3^rd BioHackathon Germany – Call for project proposals open

• promote the development of an open source data integration infrastructure that will accelerate scientific innovation. This includes areas such as FAIR, identifiers, metadata standards, ontologies and metadata catalogues
• engage technical people from the bioinformatics community within and beyond de.NBI / ELIXIR-DE to collaborate on topics of common interest aligned with de.NBI / ELIXIR-DE activities
• strengthen and enable interactions and collaborations with ELIXIR, NFDI and other bioinformatics related projects through joint activities
• provide networking opportunities for all participants.

We hope to attract interesting hacking projects and a large number of participants from de.NBI, ELIXIR Germany, other ELIXIR nodes and other interested parties and would like to encourage the participation of industry.
We have opened project proposals for 2024! 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 1 July 2024. Further information can be found here.

de.NBI/ELIXIR-DE All Hands Meeting – Save the date!

The de.NBI / ELIXIR-DE All Hands Meeting 2024 will take place in Berlin on 28 - 29 November 2024. This event is open for all members of de.NBI and ELIXIR-DE and is intended to exchange information, to communicate and to network. Reports on the activities of the network, especially the service centers and working groups, are planned. Information will directly be spread through internal network communication channels.

News from de.NBI/ELIXIR-DE

Re-activation of three de.NBI working groups
At their last meeting in May 2024, the Central Coordination Unit (CCU) of de.NBI decided to reactivate the former SIGs “Training”, “Service” and “Cloud” to support, unify and further develop the network's activities. The participants in these working groups are currently being nominated by the service centers. Further members of de.NBI who are interested in participating in these working groups are welcome to contact the This email address is being protected from spambots. You need JavaScript enabled to view it..
The formation of other working groups will be subject of further discussions.

ELIXIR Germany Node Review: achieving milestones and charting the path forward
The German Node underwent a periodic review by the ELIXIR SAB on 14 February 2024 to evaluate its progress and receive recommendations. The SAB congratulated the Node on securing permanent funding and commended its resilience during a challenging restructuring phase. They emphasized the significance of the de.NBI Cloud within the network and also called for Node to maintain its computing infrastructure while expanding its capacity to meet the growing demand. Additionally, they recommended finding ways to integrate groups that are currently not affiliated with the Node but interested in contributing to its activities. Overall, the report was highly positive and the SAB expressed satisfaction with the progress made.

  News from ELIXIR

• NSCoS—ELIXIR Nodes Support CoS
• PeoplePulse—Facilitating personal and professional growth through strategic programs within ELIXIR
• TtT—ELIXIR Train the Trainer

These projects aim to equip the Nodes with effective management skills, enhancing both internal node operations and the overall effectiveness of ELIXIR.

In addition, the ELIXIR Infrastructure Services CoS (24-TECH-infraserv) was launched within the Technology Tier on 1 April 2024. Within this project the two fundamental ELIXIR Infrastructure Services ELIXIR Authentication and Authorization Infrastructure (AAI) and the Training e-Support System (TeSS) receive funding. This project will introduce a new model of core operational, maintenance, and governance funding for these services, intended to complement feature development funding from other sources. An oversight team will evaluate the Infrastructure Services for impact and value for money, develop a protocol for managing the portfolio and its selection, and provide recommendations for future continuation or modification of the funding model. Currently, two additional services, ELIXIR Beacon Network and ELIXIR Research Software Ecosystem are under consideration as future Infrastructure Services. Find more information here.

ELIXIR-DE is co-leading two out of these four projects, demonstrating our active involvement and leadership within the ELIXIR network.

New Focus Group in ELIXIR
ELIXIR has launched the new Focus Group "Domestic Animals Genome and Phenome Focus Group" led by Emily Clark (UK), Martien Groenen (NL), Peter Harrison (EMBL), Catherine Larzul (Fr), 3 June 2024. This group aims to facilitate genotype-to-phenotype analysis for both farmed and companion animal species. Bridging researchers and data scientists across different species and countries is crucial to expedite genotype-to-phenotype research in domestic animals and establish a unified, transparent, and standardized data lifecycle. The group is still looking for members, and interested individuals are welcome to subscribe to the mailing list here.

New version of the ELIXIR Handbook of Operations

ELIXIR has released the 7^th edition of its Handbook of Operations. This handbook serves as a centralized resource for ELIXIR's operational framework, encompassing standard procedures and processes. The handbook is intended for ELIXIR staff, but it may also be useful for external collaborators. 

Since 2013, ELIXIR partners with the open research publisher F1000 on the ELIXIR Gateway, which acts as a hub for ELIXIR articles, documents, slides, and posters. The ELIXIR Gateway Advisory Board has recently been renewed. One of the new members is Irena Maus, Node Coordinator of the ELIXIR-DE. The Advisory Board reaffirms ELIXIR’s commitment to transparent and open communication in the research community. Insights from the Board members emphasize their shared goal of shaping ELIXIR’s future and providing a central location for bioinformatics and computational biology information which is available to the wider research community.

Review on the ELIXIR All Hands Meeting 2024

The eleventh ELIXIR All Hands meeting 2025 will take place in Thessaloniki, Greece.

Review on the BrAPI Hackathon in April 2024

The hackathon's outcomes are set to influence BrAPI's future development, with teams committed to ongoing collaboration. For more details and future events, visit BrAPI's official website.

Review on the de.NBI Spring School 2024

The de.NBI Spring School 2024 -Bioinformatics for Microbial Omics took place from 18-22 March at Bielefeld University. The training event was jointly organized by the Service Center BiGi and the de.NBI/ELIXIR-DE Administration Office. Out of 72 applications, 21 candidates were selected and invited to Bielefeld (see foto). The aim of this de.NBI Spring School was to provide insights into microbial bioinformatics for genomics, pangenomics, metagenomics and multi-omics analysis. Participants were introduced to the genomics workflow and gained an understanding of the capabilities and limitations of genome sequencing and sequence analysis. Keynotes were given by Oliver Schwengers (University Gießen), Jochen Blom (University Gießen), Florian Centler (University of Siegen) and Sandra Smit (Wageningen University & Research). 

News on the de.NBI Cloud

• News on de.NBI Cloud facilities:
  • de.NBI Cloud Bielefeld successfully passed their certification audit for their ISO27001:2022 ISMS certification in Mid-March.
  • de.NBI Cloud Gießen will migrate to their new datacenter infrastructure in mid-June of 2024.
  • de.NBI Cloud EMBL will decommission its OpenStack project offering by 30 June 2024. All affected projects have been contacted to discuss migration paths to other de.NBI Cloud locations or to EMBL’s Kubernetes environment. Please contact us in case of questions.

• de.NBI Cloud activities:
  • The de.NBI Cloud Portal team presented SimpleVM at this year’s ELIXIR All Hands Meeting in June in Uppsala, Sweden and will present both SimpleVM and the de.NBI Cloud at the EGI conference in September 2024 in Lecce, Italy.
  • The de.NBI Cloud Trusted Research Environments were presented as part of the EOSC ENTRUST Blueprint Roadmap Workshop in May 2024. The de.NBI Cloud participates in EOSC ENTRUST as part of the providers’ forum.
  • The de.NBI Cloud Federation was presented to the NFDI AG Multi-Cloud in May 2024. 

• Current figures on the de.NBI Cloud: Number of users: 3262, number of active projects: 661, number of publications referencing the use of the de.NBI Cloud: 1008. This equals an increase of ~7% in users, ~4.9% in projects and of ~14.8% in publications, respectively, since February 2023.

• Two new testimonials on the use of the de.NBI Cloud for Single Cell Meta Analysis and Studying the dynamics of m6A modifications in mouse brain have been published.

News on Services

PanBARLEX is a web portal that offers convenient access to gene annotations and orthologous gene groups of 76 different barley genotypes that together define a pangenome. The portal encompasses a total of 3,797,824 annotated genes, with 3,730,725 genes identified as orthologs grouped into 95,237 orthogroups determined through an analysis with OrthoFinder. The portal features versatile entry points, including the ability to locate genes by their IDs, conduct searches based on functional annotations and perform gene queries through a BLAST database search using user-defined DNA or amino acid query sequences. PanBARLEX serves as a comprehensive and valuable resource, combining extensive gene annotations, user-friendly entry points and useful analytical tools to advance research and understanding of the barley pan genome.

Galaxy Annual Report 2023 published

The Freiburg Galaxy Team published the Galaxy Annual Report 2023 which provides a summary of the Galaxy activities and achievements in 2023. The Galaxy framework is an open-source platform for FAIR (findable, accessible, interoperable, reusable) data analysis. Galaxy has become one of the largest and most widely used open source platforms for the analysis of scientific data used by over 500,000 users worldwide.
More detailed information can always be found at the group homepage, The European Galaxy Project https://galaxyproject.eu.

• Alfred: Update 0.3.1 of this NGS alignment quality control method, was released in March 2024.
• BacDive underwent a mini update in May 2024: pages now contain links to the new PhageDive database for information on prokaryotic viruses. Furthermore, new 16S rRNA gene sequences were automatically matched to BacDive strains. Additionally, several small bugs were fixed to improve the BacDive user experience.
• Bakta: v1.9.3 fixed a regex in the CRISPR parser skipping spacers, wrong Piler-CR CRISPR array stop position, and added paredt ID to CRISPR repeat/spacer features in GFF3 outputs
• Bioconductor 3.19 released, consisting of 2300 software packages, 430 experiment data packages, 926 annotation packages, 30 workflows and 5 books. There are 80 new software packages, 10 new data experiment packages, 5 new annotation packages, no new workflows, 1 new book, and many updates and improvements to existing packages. This release also includes updated Bioconductor Docker containers.
• CNApy (CellNetAnalyzer for python) update 1.1.11:  Besides a multitude of bug fixes one can now easily take a map screenshot, EFMs can now be easily normalized and scenario-dependent annotations were added (e.g., for scenario-dependent variances or thermodynamic parameter values).
• COPASI: stable release 4.43 (Build 288). More information can be found in the changelog.
• EURISCO, European Search Catalogue for Plant Genetic Resources, has been extended by national inventory data of eight countries.
• European Galaxy Server: The tools on UseGalaxy.eu were updated by an automated tool update and installation process.
• Galaxy: The new release v 24.0 contains several improvements to the workflow user interface and card view.
• iTOL v6: Features and improvements of the v6 update are described by Letunic and Bork in Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool.
• OpenMS 3: In their paper "OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data" published by Pfeuffer et al. the extention of the capabilities of OpenMS beyond bottom-up proteomics to include high-throughput workflows in top-down proteomics, metabolomics, structural biology and oligonucleotide mass spectrometry, are described.

Recent Publications by de.NBI partners

• Hauswedell H, Hetzel S, Gottlieb SG, Kretzmer H, Meissner A, Reinert K. Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics. 2024. https://doi.org/10.1093/bioinformatics/btae097
• Bauer J, Klamt S. OptMSP: A toolbox for designing optimal multi-stage (bio)processes. J Biotechnol. 2024; 383:94-102. https://doi.org/10.1016/j.jbiotec.2024.01.009
• Hönig SMN, Flachsenberg F, Ehrt C, Neumann A, Schmidt R, Lemmen C, Rarey M. SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. J Comput Aided Mol Des. 2024; 38(1):13. https://doi.org/10.1007/s10822-024-00551-7
• Marconato L, … Huber W, Gerstung M, Moore J, Theis FJ, Stegle O. SpatialData: an open and universal data framework for spatial omics. Nat Methods. 2024 Mar 20. https://doi.org/10.1038/s41592-024-02212-x
• Mueller HM, … Mayer KFX et al. Integrative multi-omics analyses of date palm (Phoenix dactylifera) roots and leaves reveal how the halophyte land plant copes with sea water. Plant Genome. 2024;17(1):e20372. https://doi.org/10.1002/tpg2.20372
• Palmowski L, … Eisenacher M, Rahmel T; SepsisDataNet.NRW research group. Assessing SOFA score trajectories in sepsis using machine learning: A pragmatic approach to improve the accuracy of mortality prediction. PLoS One. 2024; 19(3):e0300739.https://doi.org/10.1371/journal.pone.0300739
• Blumenkamp P, Pfister M, Diedrich S, Brinkrolf K, Jaenicke S, Goesmann A. Curare and GenExVis: a versatile toolkit for analyzing and visualizing RNA-Seq data. BMC Bioinformatics. 2024,25(1):138. https://doi.org/10.1186/s12859-024-05761-2
• Röhl A, Netz E, Kohlbacher O, Elhabashy H. CLAUDIO: automated structural analysis of cross-linking data. Bioinformatics. 2024;40(4). https://doi.org/10.1093/bioinformatics/btae146
• Schmitz JE, Aggarwal N, Laufer L, Walter J, Salhab A, Rahmann S. EpiSegMix: a flexible distribution hidden Markov model with duration modeling for chromatin state discovery. Bioinformatics. 2024;40(4). https://doi.org/10.1093/bioinformatics/btae178.
• Gavriilidis GI, Vasileiou V, Orfanou A, Ishaque N, Psomopoulos F. A mini-review on perturbation modelling across single-cell omic modalities. Comput Struct Biotechnol J. 2024;23:1886-1896. https://doi.org/10.1016/j.csbj.2024.04.058
• Olecka M, … Hoffmann S. Nonlinear DNA methylation trajectories in aging male mice. Nat Commun. 2024;15(1):3074. https://doi.org/10.1038/s41467-024-47316-2
• Tiniakou I, … Ohler U et al. Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation. Sci Immunol. 2024 12;9(94):eadi1023. https://doi.org/10.1126/sciimmunol.adi1023
• Paulikat AD, Schwudke D, Hammerschmidt S, Voß F. Lipidation of pneumococcal proteins enables activation of human antigen-presenting cells and initiation of an adaptive immune response. Front Immunol. 2024;15:1392316. https://doi.org/10.3389/fimmu.2024.1392316
• Galvis J, … Grüning B et al. DIMet: An open-source tool for Differential analysis of targeted Isotope-labeled Metabolomics data. Bioinformatics. 2024 May 2;40(5). https://doi.org/10.1093/bioinformatics/btae282
• Reim T, Ehrt C, Graef J, Günther S, Meents A, Rarey M. SiteMine: Large-scale binding site similarity searching in protein structure databases. Arch Pharm (Weinheim). 2024; 357(5). https://doi.org/10.1002/ardp.202300661
• Steffens S, … Backofen R, … Sickmann A, et al. The challenges of research data management in cardiovascular science: a DGK and DZHK position paper-executive summary. Clin Res Cardiol. 2024;113(5):672-679. https://doi.org/10.1007/s00392-023-02303-3

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