Newsletter 34 is out now!

Next Event: 23 Nov 2023, Annual Meeting of the de.NBI Industrial Forum

• Big data Handling in Plant breeding (BioSolveIT GmbH)
• Big cohort analysis for 4D-metablomics, lipidomics and proteomics (Bruker Daltonik GmbH & Co. KG)
• Flexible and scalable infrastructure for data driven synthetic biology using cloud computing (Cambrium GmbH)
• The impact of artificial intelligence ind clinical research (Dell Technologies)
• Big data handling in the life sciecnes making data actionable (ITTM S.A.)
• Empowering insight in KNIME from big data to large language models (KNIME GmbH)
• Big Data handling in Plant breeding (KWS Saat SE)
• Empowering life science innovation through integrated data management: From instruments to the cloud with FAIR data (Wiens Synefex GmbH)

de.NBI Spring School 2024

de.NBI will continue its very successful school training program with the de.NBI Spring School 2024 on Bioinformatics for Microbial Omics to be held in Bielefeld from 18-22 March, 2024. It will be organized by the CAU and the Bielefeld-Gießen Resource Center for Microbial Bioinformatics (BiGi).
The BiGi center is specialized in the field of Omics data analysis for microbes and is well-known for its software platforms. This de.NBI Spring School will focus on genomics, pangenomics, metagenomics and multi omics analysis. During the training, participants will gain insights into state-of-the-art bioinformatics tools. Participants will be introduced to the genomics workflow and gain an understanding of the possibilities and limitations of genome sequencing and sequence analysis. The de.NBI Spring School 2024 will cover lectures and hands-on sessions by de.NBI and renowned experts in the fields and is aimed at PhD students, postdoctoral fellows or other scientists with a solid background in bioinformatics and molecular biology.
Registration will open in the second week of January 2024.

News from ELIXIR

Niklas Blomberg will step down as ELIXIR's Director at the end of this year to join the Innovative Health Initiative (IHI) as Executive Director. The ELIXIR Board has approved the recommended candidate for the Director position, and details about the new Director will be confirmed soon. In the meantime, the Board appointed Andrew Smith as interim Director, for an initial term of six months, from December 2023 to May 2024.

Alexander Goesmann elected Chair of the ELIXIR Board
Prof. Alexander Goesmann (Germany) from the Justus-Liebig University Giessen was elected the Chair of the ELIXIR Board for the years 2024 and 2025 during the ELIXIR Board meeting on 30-31 Oct 2023 in Barcelona. He succeeds Prof. Ferran Sanz (Universitat Pompeu Fabra, Spain). Additionally, Prof. Christine Orengo (University College London, UK) has been appointed Vice-Chair of the Board for 2024 and 2025, together with Zsuzsanna Dosztányi (Eötvös Loránd University, Hungary). With this, Germany holds a notable representation on the Board.

• Bridging Academia and Industry with Training: Bérénice Batut (Freiburg University), Isabela Paredes Cisneros, Lisanna Paladin, Renato Alves (all EMBL Heidelberg), and Nils-Christian Lübke (Forschungszentrum Jülich).
• Mongoose (Multi‐Objective Network Generator Of Optimized Single‐cell Experiments): Naveed Ishaque (Charité Berlin).
• Strengthening interactions between the ELIXIR Community and the Australian BioCommons with a focus on capacity building through training, especially for system and service administrators: Björn Grüning and Mira Kuntz (Freiburg University).
• Bringing together Galaxy users and developers to expand the tools available for the single-cell community: Björn Grüning (Freiburg University).

ELIXIR launched the ELIXIR Impact Toolkit
ELIXIR has released an Impact Toolkit providing practical guidance on the process of impact evaluation. Publication: De Ruyck K, Melo AMP, Stansberg C, ..., Hoffman N, ..., Maus I, ...,  Schnitzer H et al. (2023) ELIXIR’s Impact Toolkit, to support performance and impact evaluation in a distributed data research infrastructure for the life sciences. F1000Research 2023, https://doi.org/10.7490/f1000research.1119614.1

Galaxy turned 18 years old!

Since the initial publication of Galaxy: a platform for interactive large-scale genome analysis in September 2005, a multitude of subsequent papers, authored by both the Galaxy team and its users, have contributed to Galaxy's extensive citation record, exceeding 12,000 globally. This pivotal paper marked the establishment of the global Galaxy community, significantly influencing computational biology and related fields. Congratulations to the inventors, contributors, and supporters on 18 years of success! Here's to looking forward to another 18 years of continuous innovation and collaboration! More details see here.

de.NBI Summer School 2023 - a review

The 9^th de.NBI Summer School focusing on Bio Data Analysis for Life Sciences, was hosted from 25-29 September 2023 at Bielefeld University. The training event was conducted by the CAU and the ELIXIR DE Officers.
During the one-week event, 19 participants learned that modern high-throughput-omics technologies in the life science field produce large quantities of data. Besides new challenges for analyzing and visualizing big amounts of data, the management and sharing has become an important issue in the daily research process. The 2023 Summer School gave e.g. an overview of Bioschemas and their benefits for both, data producers and data consumers. Furthermore, de.NBI trainers provided introductions to recent technologies for processing and inspecting these data, e.g. the de.NBI Cloud, Galaxy or CWL. Furthermore, the course featured a number of interesting lectures and hands-on sessions by de.NBI speakers and renowned experts, e.g. the keynote speakers Nick Juty (The University of Manchester), Björn Grüning (Freiburg University) and Veit Schwämmle (University of Southern Denmark). Find the detailed program here.

Review of the BioHackathon Europe 2023

The ELIXIR BioHackathon Europe 2023, held in Barcelona, Spain from 30 Oct - 3 Nov, attracted more than 180 on-site and 160 virtual participants to work on 35 life science projects. It successfully brought together bioinformatics experts, developers, and industry professionals to collaborate, innovate, and address challenges in the bioinformatics field. The event's emphasis on open science, data integration, and interdisciplinary collaborations has paved the way for advancements in bioinformatics research. The development of open-source tools, adoption of FAIR data principles, and strengthened collaborations will undoubtedly contribute to the growth and progress of the field, ultimately benefiting the wider scientific community and society as a whole.
ELIXIR Germany was represented with a big team as depicted in the photograph and involded in numerous projects. The ELIXIR adminstration office staff was especially involved in especially project 34 “SPLASH”, where Helena Schnitzer and Daniel Wibberg co-created content for the ELIXIR training page currently under construction. Nils Hoffmann co-led projects 6 “BioModelsML” and 18 “FAIRification of mass spectral library creation” and worked with on-site and remote participants from Czechia, Germany, UK and the Netherlands on improving FAIRness and reproducibility in mass spectrometry-based metabolomics and proteomics.

The next Hacking Event is just around the corner:
The de.NBI/ELIXIR Germany administration office is looking forward to the 2^nd BioHackathon Germany 2023 in Bielefeld from 11-15 December 2023. Apart from 11 interesting hacking projects, we will offer lots of chances for diversion and networking. See you there!

News on the de.NBI Cloud

The 6^th de.NBI Cloud User Meeting 2023 will take place as a 3-day event 27-29 November 2023 in Bielefeld. It will provide hands on training to get started with your project on the de.NBI Cloud.

• News on de.NBI Cloud facilities:
  • The de.NBI Cloud site Freiburg has passed its second ISMS certification surveilliance audit according to ISO 27001.
  • The de.NBI Cloud site in Bielefeld has installed eight new GPU servers, adding a total of 32 Nvidia A40 GPUs to the site's hardware support for AI and ML applications. These will be made available successively throughout Q4 of 2023.
  • The de.NBI Cloud site at EMBL has added two new GPU servers that are available from their Kubernetes environment.
  • de.NBI Cloud sites Bielefeld and Gießen: The migration of regular projects (without cluster or workshop functionality) to the updated SimpleVM infrastructure has been completed, providing a more modern and user-friendly environment.

• Current figures on the de.NBI Cloud: Number of users: 2887, number of active projects: 581, number of publications referencing the use of the de.NBI Cloud: 800. This equals an increase of 6,3% in users, 3,2% in projects and of 5,5% in publications, respectively, since September 2023.
• Four new testimonials on the de.NBI Cloud. Users report their experiences with the de.NBI Cloud for their application of the workshop mode for the SPAAM 2023 Summer School (thematic field of ancient metagenomics), transposon element annotation, bacterial pathobiome assicciated with crown gall disease, and an extraordinary reliability of the open stack asset.

News from de.NBI and ELIXIR DE Office

Alexander Sczyrba appointed Director of section IBG-5 "Computational Metagenomics" at FZJ
Dr. Alexander Sczyrba, Professor of Computational Metagenomics at Bielefeld University, has been appointed Director of the recently founded section "Computational Metagenomics" (IBG-5) at the Institute of Bio- and Geosciences (IBG) of Forschungszentrum Jülich. The section is located as a branch office at Bielefeld University and hosts three departments: "Computational Metagenomics", Administration Office of the German Network for Bioinformatics Infrastructure (de.NBI)" and the Administration Office of ELIXIR Germany. This is an important step forward towards the continuation of de.NBI and ELIXIR Germany.

Science communication of a different kind
Johanna Nelkner, Service Coordinator at the de.NBI administration office, has won this year's LifeScienceXplained prize from Sartorius for her children's book "Bakterien und so, die leben wo?!" The prize is awarded to communicators who explain the workings of the life sciences and the resulting novel medical applications to a wide audience in a particularly understandable, innovative and creative way. The illustrated book is designed for 3-6-year-old children. They learn that bacteria live everywhere: In snow and ice, on hot volcanoes, in the deepest oceans and the highest clouds. And also in our bodies. 

News on Services

Recent updates of services: 

• Bioconductor: release 3.18 with 69 new software packages, 10 new data experiment packages, 8 new annotation packages, 1 new book, and many updates and improvements to existing packages.
• BRENDA: Now available to download in json format! Some of the central management database was migrated to new servers. A new user ssytem has been enabled with should resolve problems with undelivered registration emails, and the user database was cleaned up.
• CellNetAnalyzer: New version 2023.1 providing new features and more flexibility in loading/combining scenarios
• COPASI: Stabel release 4.40 (Build 278). It is a bug fix release and does not include new features.
• Eurisco: European Search Catalogue for Plant Genetic Resources. National inventories of 2 further countries updated.
• FAIRDOM-SEEK: Release 1.14.0 which is a major release that contains a number of improvements, upgrades and bug fixes.
• Galaxy: Release 23.1 now containing a universal notification framework. Check out the highlights here.
• European Galaxy Server: A lot of new exciting developments have been made in Galaxy for the annotation of genomes! Many state-of-the-art genome annotation tools were integrated into Galaxy! For further details and a complete list see here.
• Galaxy Europe has a brand new subdomain, an approach to observation and modelling of the Earth System, Environment and Biodiversity. Further details are outlined here.
• IndelCallingWorkflow: Release 2.4.1-2 with minor changes on the comparison-operator in checkSampleSwap_TiN.pl (to allow for + signs in PID names) and local control AF annotations from WES cohort via deepAnnotation pipe added.
• MassBank: Server was updated to system version 2.2.4 and MassBank-data release 2023.09 was deployed with the DOI: 10.5281/zenodo.8308157. Many new mass spectra were added.
• Mercator4 v.6 released.
• MGX 2.0: Public release supports metagenome coassembly, taxonomic binning and de novo metatranscriptome assembly.
• SearchGUI:  Version 4.2.17, updated Sage to version 0.13.3 and bug fix.
• STRING: updated version 12.0: 59'309'604 proteins from 12535 organisms; 27’541’372’833 interactions included.  

Recent Publications by de.NBI partners

• Mehta S, Bernt M, Chambers, M, Fahrner M, Föll MC, Grüning B et al. A Galaxy of informatics resources for MS-based proteomics. Expert Review of Proteomics, 20:11, 251-266, https://doi.org/10.1080/14789450.2023.2265062
• de Jonckheere B, Kollotzek F, ..., Kopczynski D, ..., Hoffmann, N ..., Ahrends R. Critical shifts in lipid metabolism promote megakaryocyte differentiation and proplatelet formation. Nature Cardiovascular Research volume 2, pages 835–852 (2023). https://doi.org/10.1038/s44161-023-00325-8
• C, Zötzsche S, Kühnl F, Fallmann J, Stadler PF, Findeiß S. Tailored machine learning models for functional RNA detection in genome-wide screens. NAR Genom Bioinform. 2023 Aug 21;5(3):lqad072. https://doi.org/10.1093/nargab/lqad072
• Walker TWN, Schrodt F, ..., Neumann S et al. Leaf metabolic traits reveal hidden dimensions of plant form and function. Science Advances 2023, 9 (35), art. no. eadi4029. https://doi.org/10.1126/sciadv.adi4029
• Furrer R, Heim B, ..., Nordström KJV, ..., Walter J, Handschin C. Molecular control of endurance training adaptation in male mouse skeletal muscle. Nature Metabolism 2023. https://doi.org/10.1038/s42255-023-00891-y
• Hardt R, ..., Schork K, Eisenacher M, Gieselmann V, Winter D. Proteomic investigation of neural stem cell to oligodendrocyte precursor cell differentiation reveals phosphorylation-dependent Dclk1 processing. Cellular and Molecular Life Sciences 2023, 80 (9), art. no. 260. https://doi.org/10.1007/s00018-023-04892-8
• Wu Y, Seufert I, ..., Brors B et al. DNA-methylation signature accurately differentiates pancreatic cancer from chronic pancreatitis in tissue and plasma. Gut. 2023 Sep 14:gutjnl-2023-330155. https://doi.org/10.1136/gutjnl-2023-330155
• Sieg J, Rarey M. Searching similar local 3D micro-environments in protein structure databases with MicroMiner. Brief Bioinform. 2023 Sep 22;24(6):bbad357. https://doi.org/10.1093/bib/bbad357
• Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, Pühler A, Sczyrba A, Schlüter A. Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms 2023, 11 (10), art. no. 2412. https://doi.org/10.3390/microorganisms11102412
• Valdivia DI, Rosales MH, Geis M, Stadler PF, Hellmuth M. Hierarchical and modularly-minimal vertex colorings. Art of Discrete and Applied Mathematics 2023, 6 (2), art. no. 9b6. https://doi.org/10.26493/2590-9770.1422.9b6
• Kopczynski D, Hoffmann N, ..., Schwudke D, Ahrends R. LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies. Anal Chem. 2023 Oct 17;95(41):15236-15244. Epub 2023 Oct 4. https://doi.org/10.1021/acs.analchem.3c02449
• Martens M, Stierum S, ..., Neumann S et al. ELIXIR and Toxicology: a community in development. F1000Res. 2023 Oct 3;10:ELIXIR-1129. https://doi.org/10.12688/f1000research.74502.2
• Weil HL, Schneider K, ..., Grüning B, ..., Usadel B, Garth C, Mühlhaus T. PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research. Plant J. 2023 Oct 11. https://doi.org/10.1111/tpj.16474
• Tiozon RJN, Sreenivasulu N, ..., Usadel B, Fernie AR. Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice. Commun Biol. 2023 Oct 2;6(1):1000. https://doi.org/10.1038/s42003-023-05379-9
• Schmidt TSB, ..., Bork P. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Res. 2023 Oct 28:gkad943. https://doi.org/10.1093/nar/gkad943
• Markus D, Pelletier A, Boube M, Port F, Boutros M et al. The pleiotropic functions of Pri smORF peptides synchronize leg development regulators. PLoS Genet. 2023 Oct 30;19(10):e1011004. https://doi.org/10.1371/journal.pgen.1011004
• Naake T, Rainer J, Huber W. MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. Bioinformatics. 2023 Oct 3;39(10):btad618. https://doi.org/10.1093/bioinformatics/btad618
• Weber T, Cosenza MR, Korbel J. MosaiCatcher v2: a single-cell structural variations detection and analysis reference framework based on Strand-seq. Bioinformatics. 2023 Oct 18:btad633. https://doi.org/10.1093/bioinformatics/btad633
• Velten B, Stegle O. Principles and challenges of modeling temporal and spatial omics data. Nat Methods. 2023 Oct;20(10):1462-1474. https://doi.org/10.1038/s41592-023-01992-y
• Choubey J, Wolkenhauer O, Chatterjee T. Systems Biology Approach to Analyze Microarray Datasets for Identification of Disease-Causing Genes: Case Study of Oral Squamous Cell Carcinoma. Methods Mol Biol. 2024;2719:13-31. https://doi.org/10.1007/978-1-0716-3461-5_2
• Raab R, Küderle A, ..., Eils R, Wagener H, Eskofier BM. Federated electronic health records for the European Health Data Space. Lancet Digit Health. 2023 Nov;5(11):e840-e847. https://doi.org/10.1016/S2589-7500(23)00156-5
• Ono Y, Ito R, ..., Russell RB et al. Chemogenetic activation of G12 signaling enhances adipose tissue browning. Signal Transduction and Targeted Therapy 2023, 8 (1), art. no. 307. https://doi.org/10.1038/s41392-023-01524-2
• Fuchs S, ..., Fallmann J, ..., Stadler PF, ..., Rajewsky N et al. Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN. Nature Communications 2023, 14 (1), art. no. 3936. https://doi.org/10.1038/s41467-023-38747-4

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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.