denbi Quarterly Newsletter a1

Issue 03/2023 

denbi Iconde.NBI Summer School 2023 from 25-29 September 2023

Summer School 2023 2zb

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 8th 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
Keynote speakers are Björn Grüning (Freiburg University), Nick Juty (Manchester University) and Veit Schwämmle (University of Southern Denmark, Odense).
The Summer School is organized by the de.NBI/ELIXIR DE administration office and the ELIXIR DE Officers at ForschungszentrumJülich.  A total of 20 international participants will be welcomed in Bielefeld.

denbi Icon2nd BioHackathon Germany, 11-15 Dec 2023

LOGO 2023 After the success of the first BioHackathon Germany last year in Lutherstadt Wittenberg, de.NBI and ELIXIR Germany are hosting the 2nd BioHackathon Germany 2023 in Bielefeld from 11-15 December 2023. We hope to attract numerous participants from de.NBI, ELIXIR Germany, other ELIXIR nodes as well as other interested parties and would like to encourage industry involvement.
We will offer 11 interesting projects in various areas, e.g. training, single cell omics, Bioschemas, plant bioinformatics, etc. We will offer remote access - available for those who cannot attend the meeting in person. Places for the in-person event are limited, however virtual participation is possible alternatively.
Registration is open until 17 November 2023. Selection of participants will be on a first-come, first-served basis.

denbi Icon News on the de.NBI Cloud

  • The 6th 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

IF annual 2023 timeThe 4th Annual Meeting of the de.NBI Industrial Forum will take place virtually Thursday, 23 November 2023. The annual meeting connects academic and industrial stakeholders by giving insights in recent research developments in the Life Sciences and showcasing current industrial topics. This year’s meeting will include presentations by academic experts and will feature industrial use cases on "Big Data Handling in the Life Sciences".
More information on the agenda as well as relevant organizational information will soon to be provided here. Save the date!

denbi Icon News on ELIXIR DE

denbi Icon 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! 

Tanja Dammann-Kalinowski has taken over the lead of the de.NBI Administration Office. The function of the ELIXIR Head of Node is carried out by Deputy HoN Alf Pühler. The management of the ELIXIR Germany office is filled by Irena Maus as ELIXIR Germany Node Coordinator. We are available for all questions from the network.

denbi IconRDM Trainer Network Meeting - Review

fellowship data meeting banner horizontal

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.

The “Fellowship of the Data” meeting will be continued next year 5-7 June 2024 in Jena with ELIXIR DE being once again part of the organisation committee.

de.NBI Blog

3 cuttedIn May 2023, we have launched the new format de.NBI Blog, which comprises 12 articles by now. Topics range from indroductions to the de.NBI network, state-of-the-art services, de.NBI Cloud, benefits of training, deciphering soil metagenome data, microscopy image analysis or differential gene expression to investigation of crop plants. It's worth a read!
If you are interested in sharing your experience or describing your tools, please write an email to Johanna (This email address is being protected from spambots. You need JavaScript enabled to view it.) for further information. Follow us via the de.NBI website or via twitter or LinkedIn.

denbi Icon News on Services

Recent updates of services: 

 denbi Icon 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.
  • 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.
  • Liao WW, Asri M, Ebler J, ...,  Korbel JO et al. A draft human pangenome reference. Nature. 2023 May;617(7960):312-324.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Waldl M, Spicher T, ..., Stadler PF. Local RNA folding revisited. J Bioinform Comput Biol. 2023 Jul 28:2350016.
  • 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.
  • 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.
  • Rocha-Martins M, ...., Myers EW, Norden C. Neuronal migration prevents spatial competition in retinal morphogenesis. Nature. 2023 Aug;620(7974):615-624.
  • 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. 

  denbi Icon  Upcoming Events

The next de.NBI training events are announced on
Upcoming scheduled events:
22 Aug 2023  ProteinsPlus – Supporting Structure-Based Design on the Web - CIC Summer School  Halle (Saale)
10 Sep 2023 1001 Reasons for a Data Management Plan - GCB2023  Hamburg
18-22 Sep 2023  Applied Metaproteomics Workshop Magdeburg 2023  Magdeburg
20-21 Sep 2023 Workshop on Computational Pangenomics  Online
20 Sep 2023
Research Data Management (RDM) - Intro Series (4. Iteration) , 16 units Online
25-29 Sep 2023 de.NBI Summer School 2023 - Bio Data Analysis for Life Sciences  Bielefeld
04-05 Oct 2023 ELIXIR Galaxy Community Meeting  Freiburg
16-18 Oct 2023 ELIXIR Metabolomics Joint Community and Industry F2F/hybrid meeting Heidelberg
19 Oct 2023 GHGA Webinar: Intro to the Data Stewardship Wizard & ELIXIR Research Data Management Kit - with de.NBI  Online
26 Oct 2023 Webinar: Making container Services integratable, sustainable and widely used Online 
02-03 Nov 2023 DNA Methylation: Design to Discovery 2023  Online
23 Nov 2023 4th Annual Meeting of the de.NBI Industrial Forum 2023 Online 

28-30 Nov 2023

Tools for Systems biology modeling and data exchange: CellNetAnalyzer, COPASI, SABIO-RK, FAIRDOMHub/SEEK 2023  Magdeburg
11-15 Dec 2023 2nd BioHackathon Germany Bielefeld


Responsible for contents:
T. Dammann-Kalinowski, I. Maus, D. Wibberg
de.NBI - German Network for Bioinformatics Infrastructure, Forschungszentrum Juelich GmbH - IBG-5, Branch Office at Bielefeld University, 33594 Bielefeld, Germany
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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.image