denbi Quarterly Newsletter a1

Issue 04/2022

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

IF annual 2022The 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 hereRegistration is free of charge and open until 23 November 2022! 

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

Logo CLUM 2022This year's de.NBI Cloud User meeting will take place at the Forschungszentrum Jülich on 6-7 December 2022. 
The meeting provides the ideal opportunity for our current users to learn more about best practices in cloud computing and showcases  the capabilities provided by the de.NBI Cloud that could help accelerate their research in future projects to newcomers and prospective future users. The agenda  covers talks and workshops on topics in cloud computing, such as container orchestration using Kubernetes, the application of infrastructure as code technologies but also bioinformatics related workshops such as an introduction to Bioconda and BioContainers as well as introduction to Common Workflow Language (CWL). Take the opportunity to get in personal contact with our cloud staff. Registration is open until 20 November 2022.  

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

LOGO FINAL 1Following the success of the BioHackathon Europe organized by ELIXIR Europe, ELIXIR Germany is planning to run the first BioHackathon Germany 2022 in Lutherstadt Wittenberg from 12-16 December 2022. We hope to encourage ELIXIR Germany and non-ELIXIR Germany participants to take part, as well as to attract industry engagement.
We will offer 11 interesting projects in different areas, e.g. training, lipidomics, metabolomics, Bioschemas, plant bioinformatics etc. We are planning to hold the BioHackathon Germany with remote access - available for those that cannot attend the meeting in person. We believe this hybrid format will allow everyone to participate in the BioHackathon Germany and deliver optimized outcomes from the selected projects. Seats are limited for face-to-face participation. The registration is based on a first-come, first-served basis. Registration is open until 20 November 2022! 

denbi Icon 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.  

denbi Icon New Co-Lead for the ELIXIR Metabolomics Community 

Steffen Neumann from the Leibniz Institute of Plant Biochemistry in Halle (Saale) has been elected as the new ELIXIR Metabolomics Community co-lead in September 2022 as a representative of ELIXIR Germany. The other new co-lead is Maria Klapa from ELIXIR Greece.
steffen neumann ELIXIR
The ELIXIR Metabolomics Community joins forces with experimental scientists and developers to provide the resources, analysis tools and infrastructure to  analyze and interpret metabolomics data. The community aims to establish an infrastructure of services, standards, and datasets to help researchers discover, annotate and analyze metabolomics data from around Europe. Steffen's contribution to the community is focused on using modern bioinformatics approaches in plant biochemistry research as well as the support of data management according to the FAIR principles. We wish Steffen every success in further developing the Metabolomics Community! Find more information on Steffen’s research here.

 denbi Icon Harald Wagener elected new Lead of the ELIXIR Compute Platform

harald_wagener_ELIXIR 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!

denbi Icon News from de.NBI and ELIXIR DE Office

Team of ELIXIR DE Officers is growing!

WinkelhardtWe 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

WiDS cover interviewsWithin 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

denbi Icon News on Services

Three new de.NBI services have been added to our portfolio:
  • 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
Recent updates of services: 
  • 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. 

denbi Icon 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

denbi Icon Upcoming Events

The next de.NBI training events are announced on www.denbi.de/training.
Next scheduled events:
16-17 Nov 2022 Let's make a plan! Using DMTPTool to outline our Research Data Management - 2nd course  Online
23 Nov 2022  6th Differential Analysis of Quantitative Proteomics Data using R Online
23 Nov 2022    Joint de.NBI & NFDI4Microbiota Training Course on Metagenome Analysis Bielefeld
24 Nov 2022 3rd Annual Meeting of the de.NBI Industrial Forum Online
30 Nov-01 Dec 2022 Let’s make a Plan! Using DMPTool to outline our Research Data Management - 3rd course   Online
05-09 Dec 2022 Applied Metaproteomics Workshop Magdeburg 2022 Magdeburg
06 Dec Annual BRENDA User Event Online
06-07 Dec 2022 5th de.NBI Cloud User Meeting. Registration open until 20 Nov 22!  Jülich
12 Dec 2022 7th de.NBI Genomics Training Course  Gießen
12-16 Dec 2022 1st Biohackathon Germany. Registration open until 20 Nov 22! Lutherstadt Wittenberg (Leucorea)


Responsible for Contents
A. Tauch, T. Dammann-Kalinowski
de.NBI - German Network for Bioinformatics Infrastructure c/o Forschungszentrum Juelich GmbH - IBG-5 Branch Office at Bielefeld University, 33594 Bielefeld, Germany
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