NFDI4Microbiota, NFDI4BIOIMAGE, and DataPLANT invite researchers to join an online session exploring the Use Case LichenMetaImage, focused on “Imaging of Natural Microbial Networks of Lichen.” The event will be held on Tuesday, November 19th, from 13:00 to 14:00 CET.

The LichenMetaImage Use Case addresses the challenges of archiving and FAIRifying (Findable, Accessible, Interoperable, and Reusable) bioimaging files, including precise metadata annotation following the REMBI (Recommended Metadata for Biological Images) guidelines. Given the unique complexity of lichens—cross-kingdom communities consisting of fungi, algae, cyanobacteria, and a newly discovered microbiome—the project aims to create a tailored metadata template to capture the specific needs of lichen imaging. Reliable workflows and standardized metadata will be developed to support reproducibility and data sharing within the scientific community.

This initiative also envisions integrating lichen imaging with long-read sequencing data from Oxford Nanopore and PacBio, providing insights into the spatial organization of specific organisms within the lichen thallus.

Presentations will be led by experts from Heinrich Heine University and the DataPLANT community, including:

• Ksenia Krooß (NFDI4BIOIMAGE)- Specialist in molecular plant biology, microscopy, and metadata annotation.
• Sabrina Zander (CRC MibiNet) - Expert in data structure and metadata management within the DataPLANT Annotated Research Context (ARC) framework.
• Vivien Rosenthal - Specialist in lichen metagenomics and imaging techniques.

Join us to discover new tools and workflows for advancing lichen research, fostering collaboration, and setting a foundation for future microbiome studies across NFDI4Microbiota and CRC MibiNet.

Event Link : Zoom Meeting Meeting ID : 694 8405 5260
Passcode : 336495

The consortia DataPLANT, NFDI4Biodiversity and NFDI4Microbiota have taken a significant step towards closer cooperation by signing a joint Memorandum of Understanding (MoU). The aim is to pool expertise, energies and technologies in order to provide even better support to the scientific community in the management and processing of biological data.

The focus of the collaboration is to harmonize research data management strategies across consortia. The target groups of the consortia in plant sciences, biodiversity and microbiology use similar methods and generate comparable data types, for which software-based services are being developed. A number of points of contact have already been identified in the past and joint activities have been initiated, which are now to be pursued and expanded. “The preliminary work of the three consortia complements each other perfectly. Through even closer, now also formalized cooperation, we can support researchers in the field of biology even better and facilitate their access to data, services and resources,” says Frank Oliver Glöckner (Alfred Wegener Institute for Polar and Marine Research and University of Bremen - MARUM), spokesperson of NFDI4Biodiversity. Frank Förstner, spokesperson for NFDI4Microbiota, adds: “We are delighted that the three consortia will be working even more closely together in the future on overarching solutions for the life sciences community. The MoU forms an important basis for synergistically bringing together significant parts of our activities.”

A major topic area here involves a cross-consortia training portfolio. “Joint training courses bundle the expertise of the three consortia and enable a broad range of courses for various target groups,” explains Dirk von Suchodoletz (University Freiburg), spokesperson for DataPLANT. The aim is to be able to offer researchers, whose work often extends beyond the boundaries of the consortium’s subject areas, needs-based and interdisciplinary support.

Another key aspect of the collaboration is strengthening the joint infrastructure, such as the de.NBI cloud, which is already used by all three consortia. The aim is to better represent the needs of the NFDI to cloud operators and to jointly drive forward the further development of modern technologies such as the multicloud and the research data commons.

Other areas of collaboration will include joint programming work for data management services and standards, joint partner facilities and staff, and coordinated outreach activities. “Our collaboration will strengthen all three consortia and promote new, joint projects for the community,” says NFDI4Microbiota spokesperson Alice McHardy (Helmholtz Centre for Infection Research).

As Timo Mühlhaus (University of Kaiserslautern-Landau), co-spokesperson of DataPLANT, also emphasizes: Although the life science consortia were established from within their disciplines, “the management of research data is always a collaborative endeavor that enables researchers to share their data across disciplines and work together.” The future focus on even closer collaboration therefore has the potential to fundamentally change how research can be conducted and disseminated. “It’s clear that teamwork is not just one aspect, but the driving force behind our most significant discoveries.”

The cooperation between DataPLANT, NFDI4Microbiota and NFDI4Biodiversity, which will be established as a Biodata Interest Group within the NFDI, is therefore open to further, specialist cooperation partners: “Our Memorandum is just the beginning. We are already in contact with other NFDI consortia that work with biological data and are interested in joining,” says Barbara Ebert (Gesellschaft für Biologische Daten e.V.), deputy spokesperson for NFDI4Biodiversity.

Do you want to take your knowledge about FAIR and Open Data to the next level? Are you interested in learning something new in interesting Hands-on Workshops? Do you want to gain insights on the work of our consortium, NFDI4Microbiota?

Yes? In this case join the NFDI4Microbiota Annual Conference!

On two days we are diving deep into the main topics of NFDI4Microbiota:

• The services we offer to support you in YOUR research cycle
• How to make YOUR research data FAIR and Open

The Conference will take place in Leipzig from December 4th to 5th.

There will be Poster Sessions on each day with additional services, such as a software marketplace and Data Steward consultation. The days are starting with interesting keynotes, followed by a comprehensive overview on the services we offer on day one and an exciting panel discussion about encouraging Cultural Change to FAIR and Open Data on day two.

The afternoons are filled with Hands-on Workshops on different related topics and said poster sessions.

Please click here for registration and the program for the two days. We will keep you updated there and on our Social Media about the announcements of the keynote speaker and Workshop topics.

We are looking forward to meet you in Leipzig!

The NFDI4Microbiota Helpdesk team is
waiting for your questions! Get
in touch!

The NFDI4Microbiota Helpdesk is the point of contact for all questions related to microbial (omics) data and associated metadata but also infrastructure, training and community involvement. We welcome questions from anyone - students, researchers, data stewards, and more - working with this type of data, regardless of organism (viruses, bacteria, archaea, eukaryotic microorganisms) or data type (e.g. nucleic acid sequences, functional genomics, image data, etc.) for the microbiology research community.

Your question will be answered by one of the NFDI4Microbiota experts, which includes data
stewards, researchers, or software developers. Our experts cover a wide range of topics and
questions like:

• NFDI4Microbiota services: Do you want to use our services but you don’t know how to? We answer your questions regarding our services such as the open data storage platform ARUNA, the microbial strain database StrainInfo, the virus database VirJenDB, or our Knowledge Base.
  
• Research Data Management (RDM): How to organize your data? How to share, publish, and archive your data? How to use the RDM platform Coscine?
  
• FAIR Data Principles: How can you make your data FAIR? How to FAIRify your database? What metadata standards and ontologies should you use?
  
• Data Management Plans (DMPs): Which template should you use? What DMP tools are available? How to set up a DMP (using the Research Data Management Organizer (RDMO))?
  
• Electronic Lab Notebooks (ELNs): How to choose an ELN? How to then implement it? How to work with eLabFTW or eLabJournal?
  
• Reproducible data analysis: How can I best use bash, Python and R for my analyses? How to use Workflow Management Systems (WMSs) and software containers? How to use best-practice bioinformatic workflows on our cloud-based workflow manager CloWM?
  
• Data discovery and reuse: How to find existing and trusted datasets for reuse? How can you license your data so that others can reuse it appropriately?
  
• Training: What are the upcoming training events offered by NFDI4Microbiota ? What training is available on demand? Where can you find materials from past training events?
  

You can contact us either by filling out our contact form or by email: helpdesk@nfdi4microbiota.de.
We look forward to hearing from you!

Are you familiar with electronic lab notebooks and how they work? Not yet?

Then we highly recommend that you read the latest paper by Data Steward Justine Vandendorpe (et.al.). Published in PLOS Computational Biology, Ten simple rules for implementing electronic lab notebooks (ELNs) provides invaluable insight and practical steps for selecting and implementing ELNs at your institution.

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.

In addition to the publication, ZB MED did a short interview with Justine about her article. Watch the video for a quick introduction to the topic.

Join our NFDI4Microbiota Symposium at the Annual VAAM & DGHM conference in Würzburg!

On Wednesday, June 5th, we will give an overview of our latest services, databases and workflows for the microbiology community. Have a look at our program!

NFDI4Microbiota Symposium: Public Infrastructure for Making Your Research Data Open and FAIR

• Welcome and Introduction by Konrad Förstner (ZB MED)

• Developing and Maintaining Best-Practice Workflows and Services for Processing Microbiological Research Data by Hesham Almessady (HZI)

• Use Case Metaprot: Standardization and Metadata in Microbial Community Proteomics by Kay Schaller (ISAS)

• StrainInfo: A Central Database for Resolving Microbial Strain Identifiers by Lorenz Reimer (DSMZ)

• VirJenDB: Toward a Community-Curated and Open-Source Virus Meta(data) Analysis Platform by Noriko Cassman (University Jena)

When and Where? On 5 June 12:45 to 14:00 CEST in Raum 13!

Visit us also at our NFDI4Microbiota Booth to learn more about new services, training and Use Cases from our NFDI4Microbiota team. See you there!

This year we have launched the NFDI4Microbiota Coffee Talk Series! These 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.

Please join us online at 2:30 PM - 3:30 PM CEST in Zoom

• Meeting-ID: 633 6649 6382
• Password: 490003.

Timeline for 2024

Remember the Use Case submission call? We have good news! 3 new topics will help us and YOU to

1. create knowledge graphs for linked microbial data – MicroBioKG by Vanessa Scharf and Konrad Förstner
2. solve collection & extraction for image metadata – LichenMetaImage by Stephanie Weidtkamp-Peters and Björn Usadel
3. use & contribute to a curated database for viral sequences – VirJenDB by Noriko Cassman and Manja Marz

Join the Use Case presentations on Tuesday, 2023-03-26 at 1:00-2:30 PM CET

Zoom-Meeting: 630 7779 8681 Passcode: 973383

Did you know that NFDI4Microbiota also helps shaping NFDI? For example, our speaker, Konrad Förstner is also part of the Scientific Senate of NFDI. In this way we are involved in the strategic orientation of the NFDI in general. The Scientific Senate is the substantive and strategic body of the NFDI. The main tasks include the consolidation of project progresses of the consortia, decision making regarding interdisciplinary standards and metadata standards and the decision on integration of new services into NFDI. The Scientific Senate is chaired by the Director of the Association, Prof. Dr York Sure-Vetter, and consists of twelve other experts.

Learn more about NFDI here

Learn more about Konrad Förstner here

Do you want to know more about Electronic Lab Notebooks for your research projects? Join our first NFDI4Microbiota Coffe Talk on 26th February from 15:30 - 16:00 with Justine Vandendorpe discussing the benefits and key features of Electronic Lab Notebooks for FAIR research.

Join the meeting on 26th February at 15:30 and log in here: Zoom Meeting-ID: 647 3481 9818 Passcode:269915 

Update: You can still join the Knowledge Base Content & Coding Sprint online!

Are you a microbiology researcher, research data management enthusiast or developer? We need your help! Join the NFDI4Microbiota Knowledge Sprint on February 15-16, 2024 online. Find out more about the program!

Join the meeting and log in here: Zoom Meeting ID 889 8299 1488 Passcode:033653 

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! By contributing to the content or improving the code.

Are you a microbiology researcher, research data management enthusiast or developer? We need your help! Join the #NFDI4Microbiota Knowledge Sprint on February 15-16, 2024 online or on site in Cologne.  

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! By contributing to the content or improving the code.

If you would like to help the community, join us and register here by January 31: Registration page

There are new NFDI4Microbiota services online! We are introducing them in our online Community workshop on February 5, 2024, 10-12:00. Join us and log in here: Meeting ID 687 5464 7684, Passcode: 363736

We will talk about the knowledge base, which provides information about research data management, software development and much more. For more info, check the Knowledge base

Learn how you can use the ARUNA storage to store your (meta-)data according to FAIR principles. For more info about ARUNA, check here: ARUNA Object Storage

And discover StrainInfo, providing microbial strain identifiers, and the new virus database VirJen.

We look forward to an exciting event. See you there!

We are happy to announce the open call for the NFDI4Microbiota Use Cases for 2024!
More details, the application guideline and all application documents can be found on the Use Case submission subpage.

The call is open from 2023-12-18 until 2023-01-31. Applications can be submitted to mmagel@ukaachen.de by the end of then.

What are Use Cases and why should you be interested in submitting yours?

In a nutshell, Use Cases will help us to test and fine-tune solutions developed within NFDI4Microbiota based on ongoing scientific projects and generate scientific results or reusable tools. Share your ideas with the consortium to identify new needs or provide new solutions to implement.
At the end, the Use Case outcomes will benefit the broad microbiology research community.

Your Use Case ideas, issues and solutions can range from - but are not limited to topics on research data management, databases, standardizing data and metadata, enhancing and supporting reusability in your field.

Be part of a FAIR solution in microbiology research!

Between the 5th 6th December, the final presentation of the cross-consotia hackathon were given by the participants. The Cross-consortia Hackathon DataXplorer was co-organized with NFDI4Eearth and NFDI4Biodiversity. The diverse challenges were related to earth system sciences, biodiversity and microbiology. One specific challenge involved the inspection of colour information in scanned raster maps. Another challenge entailed the development of a a web-based question-answering system to help researchers to find answers related to research data management. Additionally, a microbiome-related challenge aimed to develop a user-friendly and feature-rich meta-data annotation tool for metaproteomic experiments. The presentations and results during the presentations were impressive! You can find them here. The hackathon event was held mainly online, the end-presentations were hybrid, with an in-person meeting in Frankfurt. The meeting was combined with a social event: a torchlight tour in the Senckenberg museum. The next cross-consortia hackathon will be held in the beginning of 2025, this time with even more consortia.

Interested in metaproteomics and a hands-on training workshop and getting to know the faces behind NFDI4Microbiota’s Use Case MetaProt?

Join the “Applied Metaproteomics workshop Magdeburg 2023” for training on experimental design, sample preparations, LC-MS measurements, data analysis and metadata suggestions based on standards developed by MetaProteomics Initiative and NFDI4Microbiota.

Organizers

Dirk Benndorf, Patrick Hellwig, Kay Schallert, Robert Heyer, Nico Jehmlich

When and where?

18th to 22nd September
Otto von Guericke University in Magdeburg, Germany

Registration

Registration fee: 100 € (incl. coffee and snacks)
Get the agenda and registration information from
mpa@ovgu.de

Program light

For more information and full agenda, please contact mpa@ovgu.de

Monday from 09:00 - 18:00
Tuesday from 08:00 - 16:00
Wednesday from 09:00 - 17:00
Thursday from 09:00 - 17:00
Friday from 08:00 - 13:00

We are glad to announce, that the NFDI4Microbiota Flex Funds 2024 call is open now. More details, the application guideline and all application documents can be found on the Flex Funds announcements page.

The call is open from 2023-07-11 until 2023-08-20. Applications can be submitted to contact@nfdi4microbiota.de by then.

As 2023 is themed around community engagement, we will present our services to the public during the first NFDI4Microbiota online Lecture Talks on April 24 from 11:00-12:30 CEST. The talks will last 20 minutes each and will cover the following NFDI4Microbiota services for the community: the NFDI4Microbiota Knowledge Base, Use Cases, Workflows, and Training.

Date and time:

24.04.2023

11.00 - 12.30 PM CEST

Webcast via Zoom:

Meeting ID: 857 7139 3336

Passcode: 095511

What are ELNs and LIMS? Why should scientists use them and what are the benefits? Besides the introduction to the topic and the tools, this world café aims to identify the needs in the microbiology community. To identify the needs of the German microbiology research community on Electronic Lab Notebooks (ELNs), we are organizing a world café on 2023-02-24 10:00 - 12:00. After an introduction, we will discuss topics such as General Needs, Interoperability, Ergonomics and Processes & Worflows. Ultimately, we would like to help the microbiology sub-communities to select and implement an ELN in their research group. To participate, please register here.

During Love Data Week 2023 several NFDI consortia participate in events or training regarding the topic “Data: Agent of Change”. Togetehr with the NFDI consortia DataPLANT, NFDI4Health and NFDI4Biodiversity, NFDI4Microbiota holds a panel discussion ‘Wind of change - sharing is caring! How to improve research data and its benefits in the Life Sciences’ at the University of Bremen. Data-driven decisions in the life sciences have an immense impact on the well-being of humans and the environment, as well as on the development of research directions. Therefore, using best practice examples, experts from different areas of life sciences will discuss the importance of data-based decisions. Expect an in-depth discussion on the challenges and benefits of cultural change related to research data governance, Open Science and FAIR principles, and their impact on the daily life of every individual.

Panelists:

Prof. Dr. Konrad Förstner (NFDI4Microbiota), Björn Usadel (DataPLANT), Dr. Barbara Ebert (NFDI4Biodiversity), Prof. Dr. Dagmar Waltemath (NFDI4Health)

Moderation:

Dr. Kerstin Elbing (VBio)

Location:

Universität Bremen, Room NW2 C0290 (Hörsaal 1)

Date and time:

16.02.2023 15.00 - 17.00 PM CEST

Zoom option:

Meeting-ID: 812 3227 9619

Password: 092856

NFDI4Microbiota will attend the 1st BioHackathon Germany organized by de.NBI. The workshop ‘Extending the NFDI4Microbiota Knowledge Base’ will be held during the event from 12th to 16th december 2022 in Wittenberg. NFDI4Microbiota has initiated a dedicated Knowledge Base which will contain information on Research Data Management and Reproducible Data Analysis in the broad field of microbiology. The Knowledge Base is developed in an open, collaborative process on GitHub and offered under a permissive license (CC-BY 4.0).

Several NFDI4Microbiota members will participate in the BioHackathon and use that time as a content spring. The BioHackathon will offer a great opportunity to engage in discussions with other participants on various topics such as best practices, bioinformatical tools, Electronic Lab Notebooks and privacy issues.

Free-of-charge registration is open until 25th of November.

Project Lead: Justine Vandendorpe and Kassian Kobert

NFDI4Health, GHGA and NFDI4Microbiota particularly welcome the strategic goal of establishing a decentralized, research-compatible, networked and interoperable health data infrastructure with a central health research data portal. The plea of the German Council of Science and Humanities for a data protection compliant facilitation of data access with the possibilities of the opt-out procedure is explicitly supported by the participating NFDI consortia. Additionally, improved possibilities for the linkage of different data sources (record linkage) on a national level are pleaded for.

For “Rückmeldung der lebenswissenschaftlichen Nationalen Forschungsdateninfrastrukturen NFDI4Health, GHGA und NFDI4Microbiota zu den Positionen und Empfehlungen des Wissenschaftsrats” click here.

For the “Positionspapier zur Digitalisierung und Datennutzung für Gesundheitsforschung und Versorgung” click here.

NFDI4Microbiota will take part in the panel discussion ‘Everything FAIR and Open? Restrictions on data publications’ at JCDL 2022. The panel discussion will be held during the NFDI Satellite Event @JCDL 2022 on the 23rd of June 2022. We are looking forward to an intense exchange on different data and their handling and restrictions in the fields of Life and Social Sciences with representatives of NFDI4Health, NFDI4Biodiversity, and KonsortSWD. Our consortium will be represented by our consortial speaker Prof. Dr. Konrad Förstner. Further details can be found via this link. Please have a closer look at the different registration options!

More than a 1,000 researchers worldwide have already signed the DSI Scientific Network’s Open Letter, calling for open & equitable sharing of genetic sequence data from. You are wondering why this might be important to you?

A short summary by the DSI Scientific Network, orgnaized by Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH:

“In March 2022, negotiations on Digital Sequence Information (DSI) and benefit sharing will resume among Parties to the Convention on Biodiversity as they work to reach agreement on the new Post-2020 Global Biodiversity Framework, which sets new goals and aims to transform society’s relationship with biodiversity. The scientific community is the primary generator and user of DSI. The outcome of these negotiations will therefore shape our ability to use DSI and generate research that helps move forward sustainable development, protect biodiversity and address global health crises. Given the importance of DSI to our work, it is essential that our perspectives, expertise and experience be included in considerations of different approaches to benefit sharing for DSI. DSI is used by researchers in a wide of contexts including for studying and monitoring biodiversity, understanding ecosystem impacts from climate change, improving crops, developing new medicines, and tracking the spread and evolution of new infectious diseases. Access to DSI is therefore crucial to research supporting many of the UN Sustainable Development Goals. A wide range of organizations and experts have called for DSI policy solutions that provide equitable benefit-sharing through multilateral mechanisms that protect open access DSI.” Source and more information

We highly support this initiative and want to invite all researchers to sign the DSI ScientificNetwork’s Open Letter to ensure good research in the future.

Become an NFDI4Microbiota ambassador for your institute! You will not only increase your knowledge on topics like research data management, but also have the possibility to network and influence our work as well as getting solutions for your problems. We do adress this program specifically to young researchers like PhD candidates and PostDocs. You can get more information and register here The first Ambassador Coffe Talk will be on the 13th of June, so make sure to register by the 23rd of May, so you will receive an invitation #NFDIrocks

We are pleased to announce our next bioinformatics workshop: “Introduction to deep learning with R”, which will take place online on June 13-15, 2022. Deep learning based techniques have shown remarkable results in domains such as speech synthesis, natural language processing and image vision. Recently, these methods have been applied to the bioinformatics domain and have been shown, for example, to achieve an unprecedented level of performance for the protein folding task. In this workshop, we will explore and train deep neural networks using the R programming language on genomic datasets. Interested? Then please find additional information here. We are looking forward to seeing you in the workshop! The link for registration here

We are pleased to announce the first bioinformatics workshop: “Introduction to R”, which will take place online from 7th to 9th of March 2022. Increasingly, physicians and biologists are facing largeamounts of data that can no longer be analyzed “by hand”. The R environment offers free software facilities for data manipulation, calculation and graphical display. It thus allows handling of large data amounts, simplifies the interpretation of the data, or enables a deeper analysis Interested? Then register here. We are looking forward to seeing you in the workshop!

You are still looking for some fine FAIR data training material for higher education institutions? Our consortium member Justine Vandendorpe recently published together with other FAIR experts a teaching and training handbook. The handbook included 179 pages and is openly available on Zenodo: https://t1p.de/cwtfq. We wish you happy reading and teaching!

The good news does not stop, so better save the date! After NFDI4Microbiota finally started in October 2021, we are glad to announce our 5th Community Workshop. The event will take place (online) on the 18th of March 2022 from 10-12 AM CEST. This great opportunity will be used to kick off our ambassador program to the microbiology community. If you are not hooked yet, wait for more information to come soon.

After three months of successfull work within our consortium, the election of the consortial speaker as representative within NFDI e.V. took place at the end of 2021. We congratulate Prof. Dr. Konrad Förstner and Prof. Dr. Alice McHardy as speaker and deputy speaker of the NFDI4Microbiota consortium! We are looking forward to a fruitful cooperation with NFDI e.V. and all its members.