- Nfdi4microbiota-announce

by Hege, Cordula Almut Selma

(English version below) Liebe NFDI4Microbiota-Interessierte, wir möchten Euch herzlich zu unserem spannenden Mitmach-Event der NFDI-Konsortien NFDI4Biodiversity<https://www.nfdi4biodiversity.org/en/>, NFDI4Earth<https://www.nfdi4earth.de/> und NFDI4Microbiota<https://nfdi4microbiota.de/> einladen, bei dem sich – natürlich – alles um die Arbeit an und mit Daten dreht. Unsere DataXplorers-Webseite<https://www.nfdi.de/dataxplorers-hackathon/> ist nun online und Registrierungen darüber bis zum 01. Oktober möglich. Mit einem online Kick-Off-Event am 23. Oktober 2023 startet der Hackathon für Nachwuchs- und erfahrende Wissenschaftler:innen aus den Feldern Erdsystem-, Biodiversitäts- und Mikrobiologieforschung sowie Interessierte aus anderen Feldern, etwa Informatik oder Design. Chat-Bots programmieren, die Fragen zu Forschungsdatenmanagementthemen beantworten, Data Cubes erstellen, die Klima – mit Biodiversitätsdaten verbinden – was kann entstehen, wenn neugierige Köpfe verschiedener Disziplinen zusammenkommen und gemeinsam Neues kreieren? Wir wollen es gemeinsam mit Euch herausfinden! Der Hackathon ermöglicht es den Teilnehmenden, sich in Gruppen (von max. 5 Personen) zusammenzutun und (begleitet von Profis) ihrer Kreativität freien Lauf zu lassen. Ihr könnt euch entweder als Team oder auch alleine anmelden. Das Organisationsteam hat dafür sechs verschiedene Challenges zu unterschiedlichen Themen vorbereitet, denen Teilnehmende sich je nach Interesse zuordnen können. Für die remote Bearbeitung der Aufgaben ist mehrere Wochen Zeit, bis am 5. und 6. Dezember 2023 in Frankfurt am Main die Ergebnisse präsentiert werden. Es ist möglich an der Abschlussveranstaltung sowohl in Person, als auch online teilzunehmen. Alle weiteren Informationen zum Ablauf des Hackathons, die detaillierten Challenge-Beschreibungen finden sich auf unserer DataXplorers Homepage: https://www.nfdi.de/dataxplorers-hackathon/. Für die Teilnahme an einer Challenge und an der Veranstaltung in Frankfurt ist eine Registrierung erforderlich. Die Formulare finden sich unter dem entsprechenden Link auf unserer Webseite und hier<https://events.gfbio.org/event/38/>. Wir freuen uns, Ihr selbst dabei seid und möchten Euch auch dringend bitten, die Veranstaltung an geeignete Empfänger:innen weiterzuleiten. Auch Interessierte, die selber keine Challenge bearbeiten, sind herzlich eingeladen am Kick-Off Event und der Abschlussveranstaltung teilzunehmen. Bei Fragen könnt Ihr Euch direkt an mich und das Organisationsteam wenden: nfdi4earth-academy(a)groups.tu-dresden.de<mailto:nfdi4earth-academy@groups.tu-dresden.de> Viele Grüße, Kristin Sauerland und Cordula Hege ----- Dear NFDI4Microbiota-enthusiasts, We would like to invite you to our exciting hands-on event of the NFDI consortia NFDI4Biodiversity<https://www.nfdi4biodiversity.org/en/>, NFDI4Earth<https://www.nfdi4earth.de/> and NFDI4Microbiota<https://nfdi4microbiota.de/>, which - of course - is all about working on and with data. Registrations via our DataXplorers website<https://www.nfdi.de/dataxplorers-hackathon/> can be made until October 01st. The hackathon starts with an online kick-off event on October 23, 2023 and adresses young and experienced scientists from the fields of Earth system, biodiversity and microbiology research as well as interested people from other fields, such as computer science or design. Programming chat bots that answer questions on research data management topics, creating data cubes that connect climate and biodiversity data - what can happen when curious minds from different disciplines come together and create something new? Together with you, we are going to find this out! The Hackathon allows participants to get together in groups (of max. 5 people) and (accompanied by professionals) give free rein to their creativity. You can register either as a team or alone and get to know new people. The organizing team has prepared six different challenges on various topics, to which participants can assign themselves according to their interests. There will be several weeks to work on the tasks remotely until the results are presented in Frankfurt am Main on December 5 and 6, 2023. It is possible to participate in the final event both in-person and online. All further information about the hackathon and the detailed challenge descriptions can be found on our DataXplorers homepage: https://www.nfdi.de/dataxplorers-hackathon/. Registration is required to participate in a challenge and in-person in the event in Frankfurt. The forms can be found under the corresponding link on our website and here<https://events.gfbio.org/event/38/>. We hope that many of you participate and would like to ask you to forward the event to suitable recipients. Interested people that do not wish to participate in a challenge, are also welcome to participate in the kick-off event and in the closing event. If you have any questions, please contact me and the organising team directly: nfdi4earth-academy(a)groups.tu-dresden.de<mailto:nfdi4earth-academy@groups.tu-dresden.de> Kind regards, Kristin Sauerland und Cordula Hege [cid:1937d5ea-b3e5-4ed6-bcd1-de12c902d198] Dr. Cordula Hege Project Manager Computational Biology for Infection Research Head of Department: Prof. Alice McHardy Helmholtz Centre for Infection Research GmbH Inhoffenstrasse 7 38124 Braunschweig Germany Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477 Unsere Hinweise zum Datenschutz finden Sie hier: https://www.helmholtz-hzi.de/de/service/datenschutz/

2 years, 5 months

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NFDI4Microbiota - Community survey open until 30th of September

by Goetz, Barbara

Dear NFDI4Microbiota community, We need your help to get better! Therefore, we have designed a 15-minute survey to gain a better understanding of the knowledge and needs of our community. As an incentive and compensation for your time, NFDI4Microbiota merchandise packages and some microbiology-related items will be raffled among all participants. Please do not hesitate to forward the link to other microbiologists! The survey is open until the 30th of September and accessible via this link: https://www.2ask-survey.com/c/6238RCG6EJY12/ We count on you! Kind regards, Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Mastodon: nfdi.social/@NFDI4Microbiota<https://nfdi.social/@NFDI4Microbiota> LinkedIn: linkedin.com/company/nfdi4microbiota/<https://www.linkedin.com/company/nfdi4microbiota/> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

2 years, 5 months

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NFDI4Microbiota Newsletter #5

by NFDI4Microbiota

[Im Browser öffnen](https://b18ad.r.a.d.sendibm1.com/mk/mr/sh/OycXxko2a8zXPIR5m9M7ojCw/… NEWSLETTER ---------- Dear Reader, With our fifth NFDI4Microbiota newsletter, we would like to share news about conferences, Use Cases, training and available online videos. If you are interested in other topics we should cover, please let us know.[We are happy to hear from you!](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1eQuZUu03s625SA/… And now: Enjoy reading the newsletter! ###Community engagement – events and conferences ###Upcoming conferences In September 2023, we will be attending many conferences in order to present our work and to meet our various target communities. Please come by to meet us if you are attending – we look forward to meeting you in person! You can find our contributions to all events below and [on our web portal](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1kTcoJzby1bbhK… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarTU3MznueikKVCI/7NYh…"). - [VAAM Annual conference 2023](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1qWL395DsB7BJDC/… "https://vaam-kongress.de/programme-abstracts/scientific-programme#c6756") – oral presentation, poster and booth - [36th Workshop of the European Helicobacter and Microbiota Study Group](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo1wZ3HyApmKckv5i… "https://www.workshop.ehmsg.org/") (EHMSG) – poster - [1st Conference on Research Data Infrastructure](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo22blWn… "https://www.nfdi.de/cordi-2023/") (CoRDI 2023) – oral presentation, poster and booth - [German Conference on Bioinformatics](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo28eTlc… "https://gcb2023.de/") (GCB) 2023 – poster - [75th Annual Conference of the DGHM 2023](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2EhC0RRfUn9TkjG/… "https://dghm-kongress.de/en/") – poster - [Jahrestagung der Deutschen Gesellschaft für Epidemiologie](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2KjuFGX… "https://2023.dgepi.de/") (DGEpi) – poster ###NFDI4Microbiota will attend the 2023 Digital-Gipfel (Digital Summit) The 2023 Digital-Gipfel (Digital Summit) will take place in Jena from November 19th-21st. Various NFDI consortia including the NFDI4Microbiota will come together on the themes of the summit. [See more here.](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2QmcU5ctJ6AcyUI… "https://initiatived21.de/veranstaltungen/digital-gipfel-2023") ###Upcoming hackathon: DataXplorers – Cross-community hackathon Together with NFDI4Biodiversity and NFDI4Earth, NFDI4Microbiota is organizing a hackathon. **The hackathon will start with an online kick-off event on October 23rd and will end with a hybrid final event on December 5th-6th in Frankfurt.** The main target group are early career researchers (PhD students and postdocs) from the fields of earth system sciences, biodiversity and microbiology – but we also strongly encourage participation from other fields, such as informatics, bio-/media-informatics, and design. More experienced individuals are also welcome to participate. Challenges will be provided and mentored by partners from the consortia of NFDI4Earth, NFDI4Biodiversity and NFDI4Microbiota. Topics include developing an annotation tool for metaproteomics experiments, building of data cubes and developing machine learning methods for image annotation. You can register on our[ hackathon website](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/OycZvHuFo2WpKiuiVDFgCa… "https://www.nfdi.de/dataxplorers-hackathon/"), where we will also publish the challenge descriptions. ###Successful Workshop on "Automating Virus Taxonomy" was held in Jena The [Workshop "Automating Virus Taxonomy"](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqJHsMvatjmqq2Ba/UIlgxIX3UGmF "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZeDhCmpvvSJauqNq/Alhq…"), which took place from July 31st to Aug 2nd in Jena, Germany, was a great success. The hybrid event was co-organized by members of the International Committee for the Taxonomy of Viruses [(ICTV)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFGUXZslPb3DsR… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3Atrzn6RJZxxFTy/2DdB…"), European Virus Bioinformatics Center [(EVBC)](https://evbc.uni-jena.de/ "https://evbc.uni-jena.de/"), and the NFDI4Microbiota. About 400 people from 46 countries registered, highlighting the global interest in this important topic. After the workshop the ICTV Executive Committee discussed this year’s taxonomic proposals and approved most of the additions to the virus taxonomy. For those interested, one can find these under “Taxonomy > Proposals” on the[ ICTV website](https://ictv.global/ "https://ictv.global/"). On the third day of the workshop, a pop-up hackathon and Hands-On Workshop co-organized by Dr. Noriko Cassman (NFDI4Microbiota, FSU Jena) and David Lähnemann (DKFZ Heidelberg/DKTK site Essen-Düsseldorf) took place. About 100 online and 20 onsite participants learned how to write Snakemake workflows and/or created pipelines to automate virus classification. We are pleased to share the results of the hackathon: two Snakemake workflows for Caudoviricetes classification that follow best coding practices! Take a peek at the [mashup-phage](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaS86XCk… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbG2VrcebytN54SmM/zUFe…") and [download-and-reannotation-of-phage-genomes](https://b18ad.r.a.d.sendibm1.co… "https://github.com/ICTV-VBEG/download-and-reannotation-of-phage-genomes") workflows on the [GitHub repository of the ICTV Virus Bioinformatics Enthusiasts Group](https://github.com/ICTV-VBEG "https://github.com/ICTV-VBEG"). Also available are the Snakemake [material](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbeziWpbmUkd… "https://snakemake.readthedocs.io/en/latest/tutorial/tutorial.html") and [slides](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc3wvC2Yx0btp9… "https://slides.com/johanneskoester/snakemake-tutorial"). ###NFDI4Microbiota Use Cases ###NFDI4Microbiota is looking for your input on the Use Cases We are delighted to invite you to explore our active [Use Cases](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcSu7rFW7WTACBg… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqPKabkgVdwMPe46/pi9R…"). Whether you are a microbiologist, bioinformatician, or computer scientist, your expertise can be a valuable addition to these projects. Engage with our Use Cases, explore innovative ideas, and contribute to solutions that drive innovation in the field of microbiome research. For each Use Case you will find graphical abstracts, project descriptions, contact details of the project leaders and how to get involved [on our web portal](https://nfdi4microbiota.de/latest/usecase "https://nfdi4microbiota.de/latest/usecase"). Discover the different topics our Use Cases cover, from metaproteomics and metagenomics to multi-omics data integration: - MetaProt: Functional profiling and routine diagnosis of human microbiomes by metaproteomics - MetaProv: Provenance and usage of metagenome data - MockBench: Systematic assessment in metagenomics using high diversity Mock samples - MULTI: Integration of multi-omics data of microbial species - Strain-ID: Collecting and matching microbial strain identifiers - TAXA: Descriptions of novel taxonomic lineages Ultimately, the outputs from these projects will help you to be more effective in your daily research. Here are some examples from across the Use Cases where your input is needed and/or how you can benefit from them: You are a … - **Microbiologist** trying to identify and match culture collection numbers to a given strain: Use the service [StrainInfo](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFMXFohr1… "https://straininfo.dsmz.de/") and [provide feedback](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZeJjv1f1XMT… "https://nfdi4microbiota.de/usecases/strain-id"). - **Microbiologist** with experience in transcriptomics or proteomics analyses: Check out the [preliminary guidelines on data processing, analysis, and integration of genomics, transcriptomics, and proteomics data](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3GwaEcC3DjTWrM… "https://gitfront.io/r/user-6306825/uUtkLPVoZfbX/multi/") and [give feedback](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaSE9FRZMZ4z… "https://nfdi4microbiota.de/usecases/multi"). - **Bioinformatician** curating metagenomes datasets: Provide curated data and metadata from human gut microbiome samples. [(Use Case “MetaProt”)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarBLueWX4wGDbfYk/vRlpO11H_BGC "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcT0AZULD8NJhlHxG/msmW…") - **Metagenome analyst** frustrated with numerical bacteria names lacking functional insights: [Use the tool](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbG8YZrThanWae4e… "https://nfdi4microbiota.de/usecases/taxa") to generate functional descriptions and curate information in a human-readable format. - **Metagenome researcher** looking for sequence data: Find a unified and standardized metadata database from SRA (sequence read archive) metagenomic sequences where you can easily select relevant samples according to your research question. [(Use Case “MetaProv”)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbf5lF4Qs6emxgTl0/33R3fNXxds4O "https://nfdi4microbiota.de/usecases/metaprov") - **Bioinformatic software developer** interested in evaluating your tools: Specify the application scenario for which your tool is most likely to be used and, consequently, indicate what challenges are to be expected from a typical target microbial community in terms of complexity and diversity. What key parameters should an appropriate evaluation dataset feature? [(Use Case “MockBench”)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc42xuHO2cW3Kisr8/pk2BTZQRiSj- "https://nfdi4microbiota.de/usecases/mockbench") ###Metaproteomics Workshop organized by the NFDI4Microbiota Use Case “MetaProt” Are you interested in metaproteomics and a hands-on training workshop and getting to know the faces behind the NFDI4Microbiota [Use Case “MetaProt”](https://nfdi4microbiota.de/usecases/metaprot "https://nfdi4microbiota.de/usecases/metaprot")? Join the**“Applied Metaproteomics Workshop Magdeburg 2023”** for training on experimental design, sample preparation, LC-MS measurements, data analysis and metadata suggestions based on standards developed by the MetaProteomics Initiative and NFDI4Microbiota. **Organizers:** Dirk Benndorf, Patrick Hellwig, Kay Schallert, Robert Heyer, Nico Jehmlich **Date:** September 18th-22nd, 2023 **Location:** Otto von Guericke University Magdeburg, Germany **Registration fee:** 100 € (including coffee and snacks) **More information:**The agenda and registration details are available at [mpa@ovgu.de](mailto:mpa@ovgu.de?subject=Applied%20Metaproteomics%20Workshop%20Magdeburg%202023 "mailto:mpa@ovgu.de") ###NFDI4Microbiota Services ###Upcoming training and workshops Supporting the community through education and training is an important goal of our work. Therefore, we provide a comprehensive training program to equip the community with the skills and literacy required for efficient and data-driven microbial research. Upcoming training courses can be found in [our training calendar](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqVNIqZm7Y5… "https://nfdi4microbiota.de/training/training") and below. - [Workshop on Computational Pangenomics](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFSZy3Ww… "https://www.denbi.de/training/1588-workshop-on-computational-pangenomics") (online, Sep 20th-21st, 2023) - Workshop on BacDive, MediaDive and StrainInfo (Oct 11th, 2023, *more details coming soon*) - [Workshop on Deep Learning with R](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZePmdGU79Gcc448s/z… "https://www.dzif.de/en/event/introduction-deep-learning-r") (online, Oct 11th-13th, 2023) - [Workshop: How to describe biological data?](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3MzITRHf7sz6T… "https://biometadata-01.sciencesconf.org/") A primer to a FAIR approach for now and the future (RWTH Aachen, Oct 16th-17th, 2023, see the next article for more details) - [Workshop on Basic statistics with R](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaSKBxgOSAz9M8sL8/d… "https://www.dzif.de/en/event/basic-statistics-r") (online, Oct 25th-27th, 2023) - Joint de.NBI & NFDI4Microbiota Training Course on Metagenome Analysis (online, Nov 7th-9th, 2023, *more details coming soon*) ###Workshop: How to describe biological data? A primer to a FAIR approach for now and the future Confused about FAIR, ontologies and metadata and how they can help you and your datasets? Begin with our hands-on workshop about description of biological data on October 16th-17th in Aachen and [register here by September 20th](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarHOctLcgqPjBHR… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbGEbI6InChg6DgXO/PmaV…"). **The workshop is intended for:** - People with knowledge about microbiology - Late-stage (wet lab) researchers with datasets that are in preparation to be submitted to repositories - Early-stage researchers that will be generating large datasets - Researchers having difficulties to apply existing ontologies and metadata fields to their data set - Data stewards or broker responsible for submitting data You will learn how to use terms based on existing ontologies and controlled vocabulary. Your engagement and continuous use of these terms will help to increase future machine-actionable analyses. After the workshop, you will have successfully described your own datasets and prepared the necessary metadata for future deposition of your described datasets. **But beware during this workshop, we will not upload or publish your data, analyze/ re-analyze your data, develop an ontology or set-up an automatic transfer of your metadata to repositories.** ###Publications ###The NFDI4Microbiota Grant Proposal has been published We are pleased to announce that our DFG [grant proposal](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbfBnxJFxiYw… "https://riojournal.com/article/110501/") “NFDI4Microbiota – national research data infrastructure for microbiota research” has been published in the journal [Research Ideas and Outcomes (RIO)](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc490cWD8EQCqIUj… "https://doi.org/10.3897/rio.9.e110501"). Here you can find all information about our structure, partners, objectives, work program and strategies. ###Reading recommendation: How to make your scientific data accessible, discoverable and useful - Nature In June 2023, Nature published a Technology Feature article entitled “How to make your scientific data accessible, discoverable and useful” asking data scientists about their best practices for publishing usable, high-quality data. Here, specialists offer seven tips for effectively sharing data. [Read the full article here.](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcT6DHjAIkHTDKt… "https://www.nature.com/articles/d41586-023-01929-7") ###Media ###NFDI4Microbiota is now part of the LinkedIn network After having profiles on X (former Twitter) and Mastodon, [you can follow us now also on LinkedIn!](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqbQ15OrjS… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZFYcgIM2FJVkbGvG/s7Ez…") We are looking forward to get in touch with you there. ###Short introduction video of NFDI4Microbiota published A two-minute introduction video of NFDI4Microbiota is [now available online](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGZeVpLVJClAm7d… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGa3T20iGNH22Ug57W/Z6M6…"), giving an insight into our vision and mission, and how we aim to democratize the access to microbiota data and high-end computational analyzes. ###Online video: NFDI4Microbiota lecture talk - Training and education One focus of our consortium is the democratization of access to data and workflows for the field of microbiology. Training and education, as well as building a knowledge base on topics related to this field, are some of the means to achieve these goals. [This presentation was originally given at the second NFDI4Microbiota annual conference (April 2023).](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGaSQEfvDXmtIri… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGarNRL8AiIkZEktJm/Guda…") It provides an overview of the overall goals for training and education within NFDI4Microbiota and details on the first steps we have taken to reach these goals. We also introduce the NFDI4Microbiota Knowledge Base as part of our educational efforts. ###Online presentation: NFDI4Microbiota - Services to make data FAIR and Open The presentation "NFDI4Microbiota - Services to make data FAIR and Open" held by Barbara Goetz, member of NFDI4Microbiota, at the fifth Thuringian RDM Days on 20-21 June 2023 [has been recorded and is available online](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbfHqfY53KT5yp… "https://www.youtube.com/watch?v=cvy5nhDBYbE"). The slides of the presentation [can be found here](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbGKe0L7sobpbnIP… "https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc4F3Kl2DqKMLs6cA/7VNS…"). ###Jobs The members of the NFDI4Microbiota consortium offer specialist positions throughout Germany. The content and funding of all positions are the responsibility of the individual members. **Our partner at the Friedrich Schiller University Jena is looking for a**[**“Postdoctoral researcher (m/f/d) or PhD Candidate (m/f/d) in Frontend development of virus database and community engagement”**](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGcTCFzx… "https://jobs.uni-jena.de/jobposting/d070b59d5f1c7eaa6e77f0e1eebbdb2238de461…")**.** The application deadline is November 1st, 2023. [All vacancies are posted on the NFDI4Microbiota website as they become available.](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGYqhSjKDxL… "https://nfdi4microbiota.de/latest/jobs") Learn More About Us: -------------------- **This newsletter is brought to you by NFDI4Microbiota** Mail: [contact@nfdi4microbiota.de](mailto:contact@nfdi4microbiota.de) If you no longer wish to receive this newsletter, [click here to unsubscribe.](mailto:contact@nfdi4microbiota.de?subject=Unsubscribe&body=Dear%20NFDI4Microbiota-Team%2C%0AI%20would%20like%20to%20unsubscribe%20from%20your%20newsletter.%0A%0AKind%20regards "click here to unsubscribe") [Privacy Policy](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbGQgiZwyQVz7M… • [Impressum](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGbfNtNmu8wN… • [Disclaimer](https://b18ad.r.a.d.sendibm1.com/mk/cl/f/sh/1f8JIKXwHGc4L62zrJS…

2 years, 6 months

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NFDI4Microbiota - Flex Funds call 2024 now open

by Goetz, Barbara

Dear NFDI4Microbiota community, We are glad to announce that we just opened the NFDI4Microbiota Flex Funds call for 2024. The call is open from 2023-07-11 until 2023-08-20. A brief summary of the call: Aim of the NFDI4Microbiota Flex Funds The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and support of further data types, development of new training programs, and improvement of the ability to react to unforeseen technical challenges. Therefore, within the NFDI4Microbiota project work, flexible funding (so called 'Flex Funds') for small projects within the research community are available for the years 2023 to 2026. To implement a dynamic system that stays on track with new trends in the field, the Flex Funds will support small projects and active Use Cases from the community as they arise over time. In the following, a guideline regarding the application and allocation process is provided. Eligible topics Applications must address services to be developed and deployed that are related to the NFDI4Microbiota proposal. This could include, but is not limited to, the following topics · Data Brokerage · Infrastructure/Services · Data storage and workflow execution · Training · Community engagement and outreach · Establishment of local data stewards · Use Case connection or an active Use Case · Generation and/or curation of large, high quality data sets All details, the application guideline and the application forms are accessible here: https://nfdi4microbiota.de/flexfunds/ For further details please read the full guideline on our web portal. Please contact us via contact(a)nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de> if you have further questions. On behalf of the NFDI4Microbiota consortium. Kind regards, The NFDI4Microbiota Administration Unit Barbara Götz, Dr. Carmen Paulmann, Dr. Cordula Hege --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota Part of the Administration Unit of NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

2 years, 7 months

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4th NFDI4Microbiota Newsletter

by Paulmann, Carmen

4th NFDI4Microbiota Newsletter - PDF version in the attachment Dear Reader, With our fourth NFDI4Microbiota newsletter, we would like to share news about conferences and events, the new StrainInfo-Archive and available online videos. If you are interested in other topics we should cover, please let us know. We are happy to <https://nfdi4microbiota.de/contact-form/> hear from you<https://nfdi4microbiota.de/contact-form/>! And now: Enjoy reading the newsletter! Community engagement – events and conferences The second NFDI4Microbiota annual conference was held in April under the theme “Community Engagement” We were glad to meet some of our participants and ambassadors during the second NFDI4Microbiota annual conference in Frankfurt am Main, Germany. Our participants had the opportunity to introduce themselves by giving flash talks and presenting posters and to get insights into the aims and current achievement of our consortium. [cid:ed7b0cab-6e0f-43cc-84ac-0f457fa36069] In addition, we were able to invite two international keynote speakers who reported on their infrastructure projects. First, <https://www.wur.nl/de/Personen/Hauke-prof.dr.-H-Hauke-Smidt.htm> Prof. Dr. Hauke Smidt<https://www.wur.nl/de/Personen/Hauke-prof.dr.-H-Hauke-Smidt.htm><https://www.wur.nl/de/Personen/Hauke-prof.dr.-H-Hauke-Smidt.htm> from Wageningen University, the Netherlands, presented the work and opportunities that the <https://www.wur.nl/en/article/unlock-1.htm> UNLOCK<https://www.wur.nl/en/article/unlock-1.htm><https://www.wur.nl/en/article/unlock-1.htm> project offers to microbiology scientists. The UNLOCK infrastructure is open for exploring new horizons for research on microbial communities. The free service provides the ability to study microbial communities in a variety of environments. Our second keynote speaker, Lee Ann McCue, came all the way from the Pacific Northwest National Laboratory in the US. She is a member of the <https://microbiomedata.org/> National Microbiome Data Collective (NMDC)<https://microbiomedata.org/><https://microbiomedata.org/>. After presenting the work of NMDC, a fruitful discussion and exchange took place with our consortium. Collaboration on similar topics is planned throughout the project. [cid:6b6eed56-4d28-48f0-8b1a-182685738ce2] NFDI4Microbiota will present its work during the Thuringian RDM Days The <https://forschungsdaten-thueringen.de/rdm-days/articles/rdm-days.html> Thuringian RDM Days<https://forschungsdaten-thueringen.de/event/fdm-tage-2023-en.html> are an annual series of events during which the universities in Thuringia offer various lectures and workshops on research data management under a specific motto. These are primarily targeted at researchers in Thuringia, but are also open to researchers and other interested parties! We will present the work of NFDI4Microbiota online on June 21 at the Thuringian RDM Days 2023. ICTV/EVBC Workshop on Automating Virus Taxonomy From July 31 to August 2, 2023, the EVBC (European Virus Bioinformatics Center) and the ICTV (International Committee on Taxonomy of Viruses) are organizing a workshop on “Automating Virus Taxonomy” in Jena, Germany. Prof. Manja Marz, NFDI4Microbiota partner, is part of the organising committee. The workshop will be hybrid and can therefore be attended live or online. On the first day, Prof. Alexander E. Gorbalenya (Leiden University, the Netherlands) and several other virology experts will present on virus taxonomy and the ins and outs of classifying specific viruses. In the morning of the second day, bioinformaticians will explain how they have implemented automated classification methods. In the afternoon, both groups, virology experts and bioinformaticians, will be brought together for discussion sessions with the goal to start or deepen collaborations between participants. In addition to this program, satellite hands-on sessions (August 2, 2023) will be offered focusing on automating bioinformatics workflows (Snakemake) and virus databases (organized by NFDI4Microbiota). For more information and to register click <https://evbc.uni-jena.de/events/virus-taxonomy-workshop/> here<https://evbc.uni-jena.de/events/virus-taxonomy-workshop/>. Second in-person meeting of the NFDI management circle took place in Hamburg A strong network needs good coordination. For this reason, people from the different NFDI consortia met for a second in-person meeting to discuss different management topics at the Deutsches Elektronen-Synchrotron (DESY) in Hamburg. The meeting addressed common challenges and approaches to solutions with a focus on administrative issues. The two days in Hamburg also offered plenty of opportunities for networking and personal exchange. We are glad to be able to work in such a supportive and friendly community. [cid:a2f411ac-e731-4c06-adb2-e9bf3fa0140b] NFDI4Microbiota Services Alpha version of the StrainInfo-Archive is online In microbiology, resolving microbial strain identifiers is an important requirement. Strain identifiers represent a universal language for working with strains and can be found throughout literature, databases and culture collection catalogs. StrainInfo is a service being developed to provide a one-stop shop for strain identity information by storing culture collection numbers, their relations and associated information on taxonomy, sequence accessions and literature to help researchers in their work with microbial strains. StrainInfo was initially created by BCCM/LMG between the years 2005 and 2015 and is currently being developed by the NFDI4Microbiota partner institution DSMZ. The alpha version<https://straininfo.dsmz.de/#><https://straininfo.dsmz.de/#><https://straininfo.dsmz.de/> of StrainInfo is now online and utilizes test data provided by LMG. Media Interview on the importance of research data management in microbiology is online Is scientific work even possible today without dedicated research data management? And what role do infrastructures play in this? Elke Roesner talks about this in the new “ZB MED Nachgefragt” with Barbara Götz, microbiologist and project manager at NFDI4Microbiota, and Prof. Dr. Konrad Förstner, bioinformatician and speaker of our consortium. This <https://www.youtube.com/watch?v=xwmMuPh0LBw> video podcast<https://www.youtube.com/watch?v=xwmMuPh0LBw> (German) explains where NFDI4Microbiota stands today, the challenges to be overcome, future plans and why it is necessary to reach scientists even earlier in their careers to embed awareness of research data management in the scientific communities. [cid:89929157-3a76-48c1-990b-ca45593e0aa6] NFDI4Microbiota contributed to Love Data Week 2023 with a panel discussion on the benefits of data-driven decisions in life sciences – video is now online What needs to happen to establish conscientious research data management in the disciplines of the life sciences? How can researchers be convinced and reservations be overcome? These were the questions addressed in a highly interesting panel discussion on February 16, 2023, jointly organised by the NFDI consortia NFDI4Biodiversity, DataPLANT, NFDI4Health and NFDI4Microbiota. Panelists were Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Konrad Förstner (NFDI4Microbiota), Prof. Dr. Björn Usadel (DataPLANT) and Prof. Dr. Iris Pigeot (NFDI4Health). The discussion was moderated by Dr. Kerstin Elbing (Verband Biologie, Biowissenschaften und Biomedizin in Deutschland e. V. – VBIO). The discussion was introduced by keynote speeches from Dr. Martin Friedrichs-Manthey (NFDI4Biodiversity), Prof. Dr Björn Usadel and Prof. Dr Iris Pigeot. The event was part of the Love Data Week 2023, an international week of action to discuss and reflect on research data together. Under the motto "Data: Agent of Change" the Love Data Week 2023 was celebrated worldwide from February 13-17 with numerous events on a wide range of research data management (RDM) topics. The <https://www.youtube.com/watch?v=3k64WHbwy8I> video<https://www.youtube.com/watch?v=3k64WHbwy8I> of the panel discussion is now online! Short clip: The work of a data steward A Data Steward is, generally said, a person who is responsible for ensuring the quality of data assets, including metadata. However, the tasks of data stewards are very different and fulfill different requirements. This is also the case in the field of research. Good research data management is essential in research. Data stewards play a crucial role here, as they support researchers in this task and take on the role of intermediaries between the different fields of work. Justine Vandendorpe, one of NFDI4Microbiota’s data stewards at <https://www.zbmed.de/kontakt/justine-vandendorpe> ZB MED<https://www.zbmed.de/kontakt/justine-vandendorpe>, explains what her tasks as a data steward look like: “As a data steward within NFDI4Microbiota, I support the curation of microbial omics data and associated metadata. In practice, this means that I train researchers in research data management and reproducible data and software practices. I also advise researchers on the use of electronic lab notebooks and in writing their data management plan.” Learn more about her work in this <https://www.youtube.com/watch?v=LcoNsvfwvts> video<https://www.youtube.com/watch?v=LcoNsvfwvts>. [cid:9eed2032-837e-4e0b-b92d-88dd91632b20] NFDI4Microbiota is now part of the Mastodon network As a decentralised network, Mastodon represents an alternative to well-known social media platforms such as Twitter. Since mid of May, we have a <https://nfdi.social/@NFDI4Microbiota> new Mastodon profile<https://nfdi.social/@NFDI4Microbiota> on the NFDI instance<https://nfdi.social/home>. The instance is designed to be a place where users can share ideas about research data management (RDM) and discuss exciting topics from the NFDI consortia as well as the scientific community. You can also follow us from another server if you look for: @NFDI4Microbiota@nfdi.social Open access research data management training material publication A group of research data management (RDM) experts at our partner institution ZB MED just published an open access RDM training workshop material in Publisso<https://repository.publisso.de/resource/frl:6452660>. The ‚Online Training Workshop on Research Data Management in (Bio-)Medicine‘ is build of three main chapters: 1) General aspects of RDM, 2) Discipline-specific content, and 3) Engagement methods. This material is not only for self-study purpose, but explicitly for training purposes. It is published under the Creative Commons Attribution 4.0 International License. Social links and Contact Follow us on Twitter<https://twitter.com/nfdi4microbiota?lang=en>, <https://nfdi.social/@NFDI4Microbiota> <https://nfdi.social/@NFDI4Microbiota> Mastodon<https://nfdi.social/@NFDI4Microbiota><https://nfdi.social/@NFDI4Microbiota><https://nfdi.social/@NFDI4Microbiota><https://nfdi.social/@NFDI4Microbiota> and <https://github.com/NFDI4Microbiota> GitHub<https://github.com/NFDI4Microbiota>! Questions or suggestions<https://nfdi4microbiota.de/contact-form/>? <https://nfdi4microbiota.de/>Learn more<https://nfdi4microbiota.de/><https://nfdi4microbiota.de/> about NFDI4Microbiota! <https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…>Subscription / Unsubscription<https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…><https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…><https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…><https://lists.nfdi.de/postorius/lists/nfdi4microbiota-announce.lists.nfdi.d…> Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Dr. h.c. Dirk Heinz - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

2 years, 9 months

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Update: NFDI4Microbiota - Lecture talks on the 24th of April 2023 11-12:30 CEST + training announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, save the date for our short lecture talks on different services NFDI4Microbiota provides for its community: training, workflows, Use Cases and the NFDI4Microbiota Knowledge Base. The lectures will be webcasted on the 24th of April 2023 11-12:30 CEST. Update: Zoom login details: Meeting ID: 857 7139 3336 Passcode: 095511 We also would like to announce training offers by our partner: · 3-day Workshop on Nanopore Sequencing<https://bic.uni-jena.de/what-we-offer/training/>, 2023-04-26 - 2023-04-28, 09:00 - 16:00 CEST. · Introduction to R<https://docs.google.com/forms/d/e/1FAIpQLSd3U-NmjfZOIORKmhGsd__q1SwtWSvI3dY…>, 2023-05-15 - 2023-05-17, 10:00 - 13:00 CEST. Your NFDI4Microbiota Administration Unit, Barbara Götz, Carmen Paulmann and Cordula Hege --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

2 years, 11 months

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NFDI4Microbiota - Save the date: Lecture talks on the 24th of April 2023 11-12:30 CEST + training announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, save the date for our short lecture talks on different services NFDI4Microbiota provides for its community: training, workflows, Use Cases and the NFDI4Microbiota Knowledge Base. The lectures will be webcasted on the 24th of April 2023 11-12:30 CEST. The login details will be shared with you soon. We also would like to announce training offers by our partner: · 3-day Workshop on Nanopore Sequencing<https://bic.uni-jena.de/what-we-offer/training/>, 2023-04-26 - 2023-04-28, 09:00 - 16:00 CEST. · Introduction to R<https://docs.google.com/forms/d/e/1FAIpQLSd3U-NmjfZOIORKmhGsd__q1SwtWSvI3dY…>, 2023-05-15 - 2023-05-17, 10:00 - 13:00 CEST. Your NFDI4Microbiota Administration Unit, Barbara Götz, Carmen Paulmann and Cordula Hege --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

2 years, 11 months

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NFDI4Microbiota Newsletter 01/23

by Paulmann, Carmen

Welcome Dear Reader, With our third NFDI4Microbiota newsletter, we would like to share news about our upcoming conferences and events. In this issue, you can also read about our connecting efforts and we continue presenting recent publications, news and much more. If you are interested in other topics we should cover, please let us know. We are happy to hear from you! And now: Enjoy reading the newsletter! [cid:acbf171d-64b1-4e79-b779-c87d658e74e1] _________________________ Community engagement – events and conferences Save the date for the second NFDI4Microbiota annual conference The theme of this year's NFDI4Microbiota conference is "Community Engagement", as we want to get to know our participants and their needs, and give them an insight into our services. The conference will take place April 24-26, 2023, venue and registration information will follow shortly. On the morning of the first day, we will present our services to the community during NFDI4Microbiota lectures, which will be available online for everyone to attend. The rest of the conference will be reserved for NFDI4Microbiota participants, ambassadors, committees and the NFDI4Microbiota consortium. The first day will be a community day to connect with our participants and ambassadors. The second day will be dedicated to cross-cutting issues such as training and workflows, as well as the General Assembly. The third day will feature inspirational talks from international speakers involved in similar projects, followed by roundtable discussions about our Use Cases and a community workshop. Love is in the air! NFDI4Microbiota contributes to Love Data Week 2023 with a panel discussion on the benefits of data-driven decisions in life sciences During the Love Data Week 2023, several NFDI consortia participate in events or training regarding the topic “Data: Agent of Change”. Together with the NFDI consortia DataPLANT, NFDI4Health and NFDI4Biodiversity, we will host an in-person panel discussion on ‘Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences’ at the University of Bremen. Data-driven decisions in the life sciences have an immense impact on human and environmental well-being, as well as on the development of research directions. Therefore, experts from different areas of the life sciences will discuss the importance of data-driven decisions using best practice examples. Expect an in-depth discussion on the challenges and benefits of cultural change related to research data governance, Open Science and FAIR principles and their impact on the daily life of each individual. * Panelists: Prof. Dr. Konrad Förstner (NFDI4Microbiota), Björn Usadel (DataPLANT), Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Dagmar Waltemath (NFDI4Health) * Moderation: Dr. Kerstin Elbing (VBio) * Location: University of Bremen Bremen, Room NW2 C0290 (Hörsaal 1) * Date and time: 2023/02/16 15.00 - 17.00 PM CEST * Zoom option: Meeting-ID: 812 3227 9619, Password: 092856 [cid:967bf743-0b62-405f-9667-f0b7a6addb88] NFDI4Microbiota World Café on Electronic Lab Notebooks (ELNs) To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we will run a virtual World Café on 2023-02-24, 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Workflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here<https://us02web.zoom.us/meeting/register/tZAqceyppjwpHdRHg7uF7AqPb6Yxq4Phq3…>. NFDI4Microbiota will showcase its activities to the virology and parasitology communities In March, we will present our mission, work progress and services at the 32nd Annual Meeting of the Society for Virology <https://virology-meeting.de/> and the 30th Annual Meeting of the German Society for Parasitology<https://parasitology-meeting.de/>. The NFDI4Microbiota consortium members met at the first NFDI4Microbiota annual conference In November 2022, we met for the first time during the internal NFDI4Microbiota conference in Cologne. Presentations and fruitful discussions took place on our current work in the areas of computational infrastructure, data storage and analysis, data and metadata standards, training and outreach. In addition, our six active Use Cases<https://nfdi4microbiota.de/latest/usecase> were presented and discussed in roundtable sessions. [cid:729f6990-ab4c-44e2-8221-03696c157b63] The NFDI4Microbiota consortium met in Cologne. _________________________ Networking and Collaborations Regular exchange of NFDI4Microbiota and NMDC The National Microbiome Data Collaborative (NMDC) was initiated in July 2019 as the foundation of a community-driven US national effort aimed to develop standards, processes, and infrastructure for an integrated microbiome data ecosystem. The NMDC aims to achieve similar solutions for the US as we at NFID4Microbiota are pursuing for Germany. They are working with the community to develop and lead an integrated, open-source microbiome science gateway that leverages existing resources and enables comprehensive access to multidisciplinary microbiome data and standardized, reproducible data products. Like our NFDI4Microbiota consortium, NMDC is committed to open science and the FAIR principles. Our representatives from NFDI4Microbiota meet regularly with those from NMCD to explore synergies and to determine how best to integrate efforts in all areas, such as standards, analytical workflows, data and results sharing, and training. [cid:fb6eee7e-d580-43c5-9cc4-4fb56ca0ae39] _________________________ Publications Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities – Published in Cell Host & Microbe Microbiome research needs comprehensive repositories of cultured bacteria from the intestine of mammalian hosts. The groups of our NFDI4Microbiota partners, Prof. Thomas Clavel and Prof. Jörg Overmann, both NFDI4Microbiota partners, expanded the mouse intestinal bacterial collection to 212 strains, all publicly available and taxonomically described. This includes strain-level diversity, small-sized bacteria, and previously undescribed taxa (one family, 10 genera, and 39 species). This collection enabled metagenome-educated prediction of synthetic communities (SYNs) that capture key functional differences between microbiomes, notably identifying communities associated with either resistance or susceptibility to dextran sulphate sodium (DSS)-induced colitis. Additionally, nine species were used to amend the Oligo-Mouse Microbiota (OMM)12 model, yielding the OMM19.1 model. The added strains compensated for phenotype differences between OMM12 and specific pathogen-free mice, including body composition and immune cells in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available for future studies. In conclusion, this work improves the knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates. Microbiota research is hampered by the fact that approximately half of complex microbial communities is still unknown. Moreover, there is a lack of cultured isolates publicly available, which prevents functional studies. This published work addresses both issues by making cultured bacteria from the mouse intestine and their metadata available according to FAIR principles. Read more Toward FAIR Representations of Microbial Interactions – Published in mSystems Despite an ever-growing number of datasets that catalog and characterize interactions between microbes in different environments and conditions, many of these data are neither easily accessible nor intercompatible. These limitations present a major challenge to microbiome research by hindering the streamlined drawing of inferences across studies. Here, Charlie Pauvert from our consortium and the other authors propose guiding principles to make microbial interaction data more findable, accessible, interoperable, and reusable (FAIR). They outline specific use cases for interaction data that span the diverse space of microbiome research, and discuss the untapped potential for new insights that can be fulfilled through broader integration of microbial interaction data. These include, among others, the design of intercompatible synthetic communities for environmental, industrial, or medical applications, and the inference of novel interactions from disparate studies. Lastly, they envision potential trajectories for the deployment of FAIR microbial interaction data based on existing resources, reporting standards, and current momentum within the community. Read more _________________________ Services and Infrastructure The BacDive database of the Leibniz Institute DSMZ has been selected as a Global Core Biodata Resource The Bacterial Diversity Metadatabase (BacDive) of the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH has been selected as a Global Core Biodata Resource by the renowned Global Biodata Coalition. This makes BacDive one of the most important global databases for bacterial research. BacDive is the world’s largest database for standardised bacterial phenotypic data, developed by one of our partners. It aims to mobilise and standardise research data to improve the accessibility and comparability of phenotypic data in microbial research. Read more [cid:7991d46f-b833-4752-b89d-ac3f61cd42b2] _________________________ Media In a recent episode of the Open Science Radio Podcast the director of the NFDI, York Sure-Vetter, gives an overview of the NFDI including the potential and challenges as well as its history and international context. Listen to it. _________________________ Social links and Contact Follow us on Twitter and GitHub! Questions or suggestions? Learn more about NFDI4Microbiota! Subscription / Unsubscription Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Wissenschaftlicher Geschäftsführer: Prof. Dr. Dr. h.c. Dirk Heinz - Administrativer Geschäftsführer: Christian Scherf Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

3 years, 1 month

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NFDI4Microbiota - Happy new year + training and event announcements

by Goetz, Barbara

Dear NFDI4Microbiota community, Happy new year to all of you! We are looking ahead to the year 2023 under the motto "Community Engagement". Today we would like to point out some event and training highlights : · Love Data Week 2023<https://forschungsdaten.info/fdm-im-deutschsprachigen-raum/love-data-week/> 2023-02-16, 15:00-17:00, in person (University of Bremen) with zoom option During this international action week, we participate in the panel discussion 'Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences'<https://nfdi4microbiota.de/news/2023-01-13-lovedataweek2023> with NFDI4Biodiversity, NFDI4Health and DataPlant at University of Bremen. · NFDI4Microbiota world café on Electronic Lab Notebooks (ELNs) 2023-02-24, 10:00 - 12:00, online To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we are organizing a world café on 2023-02-24 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Workflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here<https://us02web.zoom.us/meeting/register/tZAqceyppjwpHdRHg7uF7AqPb6Yxq4Phq3…>. · Workshop: Mapping the crosstalk of heterologous ECF sigma factors to the host genome 2023-02-20 - 24 08:00 - 16:00, in person and online 2023-03-06 - 10 08:00 - 16:00, in person and online Five places available for attendance + online participation, more details<https://nfdi4microbiota.de/training/training>. Our third newsletter will be shared with you in the end of January with news from our consortium. Kind regards Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 1 month

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NFDI4Microbiota - Merry Christmas + Outlook 2023

by Goetz, Barbara

Dear NFDI4Microbiota community, We thank you for your helpful contributions in 2022! We are looking back on a very successful year and are pleased to announce that there will be a special focus on 'community engagement' in 2023. In the beginning of 2023 we will announce a few events and planned activities for 2023, as well as our next newsletter. In addition, you will have plenty possibilities to meet us in person at conferences in 2023 and actively participate in events together with other NFDI consortia. We wish you and your families a Merry Christmas, happy holidays and a Happy New Year and look forward to work with you in 2023. [cid:image003.jpg@01D9160E.61469870] On behalf of the Board of Directors and Administration Unit Kind regards Barbara Götz --- Barbara Götz, M.Sc. Microbiology Project manager NFDI4Microbiota goetz(a)zbmed.de<mailto:goetz@zbmed.de> www.nfdi4microbiota.de<http://www.nfdi4microbiota.de/> Twitter: @nfdi4microbiota<https://twitter.com/NFDI4Microbiota> Reachable: Mon.-Thu. 7:30 AM - 4 PM; Fri. 7:30 AM - 2 PM ZB MED - Informationszentrum Lebenswissenschaften Gleueler Straße 60 50931 Köln www.zbmed.de<http://www.zbmed.de/> INFORMATION. WISSEN. LEBEN.

3 years, 2 months

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