Newsletter 30 is out now!

3^rd Annual Meeting of the de.NBI Industrial Forum on 24 November 2022

The de.NBI Industrial Forum acts as an interface between academia and industry. This year’s annual meeting will take place virtually on 24 November 2022. The presentations will give insights on recent developments in Digital Health of the de.NBI and ELIXIR networks as well as in other national organizations. Members of the Industrial Forum will complement the agenda by showcasing their industrial approaches in Digital Health. The complete agenda, abstracts, and the possibility to register can be found here. Registration is free of charge and open until 23 November 2022! 

 de.NBI Cloud User Meeting 2022 on 6-7 December in Jülich

 1st BioHackathon Germany 12-16 December 2022 at Leucorea in Wittenberg

 News on the de.NBI Cloud

• Current figures on the de.NBI Cloud: number of users: 2217, number of active projects: 483, number of publications referencing the use of the de.NBI Cloud: 521. This equals an increase of 6% users and 7% active projects, respectively, since August 2022.
• The value of the de.NBI Cloud for modern life sciences is acknowledged in a new testimonial by Prof Boas Pucker, TU Braunschweig. He praises availability and ease of scalability infrastucture of the de.NBI cloud without which many of his next-generation plant science projects could not be conducted.  

 New Co-Lead for the ELIXIR Metabolomics Community 

  Harald Wagener elected new Lead of the ELIXIR Compute Platform

In September this year, Harald Wagener from the Berlin Institute of Health (BIH), has been elected as a new ELIXIR Compute Platform lead representing ELIXIR DE. The ELIXIR Compute Platform develops services in three areas: authentication and authorisation, storage and data transfer, and cloud and computing resources. Furthermore, it works with ELIXIR Communities to ensure the platform's services fit the needs of specific life science domains. Harald will lead the Compute Platform together with Ludek Matyska (ELIXIR CZ) and Juha Törnroos (ELIXIR FI). His contribution to the platform will focus on making sure ELIXIR is well connected to other initiatives such as Gaia-X and ensuring that future ELIXIR tasks will continue to drive forward compute platform services for researchers all across Europe and beyond. Find more information on Harald’s research here and here.  We wish Harald great success in driving new developments within the ELIXIR Compute Platform!

News from de.NBI and ELIXIR DE Office

Team of ELIXIR DE Officers is growing!

We warmly welcome Dirk Winkelhardt, who started his position as ELIXIR DE Officer on 1 October 2022. Dirk is working in the proteomics field, especially on identifying peptides. Therefore he uses his experience as a computer scientist and software engineer to develop new methods of assembling search spaces for peptide identification in data-dependent acquisition workflows, making it possible to search against the complete UniProt. While deploying his own tools as distributed web applications he is eager to show other researchers how they can do the same with existing software using Python, making their tool available for everybody independent of operating systems or computing resources.
As an ELIXIR Officer, one of his goals is to introduce the Sample Data Relationship Format (SDRF) to more researchers to enable better reproducibility of results. We are looking forward to working with Dirk!

New Interview Series with Female Data Scientists from Industry and Academia

Within the framework of the joint Bayer AG and de.NBI/ELIXIR Germany of the "Women in Data Science" lecture series, we are proud to launch this new interview collection aimed at celebrating women's achievements in data science for life sciences and bioinformatics. The interviews will promote the work of female researchers and highlight the diversity of research performed and career paths across Bayer AG, de.NBI, and ELIXIR DE and will appear regularly.

Bérénice Batut, co-lead of the ELIXIR Marine Metagenomics Community representing ELIXIR Germany, is the first woman we interviewed. She shared with us her experiences as a woman in the data science field and gave recommendations on building careers and advancement opportunities. Find out more about Bérénice here. 

 News on Services

• Bakta is a tool for the rapid standardized annotation of bacterial genomes and plasmids from both isolates and MAGs. Publication: Schwengers O et al. Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification, Microbial Genomics 7(11), 2021. https://doi.org/10.1099/mgen.0.000685
• Bioimage ANalysis Desktop (BAND) is a virtual desktop platform aimed at supporting interactive image analysis workflows in the cloud. The cloud based desktops are accessible with a web browser and thereby allow working on your data in the de.NBI cloud from anywhere with an internet connection. 
• PLAST (Pangenome local alignment tool) is a command line tool enabling the heuristic search for highest scoring local alignments between a nucleotide sequence query and a graphical pangenome consisting of thousands of individual genomes. Publication: Schulz T et al., Detecting High Scoring Local Alignments in Pangenome Graphs, Bioinformatics (2021) https://doi.org/10.1093/bioinformatics/btab077

• BRENDA: Core data download in json format enabled. Implementation of a new user system and new user feedback system. The annual BRENDA user event will take place on 6 Dec 2022, online. 
• COPASI: New release COPASI 4.37 (Build 264). More information can be found in the changelog.
• MassBank: Update to system version 2.2. This implements the new accession schema. 

 Recent Publications by de.NBI partners

• Koblitz J, Halama P, Spring S, ..., Overmann J, Reimer L.C. (2022): MediaDive: the expert-curated cultivation media database, Nucleic Acids Research, 2022, gkac803, https://doi.org/10.1093/nar/gkac803 
• Schumann VF, de Castro Cuadrat RR, …, Uyar B, Franke V, …, Rajewsky N, Landthaler M, Akalin A. SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution, Science of The Total Environment, Volume 853, 2022, https://doi.org/10.1016/j.scitotenv.2022.158931
• Hönig SMN, Lemmen C, Rarey M. Small molecule superposition: A comprehensive overview on pose scoring of the latest methods. WIREs Comput Mol Sci. 2022. e1640. https://doi.org/10.1002/wcms.1640
• Zangishei Z, Annacondia ML, Gundlach H et al. Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain, Plant Physiology, Volume 190, Issue 2, October 2022, Pages 1242–1259, https://doi.org/10.1093/plphys/kiac331
• Gaurav K, Arora S, Silva P, …, Mayer KFX et al. Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement. Nat Biotechnol 40, 422–431 (2022). https://doi.org/10.1038/s41587-021-01058-4
• Schulthess AW, Kal SM, Liu, F, ..., Lange M, Scholz U et al. Genomics-informed prebreeding unlocks the diversity in genebanks for wheat improvement. Nat Genet 54, 1544–1552 (2022). https://doi.org/10.1038/s41588-022-01189-7
• Handel F, Kulik A, Wex KW, ..., Wibberg D, et al. Ψ-Footprinting approach for the identification of protein synthesis inhibitor producers, NAR Genomics and Bioinformatics, Volume 4, Issue 3, September 2022, lqac055, https://doi.org/10.1093/nargab/lqac055
• Westwick E, Repo S and Maccallum P. ELIXIR All Hands 2022 – the European life sciences data infrastructure’s annual gathering [version 1; not peer reviewed]. F1000Research 2022, 11(ELIXIR):1065,  https://doi.org/10.7490/f1000research.1119120.1 
• Martins dos Santos V, Anton M, Szomolay B, …, Golebiewski M, …, Müller W, ..., Wittig U et al. Systems Biology in ELIXIR: modelling in the spotlight [version 1; peer review: awaiting peer review]. F1000Research 2022, 11(ELIXIR):1265. https://doi.org/10.12688/f1000research.126734.1
• Deutsch EW, Vizcaíno JA, Jones AR, ..., Neumann S, ..., Hoffmann N et al. The Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work. ChemRxiv. Cambridge: Cambridge Open Engage; 2022; https://doi.org/10.26434/chemrxiv-2022-ksqg1
• Young D, Joshi A, Huang L, ..., Sczyrba A et al. Simultaneous Metabarcoding and Quantification of Neocallimastigomycetes from Environmental Samples: Insights into Community Composition and Novel Lineages. Microorganisms. 2022; 10(9):1749. https://doi.org/10.3390/microorganisms10091749
• Herres-Pawlis S, Bach F, Bruno IJ, ..., Neumann S, Steinbeck C et al. Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices Angew. Chem. Int. Ed. 2022, e202203038; Angew. Chem. 2022, e202203038. https://doi.org/10.1002/anie.202203038
• Maier BD, Aguilera LU, Sahle S, …, Kummer (2022) Stochastic dynamics of Type-I interferon responses. PLOS Computational Biology 18(10): e1010623. https://doi.org/10.1371/journal.pcbi.1010623
• Großeholz R, Wanke F, Rohr L, ..., Kummer U, Harter K (2022) Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root eLife 11:e73031. https://doi.org/10.7554/eLife.73031
• Mitrofanov A, Ziemann M, Alkhnbashi OS, Hess WR, Backofen R, CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection, Bioinformatics, Volume 38, Issue Supplement_2, September 2022, Pages ii42–ii48, https://doi.org/10.1093/bioinformatics/btac466
• Singh J, Elhabashy H, Muthukottiappan P, Stepath M, Eisenacher M, Kohlbacher O et al. Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo. Nat Commun 13, 6212 (2022). https://doi.org/10.1038/s41467-022-33951-0
• Paysan-Lafosse T, Blum M, Sara Chuguransky S, …, Bork P et al. InterPro in 2022, Nucleic Acids Research, 2022;, gkac993, https://doi.org/10.1093/nar/gkac993
• Xue L, Lenz S, Zimmermann-Kogadeeva M, ..., Bork, P et al. Visualizing translation dynamics at atomic detail inside a bacterial cell. Nature 610, 205–211 (2022). https://doi.org/10.1038/s41586-022-05255-2
• Bonidia RP, Avila Santos AP, de Almeida BLS, Stadler PF et al. Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy. Entropy. 2022; 24(10):1398. https://doi.org/10.3390/e24101398
• Gornik SG, Flores V, Reinhardt F, …, Stadler PF et al. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes, Molecular Biology and Evolution, Volume 39, Issue 10, October 2022, msac191, https://doi.org/10.1093/molbev/msac19

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