"Fellowship of the Data" meeting

The international “Fellowship of the Data” meeting invites everyone interested in research data management (RDM). The meeting will take place 1 - 2 April 2025 at the “Rosensäle”, University of Jena. The agenda includes discussions and insights on the diversity of the RDM landscape in Germany and beyond, the broad range of RDM professions and tasks, an introduction into the national data competency centers (de.KCD, SODa, DataNord) and change management in RDM. Sessions will include presentations and a strong focus on networking. All disciplines are welcome!
Poster applications are possible and registration is open until 17 March.
Find more information here: https://indico.leibniz-fli.de/e/datafellows25.

New de.NBI Service User Feedback Survey

To continuously improve the services offered via de.NBI, data on user satisfaction is collected on a regular basis. We have recently supplemented and restructured the corresponding questionnaire in order to better respond to user requirements. The most recent de.NBI user feedback survey, launched at the beginning of the year, has already garnered over 100 responses. We are pleased to report that these submissions contain valuable insights and suggestions from our users. The administration office will review and forward open-response feedback to the respective service centers for their attention. A summary of the feedback will also be presented in the CCU meetings. Service providers interested in receiving individualized statistics on the feedback related to their services can contact our service coordinators via This email address is being protected from spambots. You need JavaScript enabled to view it.. We appreciate the time taken by all users who have participated in the survey thus far and encourage all service providers to promote their individual survey links through various channels, such as websites, newsletters, and other relevant platforms.

Our New Social Media Presences: BlueSky and Mastodon

As we navigate the evolving social media landscape, we are thrilled to announce our expanded presence on BlueSky and Mastodon, aligning with our commitment to community engagement and open communication. With these platforms, we bid farewell to our X channel and embrace vibrant new spaces for interaction.
BlueSky, as a decentralized network, and Mastodon, with its open-source and community-driven nature, both offer unique environments for meaningful interactions. These platforms prioritize user privacy, control, and diverse discussions, allowing us to connect and engage authentically with our audience.
Join us on BlueSky and Mastodon to engage in important conversations and be part of a growing community. These platforms prioritize meaningful exchanges, making your voice essential to our community-building efforts.
We are excited about this transition and look forward to exploring new opportunities for innovation and collaboration. Visit us at @denbi.bsky.social and @deNBI on Mastodon.science to connect. We look forward to seeing you there!

News from de.NBI/ELIXIR-DE

Julian Uszkoreit elected as new Co-Lead of the ELIXIR Proteomics Community
We are delighted to announce that Julian Uszkoreit, Professor for Medical Informatics at Ruhr-Universität Bochum, has been elected as the new Co-Lead of the ELIXIR Proteomics Community. In this role, Julian will help drive the community’s efforts to develop sustainable proteomics tools and data resources, enhance data processing pipelines, and improve the integration of proteomics with other omics disciplines.
The ELIXIR Proteomics Community aims to standardising data management, improve annotation, and support the FAIRification of resources - ensuring that proteomics data is findable, accessible, interoperable, and reusable. With Julian’s leadership, the community will continue to foster innovation and collaboration across ELIXIR and beyond. Congratulations Julian!
Learn more about the ELIXIR Proteomics Community: https://elixir-europe.org/communities/proteomics.

  News from ELIXIR

• ELEAD—2^nd Edition
  The 2^nd edition of the ELIXIR LEadership And Diversity Programme (ELEAD) has started. This ELIXIR Implementation study aims to support women in current or future leadership roles within ELIXIR. Ranging from 2025 to 2027, ELEAD second edition will comprise three major pillars: a mentoring schema, a peer-mentoring approach, and a professional workshop schedule.

  Further information can be found here: https://elixir-europe.org/internal-projects/elead2.

• Project to link human genomic data completes ELIXIR-funded project portfolio

  A two-year project to link European human genomic data from different sources has been awarded funding by ELIXIR. The project aims to develop solutions to link multi-omic sensitive data deposition databases, biobanks and derived knowledge resources.
  FEGA-Connect involves five ELIXIR Nodes (Finland, Germany, Spain, Sweden and EMBL-EBI), two ELIXIR Communities (Federated Human Data and Proteomics) and in-kind contributions from the Polish FEGA node. The project will result in more coherent data deposition, discoverability and retrieval of multi-omics datasets, providing FAIRer data and consequently accelerating research.
  The project completes the allocation of funding for the first three years of ELIXIR’s Scientific Programme 2024–28 in the scientific areas of cellular and molecular research; biodiversity, food security and pathogens; and human data and translational research. For further information please klick here.

• ELIXIR Interoperability Stories
  A set of nine stories has been created to demonstrate how biodata and software can be made more interoperable. The stories have been produced by ELIXIR’s Interoperability Platform, a pan-European group of experts working to improve interoperability across the life sciences and describe successful data reuse across the ELIXIR network, exploring how to achieve impact through interoperable data sharing. They feature a variety of scientific and technical areas covered by ELIXIR’s Communities, ranging from plant sciences to rare diseases to metabolomics, also including "Galaxy" by B. Grüning from ELIXIR Germany.
  The stories were funded through the ELIXIR Scientific Programme 2019-2023 and form of a series of presentations. The report and slides are available on Zenodo.

Biohackathon Germany: Review 2024 and Outlook 2025

BioHackathon Germany has firmly established itself as a premier event for the German life science and bioinformatics community, promoting interdisciplinary collaboration and inventive problem-solving. Here, we recap the successes of the 2024 event and preview what lies ahead for The BioHackathon 2024 was hosted at Hotel La Strada in Kassel 5-9 December alongside with two satellite events, marking a significant achievement with over 150 participants (f2f and remote), connecting developers and researchers. The "hackers" worked on 10 diffenrent projects, tackling various challenges in bioinformatics and life sciences while advancing tools for these fields. Highlights of the social program included a Kassel city tour, a visit to the Christmas market, and a lively "After-Hack-Party."
Looking ahead, the BioHackathon 2025 is set to be hosted at the Anders Hotel in Walsrode from 1 - 5 December. The event will continue to provide a forum to address pressing issues in life science and bioinformatics. The project application phase is set to commence in early April. Stay tuned! 
BioHackathon Germany remains a vital platform for innovative problem-solving and collaboration. Building on the success of the 2024 event, the 2025 BioHackathon is poised to be equally inspiring and productive, paving the way for future innovations and breakthroughs.

CLIB International Conference 2025 – Ready to Create Impact

  News on the de.NBI Cloud

• News on de.NBI Cloud facilities:
  • de.NBI Cloud Freiburg, hosting Galaxy.eu service, has been successfully recertified according to ISO 27001.
  • de.NBI Cloud Tübingen has also successfully passed their ISO 27001 recertification audit.
• de.NBI Cloud activities:
  • NFDI IAM incubator calls:  The de.NBI Cloud has successfully applied with SimpleVM to integrate with the NFDI Identity and Access Management service. This will simplify access to SimpleVM deployments for NFDI users in the future. https://incubators.nfdi-aai.de/
  • de.NBI BioHackathon output—Secure Processing Environments as a Service in the de.NBI Cloud: The de.NBI BioHackathon project on Secure Processing Environments has published its outputs on GitHub https://github.com/deNBI/2024_BioHackathon_DE_SPE and as a BioHackrXiv preprint: https://github.com/deNBI/2024_BioHackathon_DE_SPE/blob/main/2025_03_10_paper_preview.pdf
• Current figures on the de.NBI Cloud: Number of users: 3903 (3719), number of active projects: 608 (618), number of publications referencing the use of the de.NBI Cloud: 1334 (1250). This equals a decrease of ~4,9% in users, a decrease of ~1,6% in projects and an increase of ~6,7% in publications, respectively, since December 2024.

• Two new testimonials on the use of the de.NBI Cloud have been published:

  • Processing of genomics data of circulating tumor DNA, AG Scherer, University Clinic Freiburg, https://cloud.denbi.de/about/testimonials/processing-of-genomics-data/
  • DigitalTwinBridges - Digital Twin of Nibelungenbrücke, Jörg F. Unger from FB 7.7 "Modellierung und Simulation", Bundesanstalt für Materialforschung und -prüfung, https://cloud.denbi.de/about/testimonials/digitaltwinbridges/
  • Events:
    • The joint de.NBI Cloud and de.KCD User Meeting 2025 will take place in Berlin from 30 September - 2 October 2025. Annonuncement will follow soon. 

News on Services

• BacDive: A new BacDive release is online. Numerous new strains from the DSMZ catalogue as well as new data provided by DSMZ curators were added to the database. Additionally, information on type strains of newly described species was integrated from LPSN.
• bashbone has been updated to v1.4.0, including extended genomic data download by orthologs, upgrade and adaption to patched tools and further enhanced usages.
• Bioconductor version 3.20 has been released, containing 54 new software packages, 5 new data experiment packages, 4 new annotation packages, and many updates and improvements to existing packages. This release will also include updated Bioconductor Docker containers.
• BRENDA latest release 2024.1 includes 41 new and 491 updated enzyme classes.
• EURISCO: National Inventory data of eight countries have been updated and the information about in situ CWR populations was added to EURISCO.
• FAIRDOM-SEEK: major release 1.16.0 contains a number of improvements, upgrades and bug fixes. The highlights include FAIR Data Station Integration, fewer constraints on editing Sample Types, creating new Extended Metadata Types, RDF support extended as well as DataHub- and WorkforHub enhancements.
• Galaxy Release 24.2: The workflow invocation export process and the Workflow Editor have been enhanced. Furthermore, the Galaxy masthead has been revised to achieve consistency and reduce redundancy, aligning its functionality with the Activity Bar. Finally, with this release, ChatGXY — AI assistance built directly into the Galaxy interface was introduced.
• iTOL v7 was released. The management of datasets has been improved.
• KNIME Analytics Platform 5.4 is available to download. KNIME workflows can now collaboratively build with K-AI directly in the canvas. K-AI will help to build workflows node by node and document its own work. The 5.4 release also delivers a series of UI enhancements as well as new features to carry out complex data manipulations much more easily, find and configure the needed nodes faster, simplify the work with other tools such as Tableau, and create sharper looking visualizations in reports with SVG support.
• MetFrag: in January 2025, the MetFrag Command Line (MetFrag CL) pages were updated with extra details and examples.
• PANGAEA has published new 'Authors Guides' as the future authoritative guidelines for data submissions to PANGAEA. These guidelines describe in detail the requirements that data and relevant metadata will have to satisfy in order to be considered for publication in PANGAEA.

Recent Publications by de.NBI partners

• Thelen F, Hochmuth J, Griep S, Schwab B, Goesmann A, Förster F. Crypt4GH-JS: securely storing sensitive data online with client-side encryption. Bioinformatics. 2024 Dec 26;41(1):btae763. https://doi.org/10.1093/bioinformatics/btae763
• Hellwig P, Kautzner D, Heyer R, Dittrich A, Wibberg D, Busche T, Winkler A, Reichl U, Benndorf D. Tracing active members in microbial communities by BONCAT and click chemistry-based enrichment of newly synthesized proteins. ISME Commun. 2024 Dec 4;4(1):ycae153. https://doi.org/10.1093/ismeco/ycae153
• Schober I, … Overmann J, Reimer LC. BacDive in 2025: the core database for prokaryotic strain data. Nucleic Acids Res. 2025 Jan 6;53(D1):D748-D756. https://doi.org/10.1093/nar/gkae959
• Hönig SMN, Gutermuth T, Ehrt C, Lemmen C, Rarey M. Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays. J Comput Aided Mol Des. 2024 Dec 4;39(1):2. https://doi.org/10.1007/s10822-024-00581-1
• Uszkoreit J, Marcus K, Eisenacher M. A Review of Protein Inference. Methods Mol Biol. 2025;2859:53-64. https://doi.org/10.1007/978-1-0716-4152-1_4
• Marko B, ..., Eisenacher M, et al. Employing artificial intelligence for optimising antibiotic dosages in sepsis on intensive care unit: a study protocol for a prospective observational study (KI.SEP). BMJ Open. 2024 Dec 12;14(12):e086094. https://doi.org/10.1136/bmjopen-2024-086094
• Hehner J, ..., Schwudke D, Herker E. Dengue virus is particularly sensitive to interference with long-chain fatty acid elongation and desaturation. J Biol Chem. 2025 Jan 23:108222. https://doi.org/10.1016/j.jbc.2025.108222
• Varghese J, Schuster A, … Kohlbacher O, …. EyeMatics: An Ophthalmology Use Case Within the German Medical Informatics Initiative. JMIR Med Inform. 2024 Dec 5;12:e60851. https://doi.org/10.2196/60851
• Lin CL, …, Neumann S, et al. Linking Research Data with Physically Preserved Research Materials in Chemistry. Sci Data. 2025 Jan 22;12(1):130. https://doi.org/10.1038/s41597-025-04404-2
• Liang Y, … Mayer KFX, Zhou X, Wang J, Zhang L. The giant genome of lily provides insights into the hybridization of cultivated lilies. Nat Commun. 2025 Jan 2;16(1):45. https://doi.org/10.1038/s41467-024-55545-8
• Blum M, … Bork P, … Bateman A. InterPro: the protein sequence classification resource in 2025. Nucleic Acids Res. 2025 Jan 6;53(D1):D444-D456. https://doi.org/10.1093/nar/gkae1082
• Szklarczyk D, … Bork P, Jensen LJ, von Mering C. The STRING database in 2025: protein networks with directionality of regulation. Nucleic Acids Res. 2025 Jan 6;53(D1):D730-D737. https://doi.org/10.1093/nar/gkae1113
• Müller-Bötticher N, Tiesmeyer S, Eils R, Ishaque N. Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data. Small Methods. 2024 Nov 12:e2401123. https://doi.org/10.1002/smtd.202401123
• Dmitrijeva M, ...., Zeller G, Sunagawa S. The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities. Nucleic Acids Res. 2025 Jan 6;53(D1):D797-D805. https://doi.org/10.1093/nar/gkae1004
• Ahlmann-Eltze C, Huber W. Analysis of multi-condition single-cell data with latent embedding multivariate regression. Nat Genet. 2025 Jan 3. https://doi.org/10.1038/s41588-024-01996-0
• Otoničar J, … Stegle O, Ernst A. HIPSD&R-seq enables scalable genomic copy number and transcriptome profiling. Genome Biol. 2024 Dec 18;25(1):316. https://doi.org/10.1186/s13059-024-03450-0
• Leppä AM, … Korbel JO, Trumpp A. Single-cell multiomics analysis reveals dynamic clonal evolution and targetable phenotypes in acute myeloid leukemia with complex karyotype. Nat Genet. 2024 Dec;56(12):2790-2803. https://doi.org/10.1038/s41588-024-01999-x
• Jeong Y, Gerhäuser C, Sauter G, Schlomm T, Rohr K, Lutsik P. MethylBERT enables read-level DNA methylation pattern identification and tumour deconvolution using a Transformer-based model. Nat Commun. 2025 Jan 17;16(1):788. https://doi.org/10.1038/s41467-025-55920-z
• Balogh G, ...., Stadler PF, Bernhart SH. TREMSUCS-TCGA - an integrated workflow for the identification of biomarkers for treatment success. J Integr Bioinform. 2024 Dec 11;21(4):20240031. https://doi.org/10.1515/jib-2024-0031
• Wiechens E, … Hoffmann S, Fischer M. Gene regulation by convergent promoters. Nat Genet. 2025 Jan;57(1):206-217. https://doi.org/10.1038/s41588-024-02025-w

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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.