[27th October] NFDI4Microbiota Coffee Talk: Meta-omics Analysis at a Bioinformatics Core Facility â As FAIR as Possible
by Magel, Maja
Dear microbiome research enthusiasts and bioinformatics aficionados,
curious about smoother microbiome research? Grab your coffee and join us online!
Reproducible, easily shareable workflows are essential for bioinformatics. This holds true for all areas of bioinformatics research, including microbiome research. To facilitate the centralized collection of high-quality Nextflow workflows, nf-core was established with strong involvement from the Quantitative Biology Center (QBiC) core facility. These workflows are used, extended, and improved by a large community in a standardized manner, making a wide range of bioinformatics analyses more accessible and easier to execute than ever before. This presentation will introduce QBiC, discuss some challenges faced, and present examples of solutions, with a focus on data analysis.
đ˘ NFDI4Microbiota Coffee Talk: Meta-omics Analysis at a Bioinformatics Core Facility â As FAIR as Possible
presented by Daniel Straub (QBiC TĂźbingen)
đ
Date: Monday, 27th October2025
đ Time: 14:30-15:30 CET (Berlin time)
https://rwth.zoom-x.de/j/69637480434?pwd=aq6VlWq8JB8w3W4OJ3P3pI7aQcRahP.1
đ Zoom Meeting ID: 696 3748 0434
đ Passcode: 760425
>>> Feel free to share this with your peers!
PS: Struggling with nextflow and nf-core? Daniel will be offering a weekly drop-in session and offer consultation on a first come - first serve basis.
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đ˘ A new mailinglist: Offering Life Science training events beyond the microbiome universe
The Life Science associated NFDIs have joined efforts in gathering and promoting relevant Life Science training events for you.
đ If mailinglists are how you stay updated, then don't forget to subscribe!
Mailing-List: training4lifescience(a)lists.nfdi.de<mailto:training4lifescience@lists.nfdi.de>
Join via mail to:
training4lifescience-join(a)lists.nfdi.de<mailto:training4lifescience-join@lists.nfdi.de>
or subscribe with your existing Postorius-Account via:
https://lists.nfdi.de/postorius/lists/training4lifescience.lists.nfdi.de/
A teaser on what you can look forward to:
1.
NFDI4Earth Academy Coffee lecture - "Machine Learning Fundamentals with Application Examples" (Sonja Hänzelmann & Susana Simancas Giraldo, AWI)
đ
October 15th, register here<https://gfz-de.zoom.us/meeting/register/Lu8vWZhtQA2MBPLS8Wxwtg#/registration>.
Content: Introduction to Machine Learning, Supervised vs. Unsupervised Learning â key concepts and use cases, Unsupervised Learning â Finding patterns in data (Clustering, Dimensionality Reduction) and Supervised Learning â Prediction models (Classification, Regression). Level: Beginner-friendly, perfect for anyone looking to better understand and apply ML methods.
1.
in German: GFBio Data Submission und Brokerage Service<https://submissions.gfbio.org/> fßr biologische, Ükologische und Biodiversitätsdaten (Dr. Ivaylo Kostadinov, Gesellschaft fßr Biologische Daten (GFBio e.V.)
đ
October 21st, 11:00 -12:00, register here<https://www.nfdi4biodiversity.org/de/events/biodiversitea-17/>.
Looking forward to Monday!
Kind regards
Maja (Magel)
on behalf of NFDI4Microbiota's Outreach team
Carmen (Paulmann), Lina (Junctorius), Mattea (MĂźller), Maja (Magel)
https://nfdi4microbiota.de/
Maja Magel
https://nfdi4microbiota.de/
Projektkoordination NFDI4Microbiota
Institut fĂźr Medizinische Mikrobiologie
Research Group Functional Microbiome
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Tel.: +49 (0) 241 80-38117
E-Mail: mmagel(a)ukaachen.de<mailto:mmagel@ukaachen.de>
Aufzug D4, Etage 5, Raum 34
Universitätsklinikum Aachen
PauwelsstraĂe 30
52074 Aachen
3Â days, 12Â hours
NFDI4Microbiota Newsletter Quarter 4 2025
by Mueller, Mattea
Newsletter Quarter 4 2025
2025-10-02
[https://nfdi4microbiota.de/img/newsletter/fifthnewsletter/img1.png]
Dear Reader,
With our 13th NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, services and publications. If you are interested in other topics we should cover, please let us know. We are happy to hear from you!<https://nfdi4microbiota.de/support/helpdesk/>
And now: Enjoy reading the newsletter!
Consortium News
Submission of the NFDI4Microbiota second funding phase proposal
The NFDI4Microbiota consortium has submitted its renewal proposal for the second funding phase, which is scheduled to begin in October 2026, to the DFG. Building on our successful first funding phase, our aim is to expand NFDI4Microbiotaâs efforts in the next phase to enhance data accessibility and reuse while enabling AI applications. Our achievements and infrastructure from the first funding period provide a solid foundation for achieving an even greater impact across the microbiology research community and fostering a seamless flow of data. We want to strengthen collaboration with existing stakeholders while actively reaching out to previously underrepresented groups, specifically researchers working on eukaryotic microbes such as fungi and protists, and we will work more closely with data-generating facilities to capture rich metadata early on. In addition, we aim to further strengthen our portfolio of services, databases, and analytical tools, ensuring that they are robust, interoperable, and tailored to evolving community needs. These enhancements will support a more comprehensive and inclusive data infrastructure for microbiological research. To help realise the One NFDI and EOSC vision of a coherent, sustainable, and collaborative research data ecosystem across all disciplines, NFDI4Microbiota will actively engage in cross-consortial initiatives, foster interoperability, and apply the unique perspectives of microbiological science to help shape the broader NFDI landscape. The consortium thanks all those who have committed to supporting the work of NFDI4Microbiota in the next funding phase as participants.
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Community engagement â calls, events and conferences
Recap on recent workshops and conferences
NFDI4Microbiota contributed to the 17th Seeon conference of the DGHM specialist group âMicrobiota-Probiotics-Hostâ<https://www.dghm.org/seeon/> with an oral presentation and a booth. The event was marked by good food, lively discussions, and a relaxed atmosphere. Some participants even enjoyed a refreshing swim in the lake. Our surprise boxes filled with NFDI4Microbiota merchandise were especially popular â they went like hotcakes!
[https://nfdi4microbiota.de/img/newsletter/2025-Q4-newsletter/Seeon.jpg]
NFDI4Microbiota at the 17th Seeon Conference: Booth and oral presentation by Mattea MĂźller from the Helmholtz Centre for Infection Research.
[Example Image]
NFDI4Microbiota at the ISHPSSB: Charlie Pauvert from the Uniklinik RWTH Aachen (second from left) as invited speaker to a round-table.
The ISHPSSB is one of the largest biology conference without biologists as it stands for the International Society for the History, Philosophy, and Social Studies of Biology. Nonetheless, like a few other scientists, Charlie Pauvert, member of the NFDI4Microbiota Consortium, attended the 2025 edition in Porto (PT) as an invited speaker to a round-table on how multifaceted sources of knowledge (i.e., epistemic pluralism) could improve microbiome research. Together with an historian, philosophers of biology and the audience, they reflected on, for instance, what is measurable in microbiome research and how and why do we try to do it; about the microbiome researchersâ impatience to get to causal claims when our field history tells us that it takes time. Whilst microbiology is being more discussed at the IHSPSSB (e.g., healthy microbiome concepts, AMR), another personal highlight was a rethinking of replication in biology, and how scientists are actually performing micro-replication more often than they think as part of trust-establishing practices. The NFDI4Microbiota was represented not only with merchandising, but with the well-received idea to support and guide scientists towards more reproducible research in this data-centric era.
On July 1st, 2025, the Biometadata Workshop at the TUM School of Life Sciences, Freising, introduced researchers to the essentials of FAIR metadata. Through short lectures, hands-on exercises, and live demos, participants learned how to describe datasets with standardized vocabularies, validate them with the DataHarmonizer tool, and select suitable repositories for submission. Feedback emphasized the value of the practical, interactive format, particularly the individualized support and deep dive into ontologies. Organized by RWTH Aachenâs Functional Microbiome Research Group in cooperation with NFDI4Microbiota, the workshop highlighted why good metadata is the key to reproducible research. The next Biometadata Workshop will take place on October 7th, 2025, at the University of Kiel. Interested in hosting a workshop at your institution? Contact the NFDI4Microbiota Helpdesk<https://nfdi4microbiota.de/support/helpdesk/>.
[https://nfdi4microbiota.de/img/newsletter/2025_Q3_newsletter/ambassador_p...]
Join the ambassador meetings
Do you know our Ambassador Program? The mission of the NFDI4Microbiota consortium is to serve as the central hub in Germany, providing essential support to the microbiology community by facilitating access to data, analysis services, data/meta-data standards, and training. To fulfill this mission, we are running the NFDI4Microbiota Ambassador Program, dedicated to connecting and training (early career) researchers within the microbiology community. As part of our commitment, we aim to assist young scientists in expanding their research networks and disseminating knowledge on data handling, metadata standards, standardized bioinformatics workflows and further related topics. Join us in our Ambassador Program for networking and spreading FAIR principles and openness in microbiome research! For our Ambassadors, we host bimonthly Ambassador meetings with interesting topics. The next meeting will be announced soon! Get your updates and more information on the program here<https://nfdi4microbiota.de/community/ambassador/>.
Take a break and join our Coffee Talks
[https://nfdi4microbiota.de/img/newsletter/ninthnewsletter/coffee_talk_800...]
The Coffee Talk meetings provide an opportunity to learn more about NFDI4Microbiotaâs services and mission from within and around the NFD4Microbiota community. These bimonthly meetings take place online and are open to all who are interested in staying informed about current developments and topics related to data in microbiology research. Get your updates and more information on the schedule and registration information here<https://nfdi4microbiota.de/newsroom/news/2025-02-04-nfdi4microbiota-coffe...>.
Services
To support the microbial community the NFDI4Microbiota consortium established different services. The provided services align with the aims and objectives and cover different topics. Find an overview here<https://nfdi4microbiota.de/services/>.
Ask your questions to our Helpdesk!
[https://nfdi4microbiota.de/img/newsletter/2025_Q2_newsletter/Support_oran...]
The NFDI4Microbiota Helpdesk is the point of contact for the microbiology research community for all questions related to microbial (omics) data and associated metadata. We welcome questions from anyone - students, researchers, data stewards and more - working with this type of data, regardless of organism (bacteria, archaea, eukaryotic microorganisms, viruses), environment (e.g. soil, plants, host-associated and water) or data type (e.g. nucleic acid sequences, functional genomics, image data). You can contact us either by filling in our contact form<https://nfdi4microbiota.de/support/helpdesk/> or by email: helpdesk(a)nfdi4microbiota.de<mailto:helpdesk@nfdi4microbiota.de>.
Training announcements
We updated the Training section on our website! Now you get a more comfortable view on the interesting training events, courses and workshops to come. Check it out<https://nfdi4microbiota.de/services/trainings/>!
[https://nfdi4microbiota.de/img/newsletter/ninthnewsletter/Isometric_Train...]
The next courses are
* Hands-on Biometadata: How to describe biological data? Primer to a FAIR approach for now and future<https://nfdi4microbiota.de/services/training_view/?docid=67dd67f7e68a14a1...> (University Kiel, Oct 07, 2025)
* Build a nextflow based custom pipeline<https://nfdi4microbiota.de/services/training_view/?docid=6894a31e110180b6...> (online, Oct 09, 2025)
* NFDI4Microbiota and de.NBI 16S amplicon training course<https://www.uni-giessen.de/de/fbz/fb08/Inst/algorithm-bioinformatik/teach...> (Justus-Liebig-University Giessen, Oct 22-24, 2025)
* Data Visualization for Biological Sciences<https://events.hifis.net/event/3045/> (online, Nov 18-20, 2025)
* Web-based Bioinformatics & Research Data Management<https://pretix.eu/synmikro/tecmeth-bioinfo/> (Philipps-Universität Marburg, Dec 08-12, 2025)
* RNA Bioinformatics<https://pretix.eu/synmikro/tecmeth-rna/> (Philipps-Universität Marburg, Feb 09-11, 2026)
* RNA-Seq Data Processing<https://pretix.eu/synmikro/tecmeth-rnaseq/> (Philipps-Universität Marburg, Mar 09-13, 2026)
If you like to stay up to date on training opportunities in research data management for the life sciences, we recommend to subscribe to this mailing list<https://lists.nfdi.de/postorius/lists/training4lifescience.lists.nfdi.de/> offered by NFDI and designed to keep professionals, students, and researchers in the biosciences regularly informed about upcoming training sessions, workshops, and continuing education opportunities.
Social Links and Contact
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This newsletter is brought to you by NFDI4Microbiota
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