de.NBI All Hands Meeting

The de.NBI/ELIXIR-DE All Hands Meeting took plasce 28-29 November 2024 in Berlin. It was the first in-person general assemby of the network since March 2020, so there was a lot to talk about. The convention provided a good opportunity to reunite and get to know new collaborators. 124 participants were updated on the restructuring process and learnt about the developments of the service centers. The meeting led to fruitful discussions on the positioning of de.NBI in the national and international bioinformatics scene. In the poster session each partner institute presented the current work. On the second day the working groups met to discuss the stategies of the network in Services, Training and Cloud.
The meeting was concluded by the 5^th CCU meeting of the de.NBI 2.0.  

The German Competence Center Cloud Technologies for Data Management and Processing (de.KCD)

The German Competence Center Cloud Technologies for Data Management and Processing (de.KCD) is a cross-location and cross-domain contact point for teaching skills in handling data using cloud-based technologies, resources and methods, both for facilities and networked centers, as well as for researchers at all career levels. de.KCD is a BMBF project in the frame of NextGenerationEU initially running Dec 2023 to Nov 2026.
In the current phase of digital transformation, the success of forward-looking projects are increasingly dependent on the systematic and structured collection of raw and metadata, automated processing workflows and access to scalable compute and storage infrastructure. In de.KCD, these challenges are specifically addressed by bundling expertise in the field of cloud computing and data management. The partners of de.KCD, consisting of all eight de.NBI cloud locations, can build on an extremely successful cooperation within the de.NBI network, thus continuing directly on previous joint efforts. A key focus of de.KCD is the dissemination of dedicated knowledge across the board, inter alia, by reducing access barriers to technologies and methods, standardizing training materials, optimizing material and resource usage and connecting researchers and trainers to each other. Consequently, the project includes a range of measures, among others, the development of a structured training program with new training offerings, the definition and use of processes and technologies for open and sustainable training materials, teaching relevant skills in various formats and self-learning units, the implementation of best practice examples, support in the development of software stacks and workflows, and the development and provision of virtual learning and working environments. As these goals and activities complement the overall de.NBI objectives, de.KCD has applied for becoming a de.NBI associated partner project, which was positively approved by the CCU end of November 2024.

News from de.NBI/ELIXIR-DE

New ELIXIR Germany TrC and TeC deputies

We have to announce some changes in the groups of ELIXIR Germany functional positions. Sebastian Jünemann (FZJ, Bielefeld) has stepped down as Deputy Technical Coordinator (TeC) as he has now taken on other tasks. At the 4^th meeting of the Central Coordination Unit, Renato Alves (EMBL, previously Deputy TrC) was elected as the new Deputy TeC as he has good expertise in the technical field and would like to contribute to the technical ELIXIR platforms. Lisanna Paladin (EMBL Heidelberg) was elected to fill the vacant position of Deputy Training Coordinator (TrC). She has been very active in the training area and in the ELIXIR training platform for some time. She also heads the Focus Group ‘Professionalising careeers in research infrastructures’.

  News from ELIXIR

  News on the de.NBI Cloud

• de.NBI Cloud and de.KCD Activities:
  • The SimpleVM platform was demonstrated as part of the 4th NRW research data day activities of FZ Jülich on 12 November as a cloud-based tool for handling and processing of research data. This activity was offered in conjunction with the de.KCD project, which bundles existing expertise in the field of data management and analysis technologies in the cloud.
  • 7^th de.NBI Cloud User Meeting The de.NBI Cloud is organizing the 7^th de.NBI Cloud User Meeting as an online event from 2-6 Dec 2024. This year we are focusing exclusively on experienced users, while new users will be offered recurring introductory courses in SimpleVM and OpenStack starting next year. We will give our current users the opportunity to deepen their understanding of best practices in cloud computing. There will be workshops on advanced topics such as container orchestration with Kubernetes or handling cloud-based clusters with BiBiGrid.
  • European Open Science Cloud (EOSC) Symposium
    The de.NBI Cloud was represented at the EOSC Symposium 2024 (21-23 Oct 2024, Berlin) as part of a panel discussion on „Thematic contributions to EOSC“, where Nils Hoffmann shared de.NBI‘s thematic bioinformatics perspective on the EOSC node concept also in relation to other prospective nodes, like the NFDI national EOSC node or the ELIXIR Europe EOSC node.
    The de.KCD project was also represented at the EOSC Symposium by Sebastian Juenemann, who presented the Poster „de.KCD: German Competence Center Cloud-Technologies for data management and processing“. 
  • EOSC Candidate Node Selection
    The EOSC Association has recently published its selection of the first round of candidate research infrastructures and networks to potentially establish EOSC nodes. Although de.NBI / ELIXIR-DE was not selected during this first round, our partner networks ELIXIR Europe and NFDI e.V. have been selected. This will provide an opportunity to be involved in the further development of the EOSC node concept and on-boarding process. 

• Current figures on the de.NBI Cloud: Number of users: 3719 (3565), number of active projects: 618 (631), number of publications referencing the use of the de.NBI Cloud: 1250 (1096). This equals an increase of ~4.3% in users, a decrease of ~2.1% in projects and an increase of ~14.1% in publications, respectively, since September 2024.

• A new testimonial on the use of the de.NBI Cloud for Genomics and Metagenomics of Leaf Microbiome has been published.

Review of the ECCB 2024

• During the ECCB 2024 that took place 16-20 September in Turku, FI, ELIXIR Germany offered the workshop „Learn the essentials of research data management and microbial genome submissions“, by Helena Schnitzer and Daniel Wibberg (both ELIXIR DE). The workshop introduced the basics, importance, and standards of RDM and data management plans, such as the FAIR data principles. Participants received training on tools to author data management plans and were tasked to prepare and submit microbial genome data and metadata to public databases.
• The ELIXIR Interoperability Platform offered the FAIR Assessment and FAIRification Workshop: “Practical and pragmatic FAIRification targeting ELIXIR Communities”, which contained use-case contributions from the ELIXIR Metabolomics Community by Nils Hoffmann (ELIXIR DE) and from the GNA NOW project by Yojana Gadiya (Fraunhofer ITMP ScreeningPort, Germany and Enveda Biosciences, USA). The workshop offered practical advice on how to perform FAIR data assessment using the FAIRplus tools in order to find gaps in current FAIR implementation within communities and projects and potentials to improve the level of “FAIR”ness depending on community requirements and use cases.
• ELIXIR Europe offered a dedicated conference track for its communities to network and to present their current work and roadmaps. For the ELIXIR Metabolomics Community, Nils Hoffmann presented “Connecting and Embedding the ELIXIR Metabolomics Community in a Multi-Omics World”, detailing current plans for an updated community whitepaper to realign the community goals and activities with new ELIXIR communities and scientific trends. Further, the presentation covered the working programme for the science tier commissioned service, lead by the ELIXIR Metabolomics Community, titled “Next level of reproducible, comparable and integrable Metabolomics”, which will start in 2025.
• As part of the well-attended poster session, Daniel Wibberg presented the poster "Redefining Educational Excellence: The 2024 Perspective of the de.NBI/ELIXIR-DE Training Platform“, detailing de.NBI/ELIXIR-DE‘s comprehensive training program that covers a diverse area of bioinformatics disciplines and overarching topics like research data management and FAIRification, as well as the monitoring and reporting concept that ensure continued high quality of the training courses. 

Review GCB 2024: A Hub of Bioinformatics Innovation Supported by de.NBI/ELIXIR-DE

The German Conference on Bioinformatics (GCB) 2024 unfolded successfully from 30 September to 2 October at Bielefeld University, drawing together a diverse group of bioinformatics experts and researchers. The conference offered a vibrant platform for exchanging ideas and sharing the latest advancements in the German bioinformatics field.

This year's event was significantly enriched by the contributions of de.NBI/ELIXIR-DE, which played a key role in organizing an impactful conference. Notably, de.NBI hosted three workshops: "Bioinformatic Metagenome and Metaproteome Analysis for Improved Microbiome Understanding," "Computational Pangenomics Workshop," and "Learn the Essentials of Research Data Management and Data Management Plans." These workshops provided attendees with hands-on learning experiences and practical insights into cutting-edge bioinformatics techniques.

Adding to the conference's success was a de.NBI/ELIXIR-DE supported keynote talk by Tim Hubbard, Director of ELIXIR. His presentation captivated the audience with a deep dive into the rapidly evolving landscape of bioinformatics. He emphasized the essential role that collaborative infrastructures, such as ELIXIR, play in driving innovation and discovery. Tim also highlighted current trends and future directions in managing medical data, stressing the importance of global cooperation in advancing scientific progress.

The conference dinner at GCB 2024 was enlivened by the de.NBI Sound Platform - the de.NBI/ELIXIR-DE training coordinator Daniel Wibberg, who kept the dance floor busy well into the night, making it a memorable conclusion of the first day.

We look forward to welcoming everyone to the next edition, GCB 2025, in Düsseldorf. Mark your calendars and stay tuned for more information at https://gcb2025.de/.

Review BioHackathon Europe 2024

The ELIXIR BioHackathon Europe 2024 took place in Barcelona from 4-8 November, bringing together over 180 participants onsite and more than 140 online contributors. Together they worked on 31 diverse bioinformatics projects, covering a variety of important topics such as data management, AI-ready datasets, clinical research data models, and secure data access. Other key areas included bioinformatics training, BioHackRxiv preprints, and promoting gender diversity in publications, all aligning with the event’s commitment to promoting open science and inclusivity in bioinformatics.
Germany's involvement at BioHackathon Europe 2024 was significant, with many participants from de.NBI/ELIXIR Germany partner institutions contributing to the event. ELIXIR DE members palyed an active role, with Helena Schnitzer co-leading Project 10 “BioSchemas for mortals“ and Alexander Sczyrba co-leading Project 21 “Enhancing multi-omic analysis through a federated microbiome analysis service“. All worksops are listed here.
Looking ahead, the ELIXIR BioHackathon Europe 2025 will be hosted in Berlin from 3-7 November, offering another exciting opportunity for collaboration and innovation in research and technology development.

Review 5^th Annual Meeting of the de.NBI Industrial Forum – AI Ventures in the Life Sciences

The 5^th Annual Meeting of the de.NBI Industrial Forum titled “AI Ventures in the Life Science – Needs, Challenges, Opportunities” took place virtually  on 19 November 2024.

The event showcased academic research on Artificial Intelligence (AI) and Machine Learning (ML) as well as industrial use cases and applications. The keynote lecture from Lena Maier-Hein (Heidelberg University/DKFZ) shed light on the usage and possible pitfalls from AI applications in the field of medical imaging. Research updates from the de.NBI/ELIXIR-DE network were given by Holger Gohlke (HHU Düsseldorf/FZJ) and Naveed Ishaque (BIH) in the field of protein structural analysis, single-cell sequencing and spatial biology, respectively.

News on Services

Congratulations to UseGalaxy: In September 2024, the UseGalaxy Team announced, that UseGalaxy.EU has reached 100,000 users. The journey of the European Galaxy server began in 2010 when B. Grüning offered a tiny set of BLAST tools to the faculty of Pharmacy of the University of Freiburg for similarity searches of Streptomyces strains. The team was proud when 800 Galaxy users were reached – mostly local ones – using the Freiburg Galaxy server. In the year 2018, UseGalaxy was awarded to be part of the de.NBI cloud and the Freiburg Galaxy server became the European Galaxy server being able to serve more researchers. In 2022 we celebrated 50,000 users and now, this number has doubled within two years.

• BacDive underwent a feature update: BacDive's new Special Collections assemble strains that are part of the same research project or collection. This provides users with better access and makes these data sets more visible. All Special Collections can be found on a dedicated new page at https://bacdive.dsmz.de/special-collections.
• BRENDA: The BRENDA article in Wikipedia has been updated. The revised version exhibits a new structure and contains extended sections about the history of BRENDA, the annotation process and our most important tools. As of now it is available in German and in English.
• CellNetAnalyzer for python (CNApy), release v1.2.2 contains two major changes for CNApy. The much-improved installation process is introduced, now with an automatic installer for Windows, Linux and MacOS. Due to licensing issues, there will be no more new conda packages available for CNAPy. Instead, CNApy can now be installed using pip as it is now available as a PyPI package.
• DELLY has released the new version v1.3.1.
• EURISCO: National Inventory data of four countries have been updated.
• KNIME: With the release of KNIME Analytics Platform 5.3, the commitment to the community was strengthend by delivering many user-requested features — a new workflow monitor for easier debugging, a revised Home tab for faster navigation, a new Expression node to work with text and numbers in a manner akin to spreadsheet formulas, and much more. KNIME’s goal is to build an open source platform that makes working with the latest advancements in data and AI possible for everyone.
• Mercator4 (GCBN): latest version 7.0 of Mercator4 was released with more than 6600 individual protein categories. The annotation framework was updated.
• MetFrag: A new MetFrag Command Line version 2.5.1 was released. Furthermore, an updated MoNA LC-MS/MS library for MetFrag is now available on Zenodo.
• OpenMS: in the latest release 3.2.0, changes breaking backwards compatibility were made: Rename of parameters for TOPP tool FeatureFinderCentroided, PeakPickerWavelet/TOFCalibration as well as TOPP tool IDFilter with ‘nan’ as new default.

Recent Publications by de.NBI partners

• Torta F, Hoffmann N, Burla B, Alecu I, Arita M, ... Ahrends R, Wenk MR. Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards. Nat Commun. 2024 Oct 3;15(1):8562. https://www.doi.org/10.1038/s41467-024-52087-x
• Sahm A, Cherkasov A, ... Hoffmann S. The Greenland shark (Somniosus microcephalus) genome provides insights into extreme longevity. bioRxiv [Preprint]. 2024 Sep 10:2024.09.09.611499. https://doi.org/10.1101/2024.09.09.611499
• Frolova D, Lima L, Roberts LW, Bohnenkämper L, Wittler R, Stoye J, Iqbal Z. Applying rearrangement distances to enable plasmid epidemiology with pling. Microb Genom. 2024 Oct;10(10):001300. https://www.doiorg/10.1099/mgen.0.001300
• Ghosh S, Tuz AA, Stenzel M, ... Heyer R, ... Sickmann A, Gunzer M. Proteomic characterization of 1,000 human and murine neutrophils freshly isolated from blood and sites of sterile inflammation. Mol Cell Proteomics. 2024 Oct 10:100858. https://www.doi.org/10.1016/j.mcpro.2024.100858
• Hofmann N, Bartkuhn M, Becker S, Biedenkopf N, Böttcher-Friebertshäuser E, Brinkrolf K, Dietzel E, Fehling SK, Goesmann A, Heindl MR, Hoffmann S, et al. Distinct negative-sense RNA viruses induce a common set of transcripts encoding proteins forming an extensive network. J Virol. 2024 Oct 22;98(10):e0093524. https://www.doi.org/10.1128/jvi.00935-24
• Dyer NP, Päuker B, Baxter L, Gupta A, Bunk B, Overmann J, Diricks M, Dreyer V, Niemann S, Holt KE, Rahman M, Brown PE, Stark R, Zhou Z, Ott S, Nübel U. EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens. Nucleic Acids Res. 2024 Oct 23:gkae902. https://www.doi.org/10.1093/nar/gkae902.
• Rolland C, Wittmann J, Reimer LC, Sardà Carbasse J, Schober I, Dudek CA, Ebeling C, Koblitz J, Bunk B, Overmann J. PhageDive: the comprehensive strain database of prokaryotic viral diversity. Nucleic Acids Res. 2024 Oct 7:gkae878. https://www.doi.org/10.1093/nar/gkae878
• Uszkoreit J, Marcus K, Eisenacher M. A Review of Protein Inference. Methods Mol Biol. 2025;2859:53-64. https://www.doi.org/10.1007/978-1-0716-4152-1_4
• Giurgiu M, Wittstruck N, ... Reinert K, Henssen AG. Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil. Genome Res. 2024 Oct 11;34(9):1355-1364. https://www.doi.org/10.1101/gr.279123.124
• Kim J, Jeong K, Kaulich PT, Winkels K, Tholey A, Kohlbacher O. FLASHQuant: A Fast Algorithm for Proteoform Quantification in Top-Down Proteomics. Anal Chem. 2024 Oct 18. https://www.doi.org/10.1021/acs.analchem.4c03117
• Dai C, Pfeuffer J, Wang H, Zheng P, Käll L, Sachsenberg T, Demichev V, Bai M, Kohlbacher O, Perez-Riverol Y. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nat Methods. 2024 Sep;21(9):1603-1607. https://www.doi.org/10.1038/s41592-024-02343-1
• Heumos L, Ehmele P, ... Eils R, Schiller HB, Hilgendorff A, Theis FJ. An open-source framework for end-to-end analysis of electronic health record data. Nat Med. 2024 Sep 12. https://www.doi.org/10.1038/s41591-024-03214-0.
• Bonder MJ, Clark SJ, Krueger F, ... Stegle O, Reik W, von Meyenn F. scEpiAge: an age predictor highlighting single-cell ageing heterogeneity in mouse blood. Nat Commun. 2024 Aug 31;15(1):7567. https://www.doi.org/10.1038/s41467-024-51833-5.
• Capraz T, Huber W. Feature selection by replicate reproducibility and non-redundancy. Bioinformatics. 2024 Sep 2;40(9):btae548. https://www.doi.org/10.1093/bioinformatics/btae548
• Martín R, Gaitán N,... Brors B, Royo R, Hupé P, Torrents D. ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers. Cell Genom. 2024 Sep 11;4(9):100639. https://www.doi.org/10.1016/j.xgen.2024.100639
• Garcia-Santamarina S, Kuhn M, ... Bork P, Typas A. Emergence of community behaviors in the gut microbiota upon drug treatment. Cell. 2024 Sep 19:S0092-8674(24)00966-8. https://www.doi.org/10.1016/j.cell.2024.08.037.
• Rakowski A, Monti R, Huryn V, Lemanczyk M, Ohler U, Lippert C. Metadata-guided feature disentanglement for functional genomics. Bioinformatics. 2024 Sep 1;40(Suppl 2):ii4-ii10. https://www.doi.org/10.1093/bioinformatics/btae403
• Mc Cartney AM, Formenti G, Mouton A, ... Grüning B, et al. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics. NPJ Biodivers. 2024 Sep 17;3(1):28. https://www.doi.org/10.1038/s44185-024-00054-6
• Fehrenbach A, Mitrofanov A, Alkhnbashi OS, Backofen R, Baumdicker F. SpacerPlacer: ancestral reconstruction of CRISPR arrays reveals the evolutionary dynamics of spacer deletions. Nucleic Acids Res. 2024 Oct 14;52(18):10862-10878. https://www.doi.org/10.1093/nar/gkae772
• Jayakodi M, ... Bunk B, ... Gundlach H, ... Mayer KFX, ... Scholz U, et al. Structural variation in the pangenome of wild and domesticated barley. Nature, 2024. https://doi.org/10.1038/s41586-024-08187-1
• D'Anna F, Jareborg N, Jetten M, … Lübke N.-C., … Schnitzer H, … Wibberg D, … Wittig U et al. A research data management (RDM) community for ELIXIR. F1000Research 2024, 13(ELIXIR):230. https://doi.org/10.12688/f1000research.146301.2
• König P, Fiebig A, Münch T, Grüning B, Scholz U: blast2galaxy: a CLI and Python API for BLAST+ and DIAMOND searches on Galaxy servers, Bioinformatics Advances, Volume 4, Issue 1, 2024, vbae185, https://doi.org/10.1093/bioadv/vbae18

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