de.NBI Newsletter 29 /August 2022 is out!

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

The de.NBI Industrial Forum has been established in 2018 and currently comprises 36 companies. The Industrial Forum connects the members of the forum with the de.NBI network by providing access to a collection of service tools, training courses and compute facilities. After an initial kick-off meeting in 2019, the Industrial Forum organizes annual meetings as the key activity. The first one took place in 2020 focusing on the Corona pandemic and on plant breeding. In 2021, the focus of the annual meeting was on the use of artificial intelligence (AI) in companies. In addition, the national projects NFDI4Biodiversity and NFDI4Microbiota had the opportunity to present their goals.

This year, the 3rd annual meeting of the de.NBI Industrial Forum will take place in a virtual format on 24 November 2022. As a key topic the meeting will present contributions from the field "Digital Health". Further, it is planned to present the collaboration with the European organization ELIXIR. The agenda as well as the registration of the third annual meeting will be available soon and can be found at https://www.denbi.de/industrial-forum/industrial-forum-activities. Save the date!

Developments in the Community of Practice for Data Mangement and Data Stewardship

In March 2022, the Community of Practice (CoP) for data management (DM) and stewardship (DS) training in the life sciences - Developing training and sharing knowledge, best practices, and standards - started with a kick-off meeting hosted by ELIXIR-DE. The essential vision was to bring national and local DM/DS life science communities together to foster the exchange of training materials and knowledge among trainers.
In June 2022, ELIXIR agreed to fund the CoP in order to achieve long-term sustainability.
The working plan elaborated by ELIXIR-DE, ELIXIR-NO and ELIXIR-UK with a timeline from October 2022 – July 2023, the CoP aims to foster the exchange in the training DM/DS field and to set well-established standards, guidelines and best practices in training DM/DS.
It is in ELIXIR’s best interest to further develop and sustain the grassroots of this CoP. If successful, the CoP will consequently foster the exchange in the training DM/DS field as well as the creation and implementation of best practices/standards for training in DM/DS in Life Sciences, which lies at the core of the ELIXIR Training, Interoperability and Data Platforms. Currently, there is a gap to cover these needs and demands to build a bridge for it, as demonstrated throughout the first interactions of this CoP.
The next CoP events will be ELIXIR-DE’s training courses at GCB 2022 and ECCB 2022 with the topic “Boost your Data management planning” at GCB 2022 in Halle/DE on 05 September 2022 and at ECCB 2022 on 18 September 2022 in Sitges/ES.

Co-Lead of ELIXIR’s new Single Cell Omics Community

ELIXIR Communities bring together experts across Europe to develop standards, services and training within specific life science domains. To coordinate Single-Cell Omics research in Europe and beyond, ELIXIR has recently established the new Single Cell Omics Community, which has been approved by the HoN committee in May 2022. Single-cell technologies have undergone rapid developments in recent years and have revolutionized the way and the level of resolution by which life science research is conducted. The outline of the community´s activities is described in their white paper "Community-driven ELIXIR activities in single-cell omics". Naveed Ishaque (ELIXIR-DE) has been appointed as a co-lead for the ELIXIR Single Cell Omics Community. He recently started his own research group with research focus on applying computational approaches to understand the basis of molecular biological heterogeneity in data of human disease within the unit of Roland Eils at the Berlin Institute of Health. Find more information on Naveed Ishaque‘s research here.

New Co-lead for the Marine Metagenomics Community

Bérénice Batut from the University of Freiburg has been elected as the new ELIXIR Marine Metagenomics community co-lead in August Bérénice is a bioinformatician in the Freiburg Galaxy Team and is deeply involved in developing tools for data analysis focusing on microbial communities. Last year she launched and co-led microGalaxy, a community of practice around Galaxy and microbiology, intending to coordinate community efforts and provide better support for microbiome analysis in Galaxy. In addition, Bérénice co-leads the Galaxy Training Network and is a co-founder and co-lead of Open Life Science, a mentoring & training program for open science ambassadors, recently awarded several grants from Chan Zuckerberg Institute and Wellcome Trust.
In ELIXIR-DE, Bérénice holds the position of deputy training coordinator and is a liaison between the Training Platform and the Galaxy community.

We wish Bérénice every success in further developing the Marine Metagenomics Community!

News from de.NBI and ELIXIR-DE Office

Our Twitter channel #denbiOffice has 2400 followers as of August 01.

Team of ELIXIR-DE Officers is growing

We welcome Simon Gene Gottlieb as an ELIXIR-DE Officer (representing CIBI), active since 1 March 2022. Simon is a profound software engineer with focus on C++ and Linux. He is working on his PhD at the Freie Universität Berlin in the Algorithmic Bioinformatics group focusing on efficient data structures like the bidirectional FMIndex for approximate string searches. Simon also brings special knowledge surrounding the tool framework for SeqAn and OpenMS. As an ELIXIR Officer, one of his goals is to implement CWL support for SeqAn and OpenMS based tools, making these available on the Galaxy platform. If you ever feel like talking about efficient search schemes, newest C++ updates or soccer playing robots, you are welcome to contact Simon. https://www.denbi.de/team-elixir-officers/

de.NBI Cloud Brochure online

We are delighted to present our new de.NBI brochure entitled “Development and operation of the federated de.NBI Cloud“. With the life sciences becoming increasingly data-driven, cloud technology will become more important to the sector. Following this trend, the present booklet showcases the power, strength, and range of the de.NBI Cloud for the life science community by providing the ability to unlock research data and better collaborate across the ecosystem. Furthermore, it also sheds light on the role of the de.NBI Cloud in national and international projects such as NFDI, DeCOI, GHGA or EOSC-Life in the European sector of computational biosciences.

The editorial team would like to thank all involved authors. We wish you lots of pleasure reading the de.NBI Cloud brochure.

News on the de.NBI Cloud

At present, the de.NBI Cloud has 2100 registered users and 450 active projects.

Two new testimonials on the cloud web page showcase the use of de.NBI cloud resources for plant breeding driven by big data analysis and computational solutions from data science and machine learning to solve biomedical problems.

News on Services

Numerous de.NBI services have been improved in the last quarter:

• usegalaxy.eu: Usegalaxy.eu has reached 50,000 registered users in June 2022. A new publication: The Galaxy Community, The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W345–W351,https://doi.org/10.1093/nar/gkac247. As a second notable update, COVID-19 pipelines have been repurposed for research on the monkeypox virus.
• Goslin 2.0: The new version is described in: Kopczynski D, Hoffmann N, Peng B, Liebisch G, Spener F, Ahrends R. Goslin 2.0 Implements the recent Lipid Shorthand Nomenclature for MS-Derived lipid structures, Anal. Chem. 2022, 94, 16, p. 6097–6101 https://doi.org/10.1021/acs.analchem.1c05430
• BRENDA : Summer release 2022.2 is online including 42 new and 336 updated enzyme classes.
• COPASI: New release COPASI 4.36 (Build 260). More information can be found in the changelog.
• ProteinsPlus: New Publication on the platform: Schöning-Stierand K, ..., Rarey M, ProteinsPlus: a comprehensive collection of web-based molecular modeling tools, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W611–W615, https://doi.org/10.1093/nar/gkac305
• rippchen: Update on underlying bashbone library (02 June 2022). Peak calling from *IP-Seq experiments or for differential expression- and ontology analysis from RNA-Seq data.
• Vienna RNA Package: Update to version 2.5.1. (02 June 2022)
• SeqAN: Version 3.2.0 contains a compiler update.

Recent Publications by de.NBI partners

• McDonald JG, Ejsing CS, Kopczynski D, ..., Hoffmann N, ..., Schwudke D, Shevchenko A, ..., Ahrends, R et al. Introducing the Lipidomics Minimal Reporting Checklist. Nat Metab (2022). https://doi.org/10.1038/s42255-022-00628-3
• Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz MA. Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites. 2022; 12(7):584. https://doi.org/10.3390/metabo12070584
• Schulz T, Wittler R, Stoye J. Sequence-based pangenomic core detection, iScience, Volume 25, Issue 6, 2022,104413, ISSN 2589-0042, https://doi.org/10.1016/j.isci.2022.104413
• Serrano-Solano B, ..., Grüning B, Coppens F; Galaxy: A Decade of Realising CWFR Concepts. Data Intelligence 2022; 4 (2): 358–371. https://doi.org/10.1162/dint_a_00136
• Arend D, ..., Junker A, Lange M. (2022), From data to knowledge – big data needs stewardship, a plant phenomics perspective. Plant J, 111: 335-347. https://doi.org/10.1111/tpj.15804
• Jeong K, ...., Kohlbacher O. FLASHIda enables intelligent data acquisition for top–down proteomics to boost proteoform identification counts. Nat Commun 13, 4407 (2022). https://doi.org/10.1038/s41467-022-31922-z
• Childebayeva A, ..., Kohlbacher O et al. Population Genetics and Signatures of Selection in Early Neolithic European Farmers, Molecular Biology and Evolution, Volume 39, Issue 6, June 2022, msac108, https://doi.org/10.1093/molbev/msac108
• Darvish M, Seiler E, Mehringer M, Rahn R, Reinert K, Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments, Bioinformatics, 2022, btac492, https://doi.org/10.1093/bioinformatics/btac492
• Jahn B, ..., Woklenhauer O et al. On the role of data, statistics and decisions in a pandemic. AStA Adv Stat Anal (2022). https://doi.org/10.1007/s10182-022-00439-7
• Kamal, N., ..., Gundlach H, ...., Mayer FX et al. The mosaic oat genome gives insights into a uniquely healthy cereal crop. Nature 606, 113–119 (2022). https://doi.org/10.1038/s41586-022-04732-y
• Scoma A, ..., Heyer R, ..., Benndorf D et al. Lignocellulose Fermentation Products Generated by Giant Panda Gut Microbiomes Depend Ultimately on pH Rather than Portion of Bamboo: A Preliminary Study. Microorganisms. 2022; 10(5):978. https://doi.org/10.3390/microorganisms10050978
• Hiltemann S, Rasche H, ..., Maier W, ..., Grüning B, Batut B, the Galaxy Training Network, Galaxy Training: A Powerful Framework for Teaching! bioRxiv 2022.06.02.494505; https://doi.org/10.1101/2022.06.02.494505
• Fischer M, Hoffmann S. Synthesizing genome regulation data with vote-counting, Trends in Genetics, 2022, https://doi.org/10.1016/j.tig.2022.06.012
• Matic M, ..., Russell RB, Inoue A, Raimondi F. PRECOGx: exploring GPCR signaling mechanisms with deep protein representations, Nucleic Acids Research, Volume 50, Issue W1, 5 July 2022, Pages W598–W610, https://doi.org/10.1093/nar/gkac426
• Carter JA, ..., Brors B et al. Transcriptomic diversity in human medullary thymic epithelial cells. Nat Commun 13, 4296 (2022). https://doi.org/10.1038/s41467-022-31750-1
• Fremin BJ, ..., Sczyrba A et al. Thousands of small, novel genes predicted in global phage genomes, Cell Reports, Volume 39, Issue 12, 2022, 110984, https://doi.org/10.1016/j.celrep.2022.110984
• Dubois-Pot-Schneider H, ..., Salhab A, ..., Walter J, Corlu A. Transcriptional and Epigenetic Consequences of DMSO Treatment on HepaRG Cells. Cells. 2022; 11(15):2298. https://doi.org/10.3390/cells11152298
• Vlot AHC, Maghsudi S, Uwe Ohler, Cluster-independent marker feature identification from single-cell omics data using SEMITONES, Nucleic Acids Research, 2022;, gkac639, https://doi.org/10.1093/nar/gkac639.
• Mudge, JM, ..., Ohler, U et al. Standardized annotation of translated open reading frames. Nat Biotechnol 40, 994–999 (2022). https://doi.org/10.1038/s41587-022-01369-0
• Dohmen, J, Baranovskii, A, Ronen J, Uyar B, Franke V & Akalin, A. Identifying tumor cells at the single-cell level using machine learning. Genome Biol 23, 123 (2022). https://doi.org/10.1186/s13059-022-02683-1
• Schoening T, ..., Felden J, ..., Nattkemper TW, Purser A, Zurowietz M. Making marine image data FAIR. Sci Data. 2022 Jul 15;9(1):414. https://doi.org/10.1038/s41597-022-01491-3.
• Bonidia RP, ..., Stadler PF et al. BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria, Briefings in Bioinformatics, Volume 23, Issue 4, July 2022, bbac218, https://doi.org/10.1093/bib/bbac218
• Paoli L, ..., Bork P, ..., Zeller G et al. Biosynthetic potential of the global ocean microbiome. Nature 607, 111–118 (2022). https://doi.org/10.1038/s41586-022-04862-3
• Pinter N, ..., Grüning BA et al. MaxQuant and MSstats in Galaxy Enable Reproducible Cloud-Based Analysis of Quantitative Proteomics Experiments for Everyone, J. Proteome Res. 2022, 21, 6, 1558–1565, https://doi.org/10.1021/acs.jproteome.2c00051
• Uszkoreit J, ..., Eisenacher, M. Dataset containing physiological amounts of spike-in proteins into murine C2C12 background as a ground truth quantitative LC-MS/MS reference, Data in Brief, Volume 43, 2022, 108435, https://doi.org/10.1016/j.dib.2022.108435

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