opportunity to continue discussions, to code and hack as well as enjoy the Galaxy community.

• The ELIXIR Galaxy Community Face-to-face (F2F) meeting,
• The EuroScienceGateway Final Conference,
• The European Galaxy Days (EGD) meeting.

Further information and link to registration. It is recommended to register as soon as possible.

📢 New Quarterly de.NBI & ELIXIR Germany Briefing – Save the Date!

📅 8 October 2025
🕑 14 - 16 CEST
🖥️ Online 

We are pleased to introduce a new network initiative: The de.NBI & ELIXIR Germany Briefing - an online meeting (1.5 hours) designed to share updates from ELIXIR Europe, exchange information across de.NBI Service Centres, and keep all members informed about the network’s key activities.
Held three times a year and open to all members of the network, the meetings shall provide an open platform for questions and discussion to foster effective communication and collaboration within the national de.NBI & ELIXIR Germany community. 

Join us to stay up-to-date with the latest developments across our community! Please visit the webpage for further details. Agenda and dial-in link will be distributed by email.

📢 4^th Biohackathon Germany: Registration open

Following the outstanding success of the first three editions of the BioHackathon Germany, de.NBI and ELIXIR Germany are delighted to announce that we will be hosting the 4^th BioHackathon Germany in Walsrode from 1–5 December 2025. We warmly invite participants from de.NBI & ELIXIR Germany, other ELIXIR nodes, academia, and industry. Industry participation is especially encouraged to promote fruitful collaborations and foster new innovations.

Event Overview:
📅 Dates: 1-5 December 2025
📍 Location: Walsrode, Germany
🖥️ Remote Participation: Available for those unable to attend onsite

• Engaging Projects: Choose from 11 dynamic projects spanning topics such as large language models, training, bioimaging, and more. Ten projects will take place onsite (with possible hybrid participation), and one project will be conducted online.
• Flexible Participation: Attend onsite for the full week or join online for selected tracks.
• Networking Opportunities: Collaborate and connect with experts and peers across bioinformatics and related fields.

• Registration: Open since 1 September 2025
• Selection Basis: First-come, first-served
• Registration Deadline: 14 November 2025

New Collaborations in Training: de.NBI & ELIXIR-DE join forces with WGGC and DataPlant

de.NBI & ELIXIR-DE are excited to announce a new collaboration in the training field with the West German Genome Center (WGGC) and the NFDI consortium DataPlant. The WGGC is a leading sequencing hub and research consortium, providing advanced genomics technologies and expertise to support molecular life science research across Germany. DataPLANT is a German research consortium (NFDI) dedicated to providing infrastructure, tools, and standards for FAIR data management in plant science and related research fields. These partnerships bring together expertise and resources to deliver high-quality, hands-on bioinformatics data management workshops for researchers at all levels. Three joint courses are starting this fruitful cooperation:

Long Re(ad)volution – Workshop (Düsseldorf & Online, 7-9 Jul 2025)
Led by Nils Kleinbölting (BiGi), Daniel Wibberg (CAU), Anna-Maria Möller, Florian Kraft, Tassilo Wollenweber, and Daniela Dey (all WGGC), this three-day event took a deep dive into long-read sequencing. Covering everything from technology basics to hands-on PacBio/Nanopore library prep, linux command line skills, and full genome assembly workflows. In this workshop, 19 participants learned more about the power of long-read sequencing.

Easy & Quick – Visualizing NGS Count Data with Python (EPPS25, Bonn, 17 Sep 2025)
This 90-minute beginner-friendly workshop, conducted by Anna-Maria Möller, Daniela Dey (both WGGC), and Daniel Wibberg (CAU) and Sebastian Beier (GCBN), will introduce researchers to loading, exploring, and visualizing small-scale NGS transcriptomic data using Python in the Galaxy Hub’s JupyterLab environment. Participants will work with panda and seaborn to generate quick insights from their data - no prior Python experience required! More details can be found here.

Maximizing the Potential of Agricultural Research Data: A Guide to Crafting a DMP and Using ARCs (Online, 21–23 Oct 2025).
Led by experts from de.NBI & ELIXIR-DE, DataPlant and FAIRagro, this course will guide participants through the essentials of data management plans (DMPs), FAIR data principles, and Annotated Research Contexts (ARCs) with hands-on exercises tailored to agricultural and plant science data. Participants will learn the full research data lifecycle, practice using tools like ARCitect and RDMkit, and gain the skills needed to efficiently organize and share agrosystem research data in line with funder requirements and best practices. More details and registration are available here.

These collaborative workshops reflect our shared commitment to advancing bioinformatics and genomics as well as data management training in Germany. We look forward to welcoming participants from diverse backgrounds and supporting the next generation of life science researchers!

News from de.NBI/ELIXIR-DE 

de.NBI & ELIXIR Germany at ISMB/ECCB 2025
Members of the de.NBI & ELIXIR Germany network were delighted to take part in the recent ISMB/ECCB conference, held 20–24 July in Liverpool, UK, where they presented the latest developments in network services and cloud computing. Contributions to the Technology, CompMS, and Microbiome tracks highlighted the network’s expertise and promoted valuable knowledge exchange. Key highlights included simplified VM solutions and real-world use cases designed to support and advance the life science community.

Shaping the Future of Genome Medicine: de.NBI & ELIXIR-DE and GHGA at genomDE Symposium
The 4^th genomDE Symposium (10–11 July in Berlin) was co-organized by TMF, the federal Institute for Drugs an Medical Devices (BfArM), de.NBI & ELIXIR-DE and GHGA, contributing to vital discussions on the future of genomic data infrastructures in Germany and Europe. Talks by Oliver Kohlbacher and Alexander Sczyrba highlighted key advances in German bioinformatics, particularly in reproducible, scalable, and secure data analysis. The event also previewed upcoming solutions and outlined a shared roadmap - with GHGA and de.NBI & ELIXIR-DE positioned as strong partners for the genome medicine community. The message was clear: Sustainable infrastructure and cross-disciplinary collaboration are essential for shaping the future of genomics in Germany. Together, we achieve more!

  News from ELIXIR

• ELIXIR Voices in Nature: Investing in Data Resources to Make FAIR a Reality
  In a recent Nature correspondence “Invest in data resources to make FAIR a reality", leading scientists in ELIXIR and bioinformatics, among them ELIXIR Director Tim Hubbard, highlight the urgent need for sustained funding and support for data infrastructures that fully realise the FAIR principles. ELIXIR’s involvement underscores our broader commitment to ensuring that data stewardship becomes both standard and sustainable for researchers. With FAIR, now a requirement from major funders, ELIXIR’s leadership reinforces how a shared infrastructure can help bridge expertise gaps and make FAIR data practices widely achievable.

• Upcoming Webinar Series: “The ELIXIR Node of 2030”
  The ELIXIR Hub is introducing a new webinar series in which each Node will present its current activities, share lessons learned, and outline its vision for the future. The goal is to highlight successful approaches, promote peer-to-peer learning, and advance progress toward a resilient, well-connected ELIXIR network. A key theme will be how Nodes plan to shape and steer developments leading up to 2030.
  The webinar began with a Hub-led session that explored what a strong and effective Node might look like in the years ahead. ELIXIR Germany will be the first to take the stage on 24 September at 15:00 CEST. Don’t miss it - register now and be part of the conversation!

  News on the de.NBI Cloud

• de.NBI Cloud activities:
  • A workshop on virtual machines and basic Unix, using de.NBI SimpleVMs, was held at the de.KCD Summer School - Cloud Essentials for Medical Data conference on 2 July.
  • Cloud Working Group Meeting took place in Heidelberg on 1–2 July.
  • The SimpleVM-platform was presented at the ISMB/ECCB 2025 Tech-Track by Viktor Rudko.
• Current figures on the de.NBI Cloud: Number of users: 4437 (4147), number of active projects: 664 (641), number of publications referencing the use of the de.NBI Cloud: 1504 (1444). This equals an increase of ~7% in users, an increase of ~3,5% in projects and an increase of ~4,2% in publications, respectively, since June 2025.

• Events:
  • 22 September 2025, SimpleVM Workshop, German Conference on Bioinformatics (GCB) 2025, Düsseldorf. Registration for the conference is open!
  • 29 Sep – 1 Oct 2025: TEACH V conference, taking place at HIDA Hub in Berlin, with a talk on Simplifying Cloud-Based Workshops with SimpleVM.
  • 30 Sep – 2 Oct 2025: The joint de.NBI Cloud and de.KCD User Meeting, Berlin. Registration is open until 5 September. 
  • 7 Oct 2025: An Introduction to de.NBI, ELIXIR Germany and Cloud Computing with SimpleVM will be given at the 'Woche der Forschungskompetenzen' event at Bielefeld University.

News on Services

• bashbone version v1.6.0 was released, including several updates, fixes and improvements.
• FAIRDOM-SEEK version 1.17.0 released that contains a number of improvements, upgrades and bug fixes. The highlights include—among others—an extended support for Fair Data Station (FDS), further integration with the ELIXIR Norway NeLS system to support more features that can be done directly in SEEK, as well as WorkflowHub and DataHub enhancements.
• Galaxy Release 25.0 empowers users to build more kinds of collections, more intelligently. Galaxy’s collection system has been significantly enhanced, making it easier to create and manage collections—including mixed paired and unpaired datasets, nested lists, and more—directly from selected datasets. New wizard-style builders guide users step-by-step, auto-detecting data structures and offering both instant and advanced setup options, while improved rule-based import activities, clearer feedback, and numerous refinements.
• MassBank announced the official launch of the MassBank 3.0 system, a major redesign and rewrite of the MassBank platform, now live at both https://massbank.eu/ and https://massbank.jp/. MassBank now delivers a cleaner interface, faster performance, and expanded tools for exploring and sharing high-quality mass spectral data. 
• MHCquant release 3.0.0 has new features to extract chromatograms and visualize them, to compute fragment mass errors and visualize them in multiQC report and further improvements.
• OpenMS release 3.3 has important improvements to the previous version, including changes breaking backward compatibility, Low-level peak extraction helper for MSExperiments, Docker files are now part of the main OpenMS repo. Furthermore, there are added new functionalities and combatibilities. In August 2025, Tübingen University celebrated 20 years of OpenMS. 
• PanBARLEX has been updated and the list of known genes has been extended to 103 genes.

Recent Publications by de.NBI partners

• Belmann P, Osterholz B, Kleinbölting N, Pühler A, Schlüter A, Sczyrba A. Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation. NAR Genom Bioinform. 2025 Jul 17;7(3):lqaf093. https://doi.org/10.1093/nargab/lqaf093
• Sarumi OA, Bertrams W, Schwengers O, ... Goesmann A et al. LegionProfiler: A computational tool for the identification of virulence factors and classification of Legionella pneumophila serogroup 1 isolates. Bioinformatics. 2025 Jul 12:btaf398. https://doi.org/10.1093/bioinformatics/btaf398
• Walke D, ..., Heyer R. Edges are all you need: Potential of medical time series analysis on complete blood count data with graph neural networks. PLoS One. 2025 Jul 8;20(7):e0327636. https://doi.org/10.1371/journal.pone.0327636
• Behnke JS, ..., Sickmann A, Heyer RS, Urner LH. Detergent Screening With Hybrid Detergents Increases Observable Number of Protein Identities in Bottom-Up Proteomics. Proteomics. 2025 Jun 20:e70003. https://doi.org/10.1002/pmic.70003
• Ehrt C, Schulze T, Graef J, Diedrich K, Pletzer-Zelgert J, Rarey M. ProteinsPlus: a publicly available resource for protein structure mining. Nucleic Acids Res. 2025 Jul 7;53(W1):W478-W484. https://doi.org/10.1093/nar/gkaf377
• Schwacke R, Bolger ME, Usadel B. PubPlant - a continuously updated online resource for sequenced and published plant genomes. Front Plant Sci. 2025 Jun 24;16:1603547. https://doi.org/10.3389/fpls.2025.1603547
• Larralde M, Zeller G, Carroll LM. PyOrthoANI, PyFastANI, and Pyskani: a suite of Python libraries for computation of average nucleotide identity. NAR Genom Bioinform. 2025 Jul 11;7(3):lqaf095. https://doi.org/10.1093/nargab/lqaf095
• Jendrusch MA, Yang ALJ, ..., Korbel JO, Sadiq SK. AlphaDesign: a de novo protein design framework based on AlphaFold. Mol Syst Biol. 2025 Jun 17. https://doi.org/10.1038/s44320-025-00119-z
• Logsdon GA, Ebert P, ..., Korbel JO et al. Complex genetic variation in nearly complete human genomes. Nature. 2025 Jul 23. https://doi.org/10.1038/s41586-025-09140-6
• Beyvers S, Jelonek L, Goesmann A, Schwengers O. Bakta Web - rapid and standardized genome annotation on scalable infrastructures. Nucleic Acids Res. 2025 Jul 7;53(W1):W51-W56. https://doi.org/10.1093/nar/gkaf335.
• Piro VC, Reinert K. ganon2: up-to-date and scalable metagenomics analysis. NAR Genom Bioinform. 2025 Jul 17;7(3):lqaf094. https://doi.org/10.1093/nargab/lqaf094
• Feng JW, ..., Mayer KFX, Spannagl M et al. A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum. Nature. 2025 Jul 9. https://doi.org/10.1038/s41586-025-09270-x
• Ahlmann-Eltze C, Huber W, Anders S. Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines. Nat Methods. 2025 Aug 4. https://doi.org/10.1038/s41592-025-02772-6
• Rautenstrauch P, Ohler U. Shortcomings of silhouette in single-cell integration benchmarking. Nat Biotechnol. 2025 Jul 30. https://doi.org/10.1038/s41587-025-02743-4
• Schreiber F, ..., Lange M, Scholz U, Sommer B. Sustainable software development in science - insights from 20 years of Vanted. J Integr Bioinform. 2025 Jul 1. https://doi.org/10.1515/jib-2025-0007
• Hamm F, Coppin E, ..., Walter J et al. DNA methylomes undergo distinct waves of remodeling during thymic T cell development and do not acquire a proliferation-induced imprint. Cell Rep. 2025 Aug 2;44(8):116092. https://doi.org/10.1016/j.celrep.2025.116092
• Breinig M, Lomakin A, ..., Stegle O et al. Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships. Nat Biomed Eng. 2025 Jul 28. https://doi.org/10.1038/s41551-025-01437-1 

Upcoming Events

Impressum

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.