2:38 p.m.
[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/icon_n...
Quarter 2 2024
Dear Reader,
with our seventh 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
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NFDI4Microbiota joined the annual meeting of the Research Data Alliance
As a part of NFDI e.V., NFDI4Microbiota is a member of the Research Data Alliance (RDA)
Germany<https://www.rda-deutschland.de/>. The goals of the RDA, like to improve the
social and technical requirements for an increased data exchange and an easier reuse of
data, align with ours. Therefor we were happy to represent our fields of expertise at the
annual meeting on February 20th and 21st.
[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/rda_lo... to
the recent entry of NFDI e.V. into the RDA, the presence of NFDI consortia was
significantly increased compared to previous years. Alongside NFDI and NFDI4Microbiota,
other consortia like NFDI4Earth also showcased their work. In total, there were
approximately six posters related to NFDI, our NFDI4Microbiota Poster included.
The meeting proved to be insightful, offering a different perspective on research data
management than usual. Notably, several talks delved into the political aspects of
research data management. One such talk was delivered by Renate Nikolay, the Deputy
Director General for Communications Networks, Content, and Technology at the EU
Commission, focusing on “The Cornerstones of the European Data Strategy.”
Successful NFDI4Microbiota Knowledge Base Content and Coding Sprint
The NFDI4Microbiota Knowledge Base<https://knowledgebase.nfdi4microbiota.de/> is a
collection of information and references with relevance for the microbiology community in
terms of Research Data Management, Data Analysis, FAIR principles, standards, and much
more. Furthermore, information about the NFDI4Microbiota consortium are collected.
To raise awareness of this resource and to further improve it, we planned a comprehensive
Knowledge Base Content and Coding Sprint. After having to reschedule the event multiple
times, we finally found a time slot in February 2024 to hold the NFDI4Microbiota Knowledge
Base Content and Coding Sprint in Cologne.
Roughly 20 participants, mostly, but not exclusively, from NFDI4Microbiota, came together
in a 2-day concentrated effort to push the NFDI4Microbiota Knowledge Base forward. Some
joined us online, while others met at ZB MED in Cologne. A lot of content was added by
individuals and groups focusing on specific topics. Perhaps more importantly, getting so
many interested people together has allowed us to have in-depth discussions about issues
and strategies related to the Knowledge Base that might not have happened otherwise.
[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/knowle...]
We consider the NFDI4Microbiota Knowledge Base Content and Coding Sprint an overall
success. This is not just limited to the two days dedicated to the Sprint. Having people
interested in the Knowledge Base and learning about it in preparation for the Sprint
already had an impact. Leading up to the Sprint, and especially in the weeks following the
Sprint, the Knowledge Base Git repository showed a much higher level of activity than
usual.
Given the reception and success of the sprint, we are aiming to have this as a regular
recurring event. Specifically, we, and you, can look forward to the next instance of the
NFDI4Microbiota Knowledge Base Content and Coding Sprint, planned to be hosted in Marburg
on September 11th - 13th, 2024.
Community Engagement - Upcoming Events and Conferences
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[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/DGHM_V...]
Meet us in Würzburg on June 2-5, 2024
NFDI4Microbiota is attending the VAAM&DGHM Microbiology & Infection
Conference<https://dghm-vaam.de/> in Würzburg. The conference takes place on June
2-5, 2024.
We look forward to meet you in person, so feel free to step by, if you are attending and
learn more about us.
[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/n4m_am...
ambassador meetings
On January 29th we restarted the NFDI4Microbiota Ambassador program. During the first
meeting, we provided an overview of NFDI4Microbiota in general and discussed the
ambassador program. On March 25th, Sarah Schulz from EMBL delivered a talk on “Standards
and Policies” related to NFDI4Microbiota.
In July (29th) we will delve into ARUNA Object storage<https://aruna-storage.org/>;)
with detailed insights shared by Frank Förstner. November (25th) Kassian Korbert (BiBI)
will tell us about the NFDI4Microbiota Knowledge
Base<https://knowledgebase.nfdi4microbiota.de/>. The topic for September is still to
be determined.
Are you a postdoc or a PhD student in the field of microbiology, or are you interested in
data management? Or perhaps you know someone who might be interested? We warmly welcome
new participants and invite you to join our bimonthly meetings, which are held on the last
Monday of each month at 3:30 PM. Learn more about the program and register
here.<https://nfdi4microbiota.de/community/ambassador.html>
Services
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Involving our community through new Use Cases
Three new Use Cases have been accepted recently and will expand NFDI4Microbiota’s pool of
services to create targeted solutions for you and us. Our Use Cases are your explicit
invitation to get involved as they offer possibilities to engage with the research
community, so take a look at the new Use Cases to see what the future holds:
1. MicroBioKG will be explore and serve as a blueprint for how knowledge graphs can
make microbiological data FAIR, open and sustainably accessible, and how this enables
connectivity between resources. This Use Case will follow three real projects with real
data. Follow them and you will soon be able to apply the guidelines developed by Vanessa
Scharf and Konrad Förstner to your own data.
2. LichenMetaImage will explore the best of many worlds – namely lichen (fungus and
bacterial photosymbiont) and its unique interaction with its microbiome – using a
multi-omics (imaging, metagenomics, transcriptomics) approach. This Use Case will also
bridge existing imaging metadata collection efforts developed by
DataPLANT<https://www.nfdi4plants.de/> and
NFDI4BIOIMAGE<https://nfdi4bioimage.de/home/>. We are excited to see what Björn
Usadel and Stefanie Weidtkamp-Peters’ big picture will look like.
3. VirJenDB is now also a Use Case as future plans to expand the platform include
adding automated and community curated analysis workflows, data, metadata and more (see
above). By interacting with this Use Case, e.g. as an interested virologist with data
published in ENA, you could be trained in RDM topics and contribute to community curation
of the platform and datasets. These and many more interaction opportunities will be
offered soon. The faces behind this Use Case are Noriko Cassmann, Manja Marz and Shahram
Saghaei.
Collecting publicly available virus resources, metadata and sequences: VirJenDB
[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/virjen...
are pleased to announce the beta release of the VirJenDB version 0.1 which is available
here.<https://virjendb.uni-jena.de/> VirJenDB is a comprehensive virus database
based in Jena providing user-friendly access to community-curated virus sequences,
metadata, visualizations and tools. If you are interested in becoming a beta user, joining
the curation community, or helping us to improve the database, please email the VirJenDB
team<mailto:virjendb@uni-jena.de>.
Training Announcements
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[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/Isomet...]
There are several interesting training offers currently open for registration, like:
· the NFDI4Microbiota and de.NBI 16S amplicon training course (Oct 8th-10th 2024)
· Microbiota profiling by 16S rRNA gene amplicon sequencing: Data analysis Workshop
And more courses are planned. For example, there will be an “Introduction to R course” in
early May, and “Basic statistic with R” at the end of May. 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.
Join us for our next Electronic Lab Notebook (ELN) event on June 17, 2024
Our successful ELN events are going into the next round! Join the online seminar on June
17, 2024 from 13:00 - 16:00 CET. The seminar will provide you with an overview of
NFDI4Microbiota and ELNs in general, followed by in-depth presentations and discussions on
eLabFTW from different perspectives (experienced and new users, developers).
Save the date if you are interested! Registration will start soon and will be announced
here.<https://nfdi4microbiota.de/services/training.html>
Previous Training
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Joint NFDI & de.NBI Metagenomic Training Course 2023
In early February, de.NBI and NFDI4Microbiota collaborated to host a comprehensive
training course on metagenomic data at the University Bielefeld. With that the Task Area 1
of
NFDI4Microbiota<https://nfdi4microbiota.de/aboutus/work-programme/ta1-community-network-training>
completed one of its milestones.
[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/metage...]
The participants, representing over 10 different research institutes from across Germany,
were primarily at early to mid-career stages. Spanning three days, the course provided an
extensive overview of tools and bioinformatics techniques essential for analyzing
next-generation sequence (NGS) data from microbial communities, with ample hands-on
training opportunities. The first two days focused on preprocessing, quality assessment,
error management, and various genome-related tasks such as assembly, binning, and
taxonomic and functional analysis. On the final day, participants learned from experts of
the Helmholtz Centre of Infection Research (HZI) how to incoporate metagenomics worklflow
in nf-core workflows using Nextflow for automated and reproducible analysis.
[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/metage...]
In summary, the workshop proved to be both intense and engaging with lots of opportunity
to ask questions and network with peers. Special thanks to all the organizers for their
efforts in making this event a success!
Cooperations
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[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/Isomet...
joined JourFixe of the FDM initiatives
Most of the German federal states have set up initiatives for research data management
(RDM), which network with each other in a regular JourFixe, the Forum of Digital Methods
(FDM) initiatives. The aim of these initiatives is to establish recommendations and
solutions for RDM processes in the respective federal states and to incorporate these into
an overall national strategy as part of the joint JourFixe. To support those initiatives
with their profound knowledge and expertise, the NFDI consortia joined the JourFixe on
February 21, 2024.
The NFDI consortia were specifically invited to increase their presence and contribute to
the discussions. The main topic of the meeting was “International Outreach and Exchange.”
There were 25 attendees, with the majority not from NFDI4-related initiatives. Represented
at the meeting were NFDI e.V, NFDI4Objects, NFDI4Ing, Base4NFDI, NFDI4Ing, and
NFDI4Microbiota.
The JourFixe provided an opportunity for the exchange of ideas and to plan cooperation on
several projects. One of these projects is to write a paper or an abstract about the
structures and diversity of Research Data Management (RDM) initiatives and actors in
Germany and explain the complexity of the field.
2024 Flex Funds projects
The NFDI4Microbiota consortium aims to realize the dynamic adaptation of services and
support of further data types, development of new training programs, etc. Therefore,
within the NFDI4Microbiota project work, flexible funding (so called ‘Flex Funds’) for
small projects within the research community are available for the years 2023 to 2026. To
implement a dynamic system that stays on track with new trends in the field, the Flex
Funds will support small projects and active Use Cases from the community as they arise
over time. The 2024 Flex Funds call resulted in the approval of four new Flex Funds
projects funded with an overall budget of approx. 300,000 €.
Short abstracts of them will be published on the web portal in the near future. The
project titles are listed below.
* Piloting the integration of national sequencing centers with NFDI4Microbiota through
metadata capture and data submission workflows
* Prediction of novel gut biotransformation pathways
* Establishment of guidelines for metaproteomics research data management and quality
control
* Empowering All Microbiome Scientists: Building Bioinformatic Proficiency for
Advancing Microbiome Science Worldwide
The projects are funded on an annual basis. The 2025 Flex Funds call will be most likely
opened in the mid of June 2024 and can be found on the web
portal<https://nfdi4microbiota.de/newsroom/flexfunds.html>.
Recent Publications
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Best practices on how to share microbiome data
Microbiome data, metadata and analytical workflows have become ‘big’ in terms of volume
and complexity. Although the infrastructure and technologies to share data have been
established, the interdisciplinary and multi-omic nature of the field can make resources
difficult to identify and use.
Do you want to learn more about sharing of microbiome data and the way it is analyzed? If
this is the case, you should check the article “Challenges and opportunities in sharing
microbiome data and analyses”<https://www.nature.com/articles/s41564-023-01484-x>;,
published 2023 in Nature Microbiology. NFDI4Microbiota co-speaker Alice McHardy, together
with Curtis Huttenhower and Robert D. Finn, outlines in this article best practices,
challenges and opportunities in sharing microbiome data. They are also calling out
successful examples to date and suggest steps for future improvements.
NFDI4Microbiota – national research data infrastructure for microbiota research
Microbes – bacteria, archaea, unicellular eukaryotes, and viruses – play an important role
in human and environmental health. Growing awareness of this fact has led to a huge
increase in microbiological research and applications in a variety of fields. However,
Germany currently has no infrastructure to connect such projects or even compare their
results. Thus, the potential synergy of data and expertise is being squandered.
The goal of the NFDI4Microbiota consortium is to serve and connect this broad and
heterogeneous research community by elevating the availability and quality of research
results through dedicated training, and by facilitating the generation, management,
interpretation, sharing, and reuse of microbial data.
Learn more about NFDI4Microbiota and its way to achieve its goal in the article
“NFDI4Microbiota – national research data infrastructure for microbiota
research”<https://doi.org/10.3897/rio.9.e110501> by Konrad U. Förstner et.al.,
published 2023 in Research Ideas and Outcomes.
Social Links and Contact
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[https://nfdi4microbiota.de/assets/img/newsletter/seventhnewsletter/Bluesk...
is now part of the BlueSky network
To replace our now deprecated X-account, NFDI4Microbiota started a Bluesky account.
Follow us on BlueSky<https://bsky.app/profile/nfdi4microbiota.bsky.social>. We are
looking forward to get in touch with you there.
________________________________
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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