Newsletter 40

📢 Invitations open for Bioschemas hackathon in Cologne

The Bioschemas hackathon will take place in Cologne, Germany 25 – 27 June 2025 and is organised in collaboration with experts from NFDI4DS, ZB MED, the University of Manchester (UK), Forschungszentrum Jülich GmbH (DE), the Su Lab (La Jolla, US), and the University of Nantes (FR).

Join this international hackathon to connect with other bioinformaticians to improve Bioschemas and Schemas.science website based on open GitHub and add tutorials on how to use Bioschemas and its specifications. To participate, please submit your application not later than 15 June 2025 to Oxford Abstracts Webby FDOs. Please note, that there is limited capacity, and participants are expected to cover their own travel and accommodation costs. 

📢 19^th International Symposium on Integrative Bioinformatics, Gatersleben, 10 - 12 September 2025

This year, the Gatersleben Research Conference Series, an annual gathering of leading minds in plant research and life sciences, is hosting the 19^th International Symposium on Integrative Bioinformatics at the IPK in Gatersleben. This symposium serves as a dynamic platform for bioinformaticians, computer scientists, life science researchers and interdisciplinary professionals to explore the latest advancements and applications in integrative bioinformatics. Registration is open! 
Please find more information and registration here.

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

For more than 7 years, the de.NBI Cloud has provided free of charge computing resources to the life sciences community in Germany. Scientists involved in various research topics, such as metagenomics, medical imaging, epigenetics, and plant biology benefit from the opportunities provided by the de.NBI Cloud.

With our annual user meeting, we would like to highlight topics of interest to our user community. This year, we are teaming up with the Jülich Supercomputing Center, de.KCD, and BIH/Charite, offering a mix of courses for trainers, beginners and advanced users and 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 September - 2 October 2025. We look forward to welcoming you in Berlin!

📢 4^th Biohackathon Germany: Call for project proposals open

Project submissions has opened for the BioHackathon Germany 2025 that will take place in Walsrode, 1 - 5 December 2025!
Please submit your project proposal by email to This email address is being protected from spambots. You need JavaScript enabled to view it. before the deadline on 15 July 2025. Proposals should focus on bioinformatics challenges and align with de.NBI & ELIXIR Germany activities. Accommodation for two project leads per accepted project will be covered by us.
Further information can be found here.

News from de.NBI/ELIXIR-DE: de.NBI & ELIXIR Germany participated at ELIXIR All Hands Meeting 2025

This year’s ELIXIR All Hands Meeting was held at the Porto Palace Hotel, Thessaloniki, Greece, 2-5 June, with more than 400 participants. The ELIXIR All Hands Meeting is the annual opportunity to meet, greet, and collaborate within ELIXIR network as well as to showcase node- and network-wide projects and achievements. de.NBI & ELIXIR Germany was strongly represented with 27 participants and showcased their expertise and progress in 10 workshops, 4 mini symposia, 2 plenary sessions, as well as numerous poster contributions.

Once again, the team greatly valued the experience at the ELIXIR All Hands Meeting and would like to thank the organisers for a truly wonderful conference. 
Further information can be found here.
Posters and Presentations will be made available via the ELIXIR F1000 Gateway. 

  News from ELIXIR

• New Members Join the ELIXIR Scientific Advisory Board – Including a German Representative
  We are delighted to share that Prof. Dr. Fabian Theis (Institute of Computational Biology, Munich) has been appointed to the ELIXIR Scientific Advisory Board (SAB), joining the German member Prof. Dr. Detlef Weigel (MPI for Biology, Tübingen). Prof. Theis brings leading expertise in AI for life sciences, reinforcing Germany’s strong role in ELIXIR. In addition to Prof. Theis, two other distinguished experts have joined the SAB:
  
  • Prof. Dr. Anna Niarakis (University of Toulouse III-Paul Sabatier / Centre for Integrative Biology, France) – with expertise in data and tools for Cellular & Molecular Research
  • Prof. Dr. Gary Bader (University of Toronto, Canada) – known for his contributions to bioinformatics databases and infrastructure
  Dr. Janet Kelso (Max Planck Institute for Evolutionary Anthropology, Leipzig) has concluded her 12-year term as a member of the Scientific Advisory Board. 

• Open calls for Cellular and Molecular Research (CMR) and Biodiversity, Food Security and Pathogens (BFSP) proposals
  ELIXIR announced the launch of the 2025 open call for the Cellular and Molecular Research (CMR) and Biodiversity, Food Security and Pathogens (BFSP) priority areas. This call offers an opportunity for ELIXIR members to propose collaborative projects that drive innovation and deliver technical outputs aligned with the 2024–2028 ELIXIR Scientific Programme.
  The process will consist of two steps:
  • Expression of Interest: from 12 May to 16 June 2025.
  • Full proposal submission: from 23 June to 15 September 2025. (Please note that an Expression of Interest is required prior to full submission.) 
  Further details can be found here: https://elixir-europe.org/how-we-work/scientific-programme/2025-science-open-calls

• New Webinar Series: “The ELIXIR Node of 2030”
  The ELIXIR Hub is launching a webinar series where each Node will share its current status, lessons learned, and vision for the future. The aim is to showcase best practices, encourage peer learning, and support progress toward a stable, well-connected ELIXIR network.
  The series kicks off with a Hub-led session outlining what a well-functioning Node might look like in the years ahead. The first Node webinar will feature ELIXIR Germany in September (date to be confirmed). Please register and stay tuned — we look forward to your participation!

• Launch of New ELIXIR Communities Future Focus Group
  ELIXIR network announce the launch of the ELIXIR Communities Future Focus Group, led by Anne-Françoise Adam-Blondon (Head of Node, ELIXIR-FR), Wim Vranken (IDP Community Co-lead, ELIXIR-BE) and Katharina Heil (Community Programme Manager, ELIXIR Hub). This group will explore the purpose, structure, and impact of ELIXIR Communities — both individually and as a collective portfolio. Key goals include strengthening alignment with the Science Tier, improving governance and operations, and ensuring sustainable resource planning.
  👉 If you’re interested in contributing to this important work and helping shape the future of ELIXIR Communities, visit the website to learn more and get involved.

• Updated ELIXIR Branding and Communication Materials Now Available
  The ELIXIR network has updated its Brand Guidelines, Communications Strategy, and Style Guide to ensure consistent and effective messaging across the infrastructure. As part of this update, all partners are encouraged to use the new ELIXIR standard slide templates for future presentations and communication materials. Also take a look at the updated social media guidelines for ELIXIR consortium members, as well as the dedicated guidance for account managers on building a strong Node presence.

WorkflowHub: a registry for computational workflows

Workflow sharing presents opportunities to reduce unnecessary reinvention, promote reuse, increase access to best practice analyses for non-experts, and increase productivity. In reality, workflows are scattered and difficult to find, in part due to the diversity of available workflow engines and ecosystems, and because workflow sharing is not yet part of research practice. WorkflowHub provides a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows FAIR. By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. See also the recent paper describing the registry.

  News on the de.NBI Cloud 

• News on de.NBI Cloud facilities:
  • de.NBI Cloud Bielefeld has successfully passed their ISO 27001 surveillance audit on 14 - 15 April 2025.
• de.NBI Cloud activities at the ELIXIR All Hands Meeting 2025:
  • The de.NBI Cloud Federation was represented by Nils Hoffmann with a poster at the annual ELIXIR All Hands Meeting.
  • Handling of sensitive data and Secure Processing Environments in the de.NBI Cloud were featured in two sessions by Sven Twardziok (BIH/Charité) and Nils Hoffmann (FZJ/Bielefeld).
• Current figures on the de.NBI Cloud: Number of users: 4147 (3903), number of active projects: 641 (608), number of publications referencing the use of the de.NBI Cloud: 1444 (1334). This equals an increase of ~6,25% in users, an increase of ~5,4% in projects and an increase of ~8,25% in publications, respectively, since February 2025.

• A new testimonial on the use of the de.NBI Cloud has been published:
  • LIVIVO fallback and development server, Dr. Klaus Lippert, ZB MED, Cologne
    https://cloud.denbi.de/about/testimonials/livivo-development-server/

• Events:
  • de.KCD Summer School 2025 – Cloud Essentials for Medical Data, Heidelberg, 2-3 July 2025. More info and registration here.
  • SimpleVM – Effortless Cloud Computing for Research, ISMB & ECCB Tech Track, Liverpool, 20-24 July 2025.
  • SimpleVM Workshop, German Conference on Bioinformatics (GCB) 2025, Düsseldorf, 22 September 2025: https://www.denbi.de/training-courses-2025/1899-leveraging-cloud-computing-for-bioinformatics-a-simplevm-workshop-featuring-a-metagenomics-use-case-gcb2025. 
  • 8^th de.NBI Cloud & de.KCD User Meeting, Berlin, 30 Sep - 2 Oct 2025. Official news and registration will be announced soon. Save the date.

News on Services

• BRENDA Release 2025.1 includes 168 new and 1620 updated enzyme classes.
• BacDive: New genome-based predictions for Gram stain behavior, motility, oxygen tolerance and spore formation for 15,987 strains could be fully integrated into the strain data and can now be seen in the respective sections. A BacDive Feature Update addresses new Special Collections that assemble strains that are part of the same research project or collection. BacDive also introduced a new design and invites you to try it out.
• bashbone has been updated to v1.5.0 with improvements on peak calling, variant calling, BS methylation rates inference and some further items.
• Bioconductor version 3.21 has been released, now consisting of 2341 software packages, 432 experiment data packages, 928 annotation packages, 30 workflows and 5 books.
• COPASI announced the immediate availability of the stable release COPASI 4.45 (Build 298). A new tool was added which attempts to convert ODEs into reactions and a menu entry which allows definition and subsequent execution of user defined tools was also addes. Furthermore, a graphical user infertace (CopasiUI) is now provided.
• EURISCO: National Inventory data of three countries have been updated and the database underwent an extensive software update.
• FAIRDOM-SEEK: Version 1.16.2 is a patch release that includes some important bug fixes and improvements.
• LipidXplorer release 1.2.9 fixes a critical issue where the software output falsely prefered m/z candidates with lowest absolute error value instead of lowest relative value.
• MassBank release version 2025.05.1 contains 646 new spectra from BfG, 265 new spectra from NILU and 7 new spectra from CPU. Furthermore, mismatches between PubChem ids and chemical identifiers were fixed and new annotations of chemical classes from ChemOnt to many records were added.
• MebaboLights has introduced two new functionalities concerning data submission: MetaboLights will first issue a temporary submission request instead of the traditional MetaboLights study accession number. A full MetaboLights accession number will be assigned only once a study passes new validation.
• muvac v0.9.1 has some improvements due to bashbone upgrade to v1.5.0, improved hardware resources handling, introduced padded calling, and indexing on the fly.
• rippchen v0.11.0 now aligns and normalizes to spike-ins prior to peak-calling due to bashbone upgrade to v1.5.0.
• Pan-Barlex, provided as one of the Crop Analysis Tools Suite (CATS), added pan-transcriptome data for a subset of 20 of the 76 genotypes and 5 tissues. Expression data is available for 25600 of 32578 CDS clusters.
• SearchGUI 4.3.15 updated MetaMorpheus to version 1.0.9 and updated Comet to version 2025.01 rev. 1.

Recent Publications by de.NBI partners

• Hoffmann N, Ahrends R, et al. Introduction of a Lipidomics Scoring System for data quality assessment. J Lipid Res. 2025 Apr 30:100817. https://doi.org/10.1016/j.jlr.2025.100817
• Beyvers S, Jelonek L, Goesmann A, Schwengers O. Bakta Web - rapid and standardized genome annotation on scalable infrastructures. Nucleic Acids Res. 2025 Apr 24:gkaf335. https://doi.org/10.1093/nar/gkaf335
• Heyer R, Wolf M, Benndorf D, ... Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes. Microbiome. 2025 May 23;13(1):134. https://doi.org/10.1186/s40168-025-02119-5
• Revelo-Romo DM, Hurtado Gutiérrez NH, ... Overmann J, ... Omics approaches to explore the coffee fermentation microecosystem and its effects on cup quality. Food Res Int. 2025 Apr;206:116035. https://doi.org/10.1016/j.foodres.2025.116035
• 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 May 6:gkaf377. https://doi.org/10.1093/nar/gkaf377
• Olzhabaev T, Müller L, Krause D, Schwudke D, Torda AE. Lipidome visualisation, comparison, and analysis in a vector space. PLoS Comput Biol. 2025 Apr 15;21(4):e1012892. https://doi.org/10.1371/journal.pcbi.1012892
• Abaza H, Shutsko A, ... Müller W, Golebiewski M. Toward a Domain-Overarching Metadata Schema for Making Health Research Studies FAIR (Findable, Accessible, Interoperable, and Reusable): Development of the NFDI4Health Metadata Schema. JMIR Med Inform. 2025 May 21:13:e63906. https://doi.org/10.2196/63906
• Pop M, Attwood TK, ... Kohlbacher O, Lengauer T, ... Biological databases in the age of generative artificial intelligence. Bioinform Adv. 2025 Mar 20;5(1):vbaf044. https://doi.org/10.1093/bioadv/vbaf044
• D'Altri T, Freeberg MA, ... Kohlbacher O, Korbel JO, ... Stegle O, ... The Federated European Genome-Phenome Archive as a global network for sharing human genomics data. Nat Genet. 2025 Mar;57(3):481-485. https://doi.org/10.1038/s41588-025-02101-9
• Schwab RM, Gottlieb SG, Reinert K. TetRex: a novel algorithm for index-accelerated search of highly conserved motifs. NAR Genom Bioinform. 2025 Apr 17;7(2):lqaf039. https://doi.org/10.1093/nargab/lqaf039
• Klamt S, Zanghellini J, von Kamp A. Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine. Brief Bioinform. 2025 Mar 4;26(2):bbaf188. https://doi.org/10.1093/bib/bbaf188
• Bevan MW, Messerer M, Gundlach H, Kamal N, Hall A, Spannagl M, Mayer KFX. Integrating Arabidopsis and crop species gene discovery for crop improvement. Plant Cell. 2025 May 9;37(5):koaf087. https://doi.org/10.1093/plcell/koaf087
• Mayer KFX, Haberer G. Genomics: To be (or not to be) a duckweed. Curr Biol. 2025 Apr 21;35(8):R298-R300. https://doi.org/10.1016/j.cub.2025.03.021
• Olecka M, Morrison H, Hoffmann S. Signatures of Nonlinear Aging: Molecular Stages of Life: Sudden Changes During Aging as Potential Biomarkers for an Age Classification System. Bioessays. 2025 May;47(5):e202400222. https://doi.org/10.1002/bies.202400222
• Perez-Riverol Y, Bittremieux W, ... Grüning B, ... Open-Source and FAIR Research Software for Proteomics. J Proteome Res. 2025 May 2;24(5):2222-2234. https://doi.org/10.1021/acs.jproteome.4c01079
• Gustafsson OJR, Wilkinson SR, ... Grüning B, ... WorkflowHub: a registry for computational workflows. Sci Data. 2025 May 21;12(1):837. https://doi.org/10.1038/s41597-025-04786-3
• Schmerer N, Janga H, ... Backofen R, ... A searchable atlas of pathogen-sensitive lncRNA networks in human macrophages. Nat Commun. 2025 May 21;16(1):4733. https://doi.org/10.1038/s41467-025-60084-x
• Gaber F, Shaik M, ... Akalin A. Evaluating large language model workflows in clinical decision support for triage and referral and diagnosis. NPJ Digit Med. 2025 May 9;8(1):263. https://doi.org/10.1038/s41746-025-01684-1
• Romano S, Wirbel J, ... Zeller G. Machine learning-based meta-analysis reveals gut microbiome alterations associated with Parkinson's disease. Nat Commun. 2025 May 7;16(1):4227. https://doi.org/10.1038/s41467-025-56829-3
• Huang X, Gu L, Sun J, Eils R. Bridging the gaps: Overcoming challenges of implementing AI in healthcare. Med. 2025 Apr 11;6(4):100666. https://doi.org/10.1016/j.medj.2025.100666 

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