New de.NBI/ELIXIR-DE consortium treaties in effect

New de.NBI/ELIXIR-DE consortium – national contract signed

With the signing of the cooperation agreement with Forschungszentrum Jülich in December 2023, the new de.NBI/ELIXIR-DE consortium now consists of 24 contracting partners, who are also members of the German ELIXIR node. The consortium can now resume full activity. Two CCU meetings and plenary meetings each have resumed since November 2023. 

The new ELIXIR Collaboration Agreement was signed in December 2023 after the conlusion of the national agreement. Within this framework, Forschungszentrum Jülich took on the role of the Representing Entity for the German Node. The Germany node consists of the 24 contractual partners from German universities and research institutions representing a wide range of scientific expertise in various bioinformatics topics.

In December 2023, the de.NBI General Assembly has voted in favour of a double leadership for the management of the network and elected Prof Oliver Kohlbacher (University of Tübingen) and Prof Alexander Sczyrba (Forschungszentrum Jülich) as scientific spokespersons. Furthermore, the FZJ Board of Directors and the BMBF have appointed O. Kohlbacher and A. Sczyrba as the new joint Heads of Nodes of ELIXIR Germany. Thus, as scientific spokesperson of de.NBI and Head of Node of ELIXIR Germany, O. Kohlbacher and A. Sczyrba will act as double leadership and in personal union. They succeeded Andreas Tauch and Alfred Pühler as Head of Node in January 2024 and already participated in HoN meetings. The role of the Administrative Coordinator has been taken over by Dr Tanja Dammann-Kalinowski (Forschungszentrum Jülich).

Making training material FAIR is not an easy task. The ELIXIR FAIR training focus group just released a handbook to help trainers make their material FAIR. The training coordinators of ELIXIR Germany, H. Schnitzer and D. Wibberg, who are members of the FAIR training focus group, were involved in preparing the handbook. This ten-chapter book gives simple, step-by-step guidance for trainers, training coordinators, and train-the-trainers. This is a major effort of people in the ELIXIR training platform and beyond. Check it out here: FAIR training handbook.

  News from ELIXIR

On 1 March 2024, the ELIXIR Hub welcomed Tim Hubbard in his new role as ELIXIR Director. Andy Smith remains Interim Director until 31 May, with responsibilities gradually transitioning to Tim.
Tim Hubbard joins ELIXIR from King's College London where he held the position of Professor of Bioinformatics in the Department of Medical and Molecular Genetics. He has also acted as Senior Advisor at Genomics England and Associate Director of the London region of Health Data Research UK (HDR UK). He replaces Niklas Blomberg, ELIXIR’s founding Director, who started a new role as Executive Director of the Innovative Health Initiative (IHI) in January 2024.

ELIXIR has published its new Scientific Programme, setting out the European life science data infrastructure’s vision for the coming five years. The Scientific Programme forms ELIXIR’s strategy and sets out its ambitions and goals until 2028. The ELIXIR Programme is developed with extensive input from expert working groups across ELIXIR’s 22 Nodes.
The 2024-28 Scientific Programme outlines how ELIXIR will achieve its purpose of working together to accelerate the understanding of life. ELIXIR’s new strategic priorities recognise the importance of not only scientific and technological investments, but also building capacity in ELIXIR Nodes and developing ELIXIR people.

ELIXIR has launched eight new projects addressing the scientific and technological ambitions of its new Scientific Programme for 2024 to 2028. ELIXIR Germany members are participating the five technical platform projects. There is one new project for each of ELIXIR’s three priority scientific areas: Cellular and molecular research; Biodiversity, food security and pathogens; and Human data and translational research. New co-leads were recently announced for the first two areas, and the associated projects fund leadership and strategy development, ELIXIR community engagement and the provision of funding calls and pilot projects. Calls for participation in various workpackages of  the science tier projects will open by the end of March 2024. Projects covering the Programme’s Node and people development objectives will be launched later this year.  

The projects were launched on 1 January 2024 and run for three years with funding of €4.5M. Called ‘Commissioned Services’, the projects fund activities which connect experts in ELIXIR Nodes and support the long-term strategy of ELIXIR.

On 1 February 2024, ELIXIR announced the start of the EU-funded ELIXIR-STEERS project, a three-year initiative with a budget of €4M. The project is a collaboration between all ELIXIR Nodes, encompassing 36 institutes across 23 countries, plus EMBL-EBI. It aims to enhance large-scale, cross-border federated analysis in the life sciences throughout the European Research Area.
ELIXIR-STEERS addresses the need for good software and workflow management, sometimes overlooked by funders and policymakers, which is essential for reproducible and efficient analysis of life science data. By adopting common analysis tools and good workflow practices, the project aims to minimise duplication, reduce energy consumption and lower the carbon footprint in computational life science, particularly in resource-intensive applications like AI. For ELIXIR Germany Björn Grüning (Freiburg University) will participate in WP3 "Integrating optimisation criteria for environmental impact in commonly used workflow management systems".  

Review of the 2^nd BioHackathon Germany 2023

The 2^nd BioHackathon Germany hosted by de.NBI/ELIXIR-DE took place in Bielefeld from 11-15 December 2023. In this hybrid event 11 hacking projects were carried out with all in all 200 participants, 85 of them on-site. The 5-day event was accompanied by a visit to the Bielefeld Christmas market, a bowling night, a guided Dr. Oetker tour, and a party at the discotheque Stereo with DJ Tinitus on the last evening giving time for lots of networking.

Due the great success of the first two BioHackathon Germany editions, de.NBI/ELIXIR Germany will run the 3^rd BioHackathon Germany 2024 in Kassel at Hotel La Strada from 9-13 December 2024. We hope to encourage ELIXIR Germany and non-ELIXIR Germany participants to take part, as well as to attract industry engagement. More information and call for project applications will follow in April, stay tuned!

News on the de.NBI Cloud

• News on de.NBI Cloud facilities:
  • SimpleVM is now available at the German Cancer Research Centre (DKFZ) and the first six projects are already using the resources provided. SimpleVM is an abstraction layer on top of OpenStack that simplifies and streamlines the usage of different OpenStack clouds.
  • de.NBI Cloud Bielefeld is currently preparing for their ISO27001:2022 ISMS certification surveillance audit in March.
  • de.NBI Cloud Gießen is building up their new datacenter infrastructure which will also host the de.NBI Cloud hardware in the near future.
  • de.NBI Cloud EMBL will decommission its OpenStack project offering by 30 June 2024. Projects will be contacted to discuss migration paths to other de.NBI Cloud locations or to EMBL’s Kubernetes environment. Please contact us in case of questions.
  • The de.NBI Cloud governance is participating in the EOSC Entrust Provider Forum on Trusted Research Environments. 

• Current figures on the de.NBI Cloud: Number of users: 3049, number of active projects: 630, number of publications referencing the use of the de.NBI Cloud: 878. This equals an increase of 5,6% in users, 8,43% in projects and of 9,75% in publications, respectively, since November 2023.

News on Services

• BacDive has been selected as a new ELIXIR Core Date Resource, joining a list of now 32 renowned European life science data resources that are important to biological and biomedical research and long-term preservation of biological data. A New BacDive Release features the integration of a large set of phenotypic and metabolic data. BacDive now provides data on 97,334 strains, 4080 of which were newly added. The number of total filled data fields grew by almost 30% to 2,675,988 entries. The strain pages now contain links to the newly revived StrainInfo database for strain identity information and the resolution of strain identifiers 
• BRENDA: With the start of 2024, the migration of BRENDA to the DSMZ has been completed. All BRENDA services are now running on a new IT infrastructure and we can once again focus on the further development and updates.
• COPASI stable release 4.42 is available (Build 284). Some problems have been fixed and new features implemented. 
• EURISCO, European Search Catalogue for Plant Genetic Resources: As part of the project "Extension of EURISCO for Crop Wild Relatives (CWR) in situ data and preparation of pilot countries' data sets", the EURISCO infrastructure has been extended for the management of in situ CWR data, and modules for uploading, checking and integrating this data into EURISCO have been developed. Data on the first in situ CWR populations from six countries were uploaded and the web interface was expanded to include simple filter options. Further, national Inventory data of several countries were updated.
• FAIRDOM-SEEK: version 1.14.2 is a patch release that includes some important bug fixes and improvements.
• usegalaxy.eu is now an ELIXIR Recommended Interoperability Resource (RIR), an ELIXIR Service that, among other things, supports description, reporting, annotation, sustainability and provision of biological data. Through this, an RIR facilitates interoperability and (re-)usability of knowledge, thus supporting the FAIR Principles.
• PANGAEA's data warehouse functionality was enhanced to return a list of all dataset citations in various formats that are required to be cited when using the compiled warehouse output.
• SABIO-RK v. 2.21: database and software were updated, in particular by adding new publications. In addition, UniProtID’s and cellular locations were added in the Bar Chart Search. 

Recent Publications by de.NBI partners

• Schäfer RA, Rabsch D, Scholz GE, Stadler PF, Hess WR, Backofen R, Fallmann J, Voß B. RNA interaction format: a general data format for RNA interactions. Bioinformatics 2023. https://doi.org/10.1093/bioinformatics/btad665
• Schleussner N, Cauchy P, Franke V, …, Akalin A, …, Rajewsky K et al. Transcriptional reprogramming by mutated IRF4 in lymphoma. Nat Commun. 2023 Nov 7. https://www.nature.com/articles/s41467-023-41954-8
• Toussaint PA, Leiser F, Thiebes S, Schlesner M, Brors B, Sunyaev A. Explainable artificial intelligence for omics data: a systematic mapping study. Brief Bioinform. 2023 Nov 22. https://doi.org/10.1093/bib/bbad453
• Jeong K, Kaulich PT, ..., Kohlbacher O. Precursor deconvolution error estimation: The missing puzzle piece in false discovery rate in top-down proteomics. Proteomics. 2023. https://doi.org/10.1002/pmic.202300068
• Kumar A, Grüning B, Backofen R. Transformer-based tool recommendation system in Galaxy. BMC Bioinformatics. 2023 Nov 27. https://doi.org/10.1186/s12859-023-05573-w
• Dumschott K, Dörpholz H, …, Usadel B, Neumann S et al. Ontologies for increasing the FAIRness of plant research data. Front Plant Sci. 2023 Nov 30. https://doi.org/10.3389/fpls.2023.1279694
• David R, Rybina A, …, Coppens F, …, Grüning B, …, Wagener H et al. "Be sustainable": EOSC-Life recommendations for implementation of FAIR principles in life science data handling. EMBO J. 2023 Dec 1. https://doi.org/10.15252/embj.2023115008
• Sung HM, Schott J, ..., Ohler U, Stoecklin G. Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing. J Cell Biol. 2023 Dec 4. https://doi.org/10.1083/jcb.202111151
• Müller P, …, Bork P et al. High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities. Nat Protoc. 2023 Dec 13. https://doi.org/10.1038/s41596-023-00926-4
• Schmidt TSB, …, Bork P. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Res. 2024 Jan 5. https://doi.org/10.1093/nar/gkad943
• Köhler CU, Schork K, Turewicz M, Eisenacher M et al. Use of Multiple Machine Learning Approaches for Selecting Urothelial Cancer-Specific DNA Methylation Biomarkers in Urine. Int J Mol Sci. 2024 Jan 6. https://doi.org/10.3390/ijms25020738
• Flachsenberg F, Ehrt C, Gutermuth T, Rarey M. Redocking the PDB. J Chem Inf Model. 2024 Jan 8. https://doi.org/10.1021/acs.jcim.3c01573
• Schwarzl T, ..., Backofen R, Huber W et al. Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq. Nucleic Acids Res. 2024 Jan 11. https://doi.org/10.1093/nar/gkad998
• Boutros M, …, Stegle O et al. UNCAN.eu: Toward a European Federated Cancer Research Data Hub. Cancer Discov. 2024 Jan 12. https://doi.org/10.1158/2159-8290.CD-23-1111
• Espinel-Ríos S, Morabito B, ..., Klamt S, Findeisen R. Toward a modeling, optimization, and predictive control framework for fed-batch met abolic cybergenetics. Biotechnol Bioeng. 2024. https://doi.org/10.1002/bit.28575
• Witting M, …, Hoffmann N, Kopczynski D, et al. Challenges and perspectives for naming lipids in the context of lipidomics. Metabolomics. 2024 Jan 24. https://doi.org/10.1007/s11306-023-02075-x
• Pan C, Reinert K. A simple refined DNA minimizer operator enables twofold faster computation. Bioinformatics. 2024 Jan 25. https://doi.org/10.1093/bioinformatics/btae045
• Larivière D, …, Grüning B et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nat Biotechnol. 2024 Jan 26. https://doi.org/10.1038/s41587-023-02100-3
• Heyer R, …, Maus I, …, Sczyrba A, …, Reichl U, Benndorf D. Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter. Water Res. 2024 Feb 15. https://doi.org/10.1016/j.watres.2023.121020
• Rocha U, …, Stadler PF, CLUE-TERRA Consortium. MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy. Mol Ecol Resour. 2024 Feb. https://doi.org/10.1111/1755-0998.13904

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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.