de.NBI Summer School 2023 from 25-29 September 2023

The life sciences are a major player in the age of big data. Modern high-throughput omics technologies generate large amounts of high-dimensional data. Besides new challenges for the analysis and visualization of this amount of research data, its management and sharing has become an important issue in the daily research process. The main objective of the 2023 de.NBI Summer School is to provide an overview of the possibilities to process, analyze, share and integrate data using different open source platforms.

The 8^th de.NBI Summer School on Bio Data Analysis for Life Sciences will take place in Bielefeld, Germany. This training event addresses life scientists, bioinformaticians, computer scientists, systems biologists, synthetic biologists and others working with or interested in (bio)research data. The program features lectures and hand-ons about

• Hands-on de.NBI Cloud computing
• Workflows – Galaxy & CWL
• Bioschemas
• Introduction to Python
• Population genomics or Transcriptomics
• The MGX framework for microbial community analysis

2^nd BioHackathon Germany, 11-15 Dec 2023

 News on the de.NBI Cloud

• The 6^th de.NBI Cloud User Meeting 2023 will take place as a 3-day event in the second half of November 2023 in Bielefeld. Please check back soon for more information in the near future.
• Updates on de.NBI Cloud facilities: The de.NBI Cloud site Bielefeld has passed its second ISMS certification surveilliance audit according to ISO 27001.
• Current figures on the de.NBI Cloud: Number of users: 2715, number of active projects: 563, number of publications referencing the use of the de.NBI Cloud: 758. This equals an increase of 4,9% users and 18,6% publications, respectively, since May 2023.

Announcing the Annual Meeting 2023 of the de.NBI Industrial Forum

 News on ELIXIR DE

• The ELIXIR Galaxy Community Meeting 2023 organized by our ELIXIR DE partners at Freiburg University will take place on 4-5 October in Freiburg.
• Björn Grüning, co-lead of the ELIXIR Galaxy Community, is using the ELIXIR Staff exchange programm for a working visit to BioCommons Australia to enforce their Galaxy services.
• The ELIXIR Metabolomics Joint Community and Industry F2F/hybrid meeting 2023 will take place 16-18 October at EMBL Heidelberg. Steffen Neumann as Metabolomics Community Co-lead is the lead 0rganizer. 
• At the ELIXIR All Hands Meeting 2023 in Dublin (5-8 June 2023) more than 27 ELIXIR DE members attended in person.
• There were 14 talks in workshops, mini symposia and main programme by ELIXIR DE members and additionally 20 posters. Posters and many of the slides are available in the electronic programme and published slides. 
• As a collaborative effort between the Bio Network for Training (BioNT), the European Life Science Infrastructure  ELIXIR, and its de.NBI/ELIXIR DE the coopperation partners have launched a survey to inquire bioinformatics training needs. Please participate!

News from de.NBI and ELIXIR DE Office

We say goodbye to Andreas Tauch, who has left de.NBI and ELIXIR Germany on 30 June. Andreas has been involved in the planning and development of the German Network for Bioinformatics Infrastructure since the beginning of the conception phase in 2014 and has served as head of the de.NBI Administration Office since the start of the BMBF project in March 2015. Simultaneously, he has also tirelessly promoted the establishment of the German Node of ELIXIR, initially as Deputy Head of Node and after finalisation of the entire contract as HoN from June 2020.
On behalf of the entire network, we would like to thank him for his commitment and collegiality and wish him all the best for his future! 

RDM Trainer Network Meeting - Review

Over 70 international participants attended the „Fellowship of the Data – Research Data Management Trainer Network Meeting“ on-site at the Humboldt University, Berlin, 21 to 22 June 2023. The meeting was jointly organised by ELIXIR DE, ELIXIR NO, and ELIXIR UK in the realm of ELIXIR CONVERGE and the sub-working group training/further education of the DINI/nestor WG Research.
Key themes of the event were to explore the broad variety of research data management (RDM) training, to collect and exchange methods of research data management training and to get connected as a community. Thus, the agenda mirrored these efforts by offering time and opportunities to network and discuss as a group in open table exercises, an RDM game night and a poster session with introductory flash talks. As keynotes Sara Jones (GÈANT) introduced “Tips and Tricks” to RDM training while Katrin Frisch (German Research Ombudsman, focus on research data) presented examples and issues of unprofessional or wrongful handling of research data.

de.NBI Blog

 News on Services

• Silva: Webserver Jobs are now hosted in the de.NBI Cloud. 
• Bakta:  Bump version 1.8.2 released.
• OpenMS 3.0.0: New full release with numerous improvements.    
• Galaxy training network: The paper Training Infrastructure as a Service is finally published!  Authors: Rasche H, …, Serrano-Solano B, …, Grüning B et al.  
• EURISCO: European Search Catalogue for Plant Genetic Resources. National inventories of 6 countries updated.
• mOTUs: The mOTU extender is a companion tool used to extend the current mOTUs database with user provided genomes. See new publication "Reference genome-independent taxonomic profiling of microbiomes with mOTUs3".
• Pangaea: Submitting biogogical data? Let brand new templates guide you!
• KNIME: Get started with KNIME Analytics Platform 5.1 using a cheatsheet specially created to help you understand popular and new nodes included in the latest release such as Value Lookup, Table Splitter, and more.  

  Recent Publications by de.NBI partners 

• Darkow E, Yusuf D, Rajamani S, Backofen R, et al. Meta-Analysis of Mechano-Sensitive Ion Channels in Human Hearts: Chamber-and Disease-Preferential mRNA Expression. Int. J. Mol. Sc. 2023, 24(13), 10961. https://doi.org/10.3390/ijms241310961
• Wolf M, Schallert K, Knipper L, Sickmann A, Sczyrba A, Benndorf D, Heyer R. Advances in the clinical use of metaproteomics. Expert review of proteomics 2023, 1-16. https://doi.org/10.1080/14789450.2023.2215440
• Liao WW, Asri M, Ebler J, ...,  Korbel JO et al. A draft human pangenome reference. Nature. 2023 May;617(7960):312-324. https://doi.org/10.1038/s41586-023-05896-x
• Mohan K, Gasparoni G, Salhab A, ..., Hoffmann S, ..., Walter J, Nordheim A. Age-Associated Changes in Endothelial Transcriptome and Epigenetic Landscapes Correlate With Elevated Risk of Cerebral Microbleeds. J Am Heart Assoc. 2023 Aug 23:e031044. https://doi.org/10.1161/JAHA.123.031044
• Hardt R, Dehghani A, ..., Schork K, Eisenacher M et al. Proteomic investigation of neural stem cell to oligodendrocyte precursor cell differentiation reveals phosphorylation-dependent Dclk1 processing. Cell Mol Life Sci. 2023 Aug 18;80(9):260. https://doi.org/10.1007/s00018-023-04892-8
• Kremer K, Meier D, ..., Goesmann A et al. Functional Degeneracy in Paracoccus denitrificans Pd1222 Is Coordinated via RamB, Which Links Expression of the Glyoxylate Cycle to Activity of the Ethylmalonyl-CoA Pathway. Appl Environ Microbiol. 2023 Jul 26;89(7):e0023823. https://doi.org/10.1128/aem.00238-23
• Felden J, Möller L, Schindler U, Huber R, Schumacher S, Koppe R, Diepenbroek M, Glöckner FO. PANGAEA - Data Publisher for Earth & Environmental Science. Sci Data. 2023 Jun 2;10(1):347. https://doi.org/10.1038/s41597-023-02269-x
• Kontou EE, Walter A, Alka O, Pfeuffer J, Sachsenberg T, ..., Kohlbacher O, Weber T. UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. J Cheminform. 2023 May 12;15(1):52. https://doi.org/10.1186/s13321-023-00724-w
• Diedrich K, Krause B, Berg O, Rarey M. PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J Comput Aided Mol Des. 2023 Oct;37(10):491-503. https://doi.org/10.1007/s10822-023-00522-4
• Vondrackova M, Kopczynski D, Hoffmann N, Kuda O. LORA, Lipid Over-Representation Analysis Based on Structural Information. Anal Chem. 2023 Aug 29;95(34):12600-12604. https://doi.org/10.1021/acs.analchem.3c02039
• Flocco CG, Methner A, ..., Overmann J. Touching the (almost) untouchable: a minimally invasive workflow for microbiological and biomolecular analyses of cultural heritage objects. Front Microbiol. 2023 Aug 3;14:1197837. https://doi.org/10.3389/fmicb.2023.1197837
• Nowatzky Y, Benner P, Reinert K, Muth T. Mistle: bringing spectral library predictions to metaproteomics with an efficient search index. Bioinformatics. 2023 Jun 1;39(6):btad376. https://doi.org/10.1093/bioinformatics/btad376
• Schiml VC, Delogu F, Kumar P, Kunath B, Batut B, Mehta S, Johnson JE,Gruening;B et al.Integrative meta-omics in Galaxy and beyond. Environ Microbiome. 2023 Jul 7;18(1):56. https://doi.org/10.1186/s40793-023-00514-9
• Walke D, Micheel D, Schallert K, Muth T, Broneske D, Saake G, Heyer R. The importance of graph databases and graph learning for clinical applications. Database (Oxford). 2023 Jul 10;2023:baad045. https://doi.org/10.1093/database/baad045
• Vromman M, Anckaert J, ..., Hoffmann S, ...,  Stadler P et al. Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nat Methods. 2023 Aug;20(8):1159-1169. https://doi.org/10.1038/s41592-023-01944-6
• Waldl M, Spicher T, ..., Stadler PF. Local RNA folding revisited. J Bioinform Comput Biol. 2023 Jul 28:2350016. https://doi.org/10.1142/S0219720023500166
• Yao HT, Lorenz R, Hofacker IL, Stadler PF. Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. Algorithms Mol Biol. 2023 Jul 29;18(1):8. https://doi.org/10.1186/s13015-023-00236-0
• Chafra F, Borim Correa F, ..., Stadler PF, Nunes da Rocha U. StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins. Bioinform Adv. 2023 Jun 9;3(1):vbad069. https://doi.org/10.1093/bioadv/vbad069
• Rocha-Martins M, ...., Myers EW, Norden C. Neuronal migration prevents spatial competition in retinal morphogenesis. Nature. 2023 Aug;620(7974):615-624. https://doi.org/10.1038/s41586-023-06392-y
• Uliano-Silva M, ..., Darwin Tree of Life Consortium, ..., Myers EW et al. MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. BMC Bioinformatics. 2023 Jul 18;24(1):288. https://doi.org/10.1186/s12859-023-05385-y 

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