Nfdi4microbiota-announce
January 2025
nfdi4microbiota-announce@lists.nfdi.de
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NFDI4Microbiota Newsletter 1/2025
by Mueller, Mattea
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-coffe...>
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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
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