5:24 p.m.
Newsletter Quarter 3 2024
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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!<https://nfdi4microbiota.de/contact-form/>
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.
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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:
* Developing and Maintaining Best-Practice Workflows and Services for Processing
Microbiological Research Data by Hesham Almessady (HZI),
* UseCase MetaProt: Standardization and Metadata in microbial community proteomics
(Kay Schallert, ISAS),
* StrainInfo: A central database for resolving microbial strain identifiers (Lorenz
Reimer, DSMZ) and
* VirJenDB: Toward a community-curated and open-source virus meta(data) analysis
platform (Noriko Cassman, University Jena).
You can find the complete presentation online.<https://zenodo.org/records/12189067>
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
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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.
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You can contact the Helpdesk by filling out the contact
form<https://nfdi4microbiota.de/contact-form/> or sending us an
email.<mailto:helpdesk@nfdi4microbiota.de>
Community Engagement
Upcoming Events and Conferences
________________________________
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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<https://nfdi4microbiota.de/newsroom/events.html>.
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.<https://pretix.eu/n4m/2KBsprint/>
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 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.<https://nfdi4microbiota.de/community/ambassador.html>
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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.<https://nfdi4microbiota.de/newsroom/news/2024-04-26-nfdi4microbiota-coffee-talks-series>
Services
________________________________
2025 Flex Funds call just opened!
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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:
* Data Brokerage
* Workflow development
* Data storage and workflow execution
* Infrastructure/Services
* Training
* Community engagement and outreach
* Establishment of local data stewards
* Use Case connection or an active Use Case
* 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.<https://nfdi4microbiota.de/newsroom/flexfunds.html>
In case you have questions, please do not hesitate to contact us via
contact@nfdi4microbiota.de.<mailto:contact@nfdi4microbiota.de>
Training Announcements
________________________________
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There are several interesting training offers currently open for registration, like:
* Summer-School: Trends in multiomics data analysis for Microbial Ecology and
Biotechnology (July 8th-26th)
* Optimizing Microbial Research Data Utilization: Integrating Electronic Lab Notebooks
into your data management strategy (Aug 27th-29th)
* Computational Pangenomics Workshop @ GCB (Sep 30th)
* 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.<https://nfdi4microbiota.de/services/training.html> 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
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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:
* 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.
* Organizing biological data: Many attendees sought to bring order to the chaos of
their biological data.
* 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".<https://by-covid.org/news/support-implementation-sars-co... 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<https://nfdi4microbiota.de/community/usecases/virjendb> 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!
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If you would like to have more information, check the following links:
* BY-COVID<https://by-covid.org/>
* ENA<https://www.ebi.ac.uk/ena/browser/home>
* FAIR Principles<https://doi.org/10.1038/sdata.2016.18>
* ELIXIR<https://elixir-europe.org/>
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)"<https://doi.org/10.1371/journal.pcbi.1012170>;, 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".<https://doi.org/10.1007/978-1-0716-3838-5_20> 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.<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/>
If you no longer wish to receive this newsletter, click here to
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________________________________
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