2:06 p.m.
Newsletter Quarter 1 2025
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Dear Readers,
With our tenth NFDI4Microbiota newsletter, we would like to share news about conferences,
training courses, services and cooperations.
If you can think of other topics that we should cover, please let us know. We are happy to
hear from you!<https://nfdi4microbiota.de/contact-form/>
And now: Enjoy reading the newsletter!
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We wish you all a great and healthy start into 2025.
Community Engagement
Events and Conferences
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Great experiences at our 3rd Annual Conference
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The NFDI4Microbiota conference was a fantastic opportunity for the NFDI4Microbiota
community to meet in person. We presented current development of our services and future
plans during the public conference. .It was great to have several representatives from
other NFDI consortia and Base4NFDI attend the event, as it provided the chance to exchange
updates, discuss upcoming events, and align on shared goals. The keynote and panel talks
inspired discussion of the policy, infrastructure, training and support needs of our
various user communities.
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The Hands-on Workshops covered a variety of topics and were set in different styles,
according to the topics. The Use Case workshop for example was a discussion-style
workshop, were the Use Cases VirJenDB and MetaProt were presented and discussed with the
participants.
The workshop on Research Data Management on the other hand used a LEGO activity that
highlighted the importance of metadata in experimental reproducibility. The game was based
on a similar exercise by University of Glasgow.
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The workshop participants were divided into small groups of 2-3 people, each tasked with
building a vehicle using at least 10 LEGO pieces within a limited timeframe of 15 minutes.
Once the vehicles were built, each group documented their construction process by creating
Standard Operating Procedures (SOPs).
This documentation was crucial, as it provided detailed instructions on how to reconstruct
their creations accurately. The emphasis on thorough SOPs mirrored the nature of
scientific documentation, reinforcing its significance in ensuring reproducibility.
After the initial LEGO creation and documentation of SOPs, groups switched tables with
another team. They then had 15 minutes to rebuild the vehicles based solely on the
provided instructions. This phase was not only a test of clarity and precision in
documentation but also an opportunity for participants to appreciate how well-structured
metadata can aid in replicating complex experiments.
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The LEGO activity served as a playful yet impactful reminder of the vital role that
metadata plays in research. Just as accurate instructions can lead to successful LEGO
constructions, comprehensive data management is essential for fostering reproducibility
and reliability in scientific endeavors. Participants left with a renewed understanding of
collaboration and communication's importance in both science and play.
Successful first NFDI BioMed Workshop
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Several NFDI consortia supporting the work with biomedical and health data came together
for a cross-consortium workshop on biomedical research data management (RDM). The event,
jointly organized by NFDI4Bioimage, NFDI4Health, NFDI4Immuno, NFDI4Microbiota, and GHGA,
successfully brought together experts from different NFDI consortia to share knowledge,
discuss challenges, and identify opportunities for collaboration.
The workshop provided a unique opportunity for exchange within the NFDI. Participants
discussed potential joint use cases , explored areas of synergy for collaborative efforts,
and developed pathways for further collaboration in biomedical RDM.
This event was an important step in fostering collaboration and advancing research data
management to generate solutions for the Germany biomedical research community.
Community Engagement
Upcoming Events and Conferences
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Next Community Workshop coming soon!
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The upcoming Community Workshop will be held online in spring. We want to get YOUR
feedback - straight out of the community. We will discuss how we further can support your
microbiological research by providing data management infrastructure. The exact date will
be announced soon in the Event section of our
website<https://nfdi4microbiota.de/newsroom/events.html>. Stay tuned!
Use Case Conference in May 2025
Join the experts and learn more about the NFDI4Microbiota Use Cases at the Use Case
Conference on May 19. More information coming soon in the Event section of our
website<https://nfdi4microbiota.de/newsroom/events.html>.
See you in person!
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We will attend different events over the next year - find some of them below - and are
looking forward to meet you there:
* GfV 2025, March 4-7<https://virology-meeting.de/>
* VAAM 2025, March 23-26<https://vaam-kongress.de/>
* EVC 2025, April 27-30<https://eusv-congress.eu/>
* ViBiom 2025, May 13-15<https://evbc.uni-jena.de/events/vibiom2025/>
Announcing the next Knowledge Base Sprint
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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.
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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
bioinformatic 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.html>
Take a break and join our Coffee Talks
The Coffee Talk meetings provide an opportunity to learn more about NFDI4Microbiota's
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. We will
continue our Coffee Talks this year, too. Get your updates and more information on the
schedule and registration information
here.<https://nfdi4microbiota.de/newsroom/news/2024-04-26-nfdi4microbiota-coffee-talks-series>
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Services
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Foundational Guidelines published
To support our community we published NFDI4Microbiota Foundational
Guidelines<https://zenodo.org/records/13628175> on Zenodo. The Guidelines shall act
as basis for specific policies of all NFDI4Microbiota projects and services and are
supposed to help researchers to offer data handling and storage, bioinformatic tools and
services as well as training within the scope of a centralized infrastructure to a broad
scientific audience.
Training Announcements
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We updated the Training section on our website! Now you get a more comfortable view on the
interesting trainings, courses and workshops to come. Check it
out!<https://nfdi4microbiota.de/services/trainings.html> More courses will be
announced soon, e.g. the "Joint NFDI4Microbiota, de.NBI & DZIF Nextflow
Metagenomic Training Course 2025", which will take place in person in Brunswick in
April, so make sure to check the section regularly.
Previous Training
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Intense 3-day-workshop on 16S Amplicon microbiome experiments
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Evaluating the mountain of 16S rRNA amplicon sequencing data after a successful microbiome
experiment can be daunting, especially if you do not know where to start. That is why, as
part of an on-going collaboration, de.NBI and NFDI4Microbiota hosted a course on
Microbiome Analyses at Justus Liebig University in Gießen at the beginning of October. The
aim was to encourage fellow scientists to feel confident enough in their skills to
kickstart the analyses of their own data.
Over the span of three days, the 17 participants, from PhD student to PI, were first
introduced to the basic steps for running amplicon experiment analyses, including the
pitfalls and best practices connected to high-throughput computations. The main part of
the course was spent with hands-on sessions, assessing the quality of reads, using the
tools Qiita and QIIME2 to preprocess the data, and subsequently analysing it.
Cooperations
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Presentation at BY-COVID consortium meeting
The final BY-COVID consortium meeting took place in Brussels on September 10 and 11.
Noriko Cassman and Kilian Ossetek from VirJenDB attended and Kilian presented his project,
which was funded by the open call that VirJenDB was awarded. His project is a submission
web tool for the upload of virus sequences to ENA via the VirJenDB as a data broker. The
pilot tool is available here<hxxps://www[.]virjendb[.]org/submission>.
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Recent Publications
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Memorandum of Understanding on Biodata Interest Group published
We intensify the collaboration with the consortia DataPLANT and NFDI4Biodiversity as the
Biodata Interest Group. Therefore, our consortia signed a Memorandum of Understanding
(MoU) which is now published here<https://zenodo.org/records/13880944>;. Our three
NFDI-consortia will pool expertise, energies and technologies in order to provide the
scientific community with even better support in managing and processing their biological
data. The focus of the MoU is on the cross-consortium harmonization of research data
management strategies.
Lesson plan on data organization
Data Steward Justine Vandendorpe and Sophie Boße from ZB MED created a lessons plan and
slides on data organization<https://zenodo.org/records/14234219> for an interactive
workshop on the same topic. The lessons plan covers topics such as the motivation behind
good data organization, file naming, versioning, folder structure and tidy data.
Video publications on TIB AV-Portal
In addition to the written publications we provide on our website, we proudly present our
very own NFDI4Microbiota channel on the TIB
AV-Portal.<https://av.tib.eu/publisher/NFDI4Microbiota> There you can find
recordings of talks given within the consortium, for example on topics like ELNs,
workflows, our Use Cases and, of course, an introduction to NFDI4Microbiota. Some selected
video publications you can also find directly in the new media center on our
website.<https://nfdi4microbiota.de/newsroom/mediacenter.html>
Social Links and Contact
________________________________
This newsletter is brought to you by NFDI4Microbiota
Mail: contact@nfdi4microbiota.de<mailto:contact@nfdi4microbiota.de>
Web: www.nfdi4microbiota.de<https://www.nfdi4microbiota.de/>
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________________________________
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