Newsletter Quarter 3 2024
Dear Reader,
With our eighth NFDI4Microbiota newsletter, we would like to share news about conferences, training courses, cooperations and publications. If
you can think of other topics that we should cover, please let us know. We are happy to hear from you!
And now: Enjoy reading the newsletter!
Community Engagement
Events and Conferences
NFDI4Microbiota joined the VAAM&DGHM conference in Würzburg from June 2nd to 5th
To engage and connect with the NFDI4Microbiota research community, members of our consortium attended the 7th joint Microbiology & Infection Conference of
the German Society for Hygiene and Microbiology (DGHM) and the Association of General and Applied Microbiology (VAAM) in Würzburg. Our outreach team members Mattea Müller and Barbara Götz provided an informative booth at the conference on all four days.
Many researchers with diverse scientific backgrounds were interested in the services provided by our consortium. Our outreach team provided answers to all the questions the community addressed them with and
raffled divers merchandise articles among all booth visitors.
In addition, we held the NFDI4Microbiota symposium presenting our services to making microbiology research data Open and FAIR on June 5th. NFDI4Microbiota
speaker Konrad Förstner (ZB MED) introduced participants to the mission and vision of our consortium. Afterwards, a best-practice workflow development recommendation and a selection of our most interesting services was presented:
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Developing and Maintaining Best-Practice Workflows and Services for Processing Microbiological Research Data by Hesham Almessady (HZI),
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UseCase MetaProt: Standardization and Metadata in microbial community proteomics (Kay Schallert, ISAS),
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StrainInfo: A central database for resolving microbial strain identifiers (Lorenz Reimer, DSMZ) and
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VirJenDB: Toward a community-curated and open-source virus meta(data) analysis platform (Noriko Cassman, University Jena).
You can find the complete presentation online.
It was a great conference with inspiring encounters and exciting talks. We are already looking forward to interact with you at other upcoming conferences. For example “Gesundheit Gemeinsam”,
the joint conference of five different medical societies including the GDMS (German association for medical informatics, biometry and epidemiology) and the DGEpi (German society for epidemiology), which is one of our supporting societies. We will share a booth
there with NFDI4Health. And of course at our annual NFDI4Microbiota conference, which will take place in December - see the text further down.
HeFDI Data Week presentation of NFDI4Microbiota
The Hessian Federal state initiative organizes each year the HeFDI Data Week, which is aimed at researchers, educators, students and anyone interested
in learning more about topics like FAIR data.
On June 5th, Thomas Clavel and Shahram Saghaei presented our consortia speaking about: NFDI4Microbiota – Infrastructure, Microbiology, Databases
and Interaction. The presentation started with Thomas Clavel introducing NFDI4Microbiota and detailing interaction possibilities. After that, he exemplified the Use Cases, which are research projects from the community that profit from the services of NFDI4Microibota.
Sharam Saghaei who described VirJenDB - a database that aims to be the central hub to connect virus researchers with publicly available virus resources, metadata and sequences, concluded the presentation. VirJenDB
is now also an active Use Case of NFDI4Microbiota.
NFDI GEo-Chem-Life-Sciences-Helpdesks meeting in Bremen
On May 27th and 28th 2024, representatives of NFDI4Microbiota, NFDI4Health, NFDI4Biodiversity, NFDI4Chem, NFDI4Earth, NFDI4BioImage, DataPlant
und FAIRagro came together in Bremen to discuss Helpdesks and support structures. This was a great opportunity for us to meet and connect, share experiences and discuss future collaborations with consortia of closely related disciplines. Together we compiled
a competence matrix and workflows for liaising on interdisciplinary questions and for the efficient transfer of tickets between consortia to ensure that inquiries can be forwarded to the most qualified Helpdesk.
Our NFDI4Microbiota Helpdesk answers all kinds of questions and issues regarding data management and data analysis as well as queries about the
NFDI4Microbiota consortium, services, outreach, community activities, and more.
You can contact the Helpdesk by filling out the contact form or sending
us an email.
Community Engagement
Upcoming Events and Conferences
Save the date: NFDI4Microbiota annual conference December 3rd-4th, 2024
Please mark your calendar: we will have this year’s annual conference in Leipzig, Germany on December 3rd to 4th. There will be a panel discussion, interesting keynotes, helpful workshops and more you can look forward to. More
information and registration opportunity coming soon on our events page.
Take part in the next NFDI4Microbiota Knowledge base sprint
Are you a microbiology researcher, research data management enthusiast or developer? We need your help! Join
the next NFDI4Microbiota Knowledge Base Content & Coding Sprint on September 11th.
The Knowledge base offers extensive information about research data management, software development and much more. And you can help us to make this even better! Contribute to the content or improve the code. If
you are interested, get more information and registration here.
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 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 take place on July 29th, starting at 14:30 CEST. Frank
Förster of the JLU Gießen will tell us about ARUNA object storage. Did you ever wished to share your data in a domain-agnostic, fast and secure way that additionally ensures sharing accordingly to the FAIR principles? Or are you related to data management
and would like to learn about ways to share data? Be sure not to miss this talk. Get more information about the program here.
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.
The next Coffee Talk will take place on August 26th. Get
more information on the topics and the schedule here.
Services
2025 Flex Funds call just opened!
We are glad to inform you, that the 2025 Flex Funds call is open from June 10th to August 7th 2024.
What is funded?
The NFDI4Microbiota Flex Funds provide funding to perform a short one-year project from the community. The project needs to correspond to the mission of NFDI4Microbiota.
A list of matching topics is provided below.
What is the aim of the 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 (12 months) within the research community are available for the years 2023 to 2026. To achieve a dynamic system that stays on track with new trends in the field, the Flex Funds support small projects from
the community and active Use Cases.
What are eligible topics? Eligible topics are as follows:
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Data Brokerage
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Workflow development
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Data storage and workflow execution
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Infrastructure/Services
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Training
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Community engagement and outreach
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Establishment of local data stewards
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Use Case connection or an active Use Case
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Deposition of high quality data sets in public repositories
Details on the eligible topics, further information on the call and the procedure can be found on the NFDI4Microbiota
web portal.
In case you have questions, please do not hesitate to contact us via contact@nfdi4microbiota.de.
Training Announcements
There are several interesting training offers currently open for registration, like:
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Summer-School: Trends in multiomics data analysis for Microbial Ecology and Biotechnology (July 8th-26th)
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Optimizing Microbial Research Data Utilization: Integrating Electronic Lab Notebooks into your data management strategy (Aug 27th-29th)
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Computational Pangenomics Workshop @ GCB (Sep 30th)
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The NFDI4Microbiota and de.NBI 16S amplicon training course (Oct 8th-10th)
And more courses are planned. In September you can learn about “Linux Basics for Bioinformatics” and in November about “Metagenomics”.
As soon as the registration opens, you will find it on the NFDI4Microbiota website. More courses will be announced
soon, so check the website regularly for training opportunities.
Previous Training
Biometadata Workshop: How to Describe Biological Data? A Primer to a FAIR Approach for Now and the Future
Did you miss the recent Biometadata workshop in Tübingen? If so, you skipped on an incredible opportunity to dive deep into the world of biological
metadata with leading experts in the field. But don’t worry—there’s always next time!
Understanding and implementing FAIR standards is crucial in modern research. Metadata provides the context necessary for data to be understood
and reused, ensuring reproducibility, and facilitating further research. However, the process of thoroughly describing data with appropriate metadata can be complex and daunting. This workshop aimed to demystify the process, clearing the fog, and revealing
the path forward.
Designed for beginners, the workshop was perfect for those new to data submission and the collection of biological metadata in microbiome research.
It focused on using terms based on existing ontologies and controlled vocabularies, crucial for enabling future machine-actionable analyses.
Participants engaged with an online pad for interactive exercises and a team of helpers to support them when puzzled. All adhered to the Carpentries’
code of conduct to create a safe and inclusive environment. This approach ensured that everyone felt comfortable participating and asking questions.
Given the wealth of material covered in a single day, we actively monitored participants’ expectations and learning goals. Here are some of the
goals they shared:
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Uploading metadata for metagenomics data: Participants wanted to learn how to upload data and metadata to the required online repositories and understand what these repositories are.
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Organizing biological data: Many attendees sought to bring order to the chaos of their biological data.
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Identifying necessary metadata: There was a strong desire to learn what metadata needs to be collected and recorded for scientific data.
To address these goals, the workshop included a beginner’s guide to metadata and ontologies, reviewed data repositories and metadata fields, standards,
and minimal requirements. We also explored data description examples, ontologies for biological data, and introduced the DataHarmonizer tool to aid in metadata collection and validation.
Interactive exercises were a core part of the workshop. Participants worked in groups to explain their own datasets and annotate them with ontology
terms, turning what might have been a dry topic into a dynamic and engaging experience.
This free workshop was led by two Carpentries certified NFDI4Microbiota instructors from the Functional Microbiome Research Group at the Institute of Medical Microbiology, University Hospital of RWTH in Aachen.
Cooperations
BY-COVID project is about to start
A NFDI4Microbiota team consisting of Noriko Cassman and Manja Marz from FSU Jena and Konrad Foerstner from ZB MED, has secured a grant by the
BeYond-COVID (BY-COVID) consortium through a successful proposal to the open call “Support for the implementation of SARS-CoV-2 data hubs at national and regional
levels”. The proposal is titled “Validation and submission tool to facilitate virus data flow into ENA via secure intermediate storage”.
Now, that the agreement has finally been signed, the project will extend VirJenDB, the comprehensive virus database based at FSU Jena which is currently being developed as an NFDI4Microbiota
service and Use Case to connect researchers and virus research data and resources. The work in the proposed project has three planned parts: 1) virus pathogen metadata curation and integration, 2) validation
parameter evaluation and 3) submission tool development. These will be carried out to achieve the shared goals of VirJenDB and BY-COVID projects, which are to help mobilize (German) virus sequence data to the ENA. The awarded amount is 60,000 euros over 6
months in 2024. We look forward to the results of this project!
If you would like to have more information, check the following links:
Recent Publications
Ten simple rules for implementing electronic lab notebooks (ELNs)
NFDI4Microbiota Data Steward Justine Vandendorpe just published an excellent overview of ELNs. The paper “Ten
simple rules for implementing electronic lab notebooks (ELNs)”, published in PLOS Computational Biology, provides invaluable insight and practical steps for selecting and implementing ELNs.
An ELN is a software tool for documenting laboratory experiments, research data, and processes. ELNs are poised to replace paper lab notebooks
as part of the ongoing digital transformation and offer many advantages over physical lab notebooks.
Dive into Justine’s article to learn more about the ten rules to help you on your journey to implementing ELNs. Key highlights include an in-depth discussion of the benefits of open-source ELNs, an emphasis on
the importance of standardization, and a handy questionnaire to test the usability of ELNs in the supporting information.
A practical approach to using the genomic standard’s consortium MIxS reporting standard for comparative genomics and metagenomics
A group of scientists around NFDI4Microbiota co-speaker Alice McHardy published a protocol belonging to the book ”Comperative Genomics, Methods
and protocols”, published by Humana, New York. The name of the protocol is: “A practical approach to using the genomic standard’s consortium MIxS reporting standard for comparative
genomics and metagenomics”. The book belongs to the book series “Methods in Molecular Biology”.
The protocol provides a description of the structure and terminology of the GSC’s MIxS reporting standard, how to navigate ontologies for required terms in MIxS, and demonstrates practical usage through a soil
metagenome example. The Genomic Standards Consortium (GSC) collaborates with the research community to develop and maintain the Minimum Information about any (x) Sequence (MIxS) reporting standard for genomic data to enable comparative analysis of (meta)genomes
necessitates aggregation, integration, and synthesis of well-annotated data using standards.
New video publications available
In addition to the written publications we provide on our website, we proudly present our very own NFDI4Microbiota
channel on the TIB AV-Portal. 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.
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