Dear Reader,
With our ninth 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!
And now: Enjoy reading the newsletter!
Community Engagement
Events and Conferences
Performing ancient metagenomics at SPAAM summer school
The online SPAAM summer school (August 5-9) introduced essential steps to perform ancient metagenomics, including how to process next-generation assembly and how to perform de novo metagenomic assembly. The online event had a lovely design like a little RPG, in which you actual had to walk to the seminar rooms with your avatar, as shown in the picture above.
Integrated into the summer school Konrad Förstner, Hesham Almessady and Justine Vandendorpe each delivered a 15 minute talk on August 8. First, Konrad Förstner introduced NFDI4Microbiota. Subsequently, Hesham presented relevant workflows and services such as CAMI (critical assessment of metagenome interpretation) benchmarking and CloWM (Cloud online workflow manager). Lastly, Justine introduced electronic lab notebooks (ELN), including the advantages of ELN and examples. The talks were well received, attracted over 45 attendees, and generated significant interest.
Successful Knwoledge Base Coding Sprint on September 11-13, 2024
In our recent three-day coding sprint we continued to develop the NFDI4Microbiota knowledge base. New and experienced contributors collaborated to improve the platform, demonstrating the power of open collaboration.
There were 23 active pull requests, as the Sprint started, and seven contributors merged 21 of them. From 38 issues we closed 28, including fixes for broken links, formatting, and tracking key performance and nine authors made 264 commits. Finally yet importantly, we updated 55 files and 1,928 lines of code, which added notable improvements including better documentation, enhanced internal linking, and a more user-friendly design. In addition, major updates to experimental SOPs ensure a more reliable resource for researchers.
The sprint strengthened both the platform and community, setting the stage for future progress. Thanks to all that contributed during the four sessions.
Community Engagement
Upcoming Events and Conferences
Join us at the 3rd NFDI4Microbiota annual conference in Leipzig on December 4-5, 2024
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 divníng 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 the KUBUS (UFZ) Leippzig 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 said poster sessions and Hands-on Workshops on different related topics, such as “Basics in Research Data Management”, Workflows for Microbiological Data” and “First steps towards FAIR (meta)data descriptions, ontology terms and data deposition.
You can find the complete timetable here on the registration site.
Meet your peers at the CarpentryConnect Heidelberg 2024
Following the CarpentryConnect Manchester 2019, this year’s community event takes place in Heidelberg, Germany, from November 12th-14th.
The CarpentryConnect Heidelberg 2024 (CCHD2024) will feature a diverse range of sessions, such as breakouts, posters, lightning talks, workshops and curriculum co-working sessions, all centred around the Theme: “Community-led training beyond academia.” NFDI4Microbiota sponsors the event and we invite our fellow Carpentries to join: https://biont-training.eu/CarpentryConnect2024.html.
Never heard about The Carpentries communtiy? The project compromises the Software Carpentry, Data Carpentry, and Library carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researcher. It builds global capacity in essential data and computational skills for conducting efficient, open, and reproducible research.
Join the ambassador meetings
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 November 25th, starting at 14:30 CEST. Kassian Kobert of the University Bielefeld will tell us about the NFDI4Microbiota Knowledge Base and how you can contribute. 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 October 28th. Ulisses da Rocha from Helmholtz Centre for Environmental Research (UFZ) will talk about Metadata standards in connection with data quality. Get more information on the topics and the schedule here.
Services
2025 Flex Funds call closed!
Thank you to all of you who participated in our 2025 Flex Funds call. We received many exciting proposals and are now busy reviewing them. We will announce the new Flex Funds projects in one of our next newsletters.
Introducing the New Provenance Guidelines for Workflow Developers
The Task Area 3.4 of NFDI4Microbiota is pleased to announce the release of our Provenance Guidelines for Workflow Developers. These guidelines are designed to support new and experienced developers in creating bioinformatics workflows that prioritize provenance tracking, reproducibility, and transparency. By following these standards, developers can ensure that their workflows are scientifically robust, easily reproducible, and verifiable.
Why Provenance Matters
In bioinformatics, the ability to trace the origin and evolution of data within a workflow—known as provenance—is crucial. Provenance tracking ensures that every step of a workflow, from data acquisition to the final output, is documented and reproducible. This level of detail not only fosters scientific transparency but also facilitates the validation and replication of results by others in the community.
Key Components of the Guidelines
Our guidelines cover several critical areas:
- Improve Reproducibility: To enhance reproducability, we advise to pin all software versions and set random seeds.
- Version Management: Proper version control is essential for tracking changes over time. The guidelines emphasize the importance of managing and reporting versions of both the workflow and any associated software tools or libraries. Examples are given how the expected provenance output can be created.
- Data and Metadata Management: The guidelines outline best practices for managing inputs and outputs as well as metadata. Examples are given how the expected provenance output can be created.
- Detailed Documentation: Developers are encouraged to provide comprehensive documentation for every aspect of their workflows. This includes clear descriptions of inputs, outputs, and intermediate steps, as well as the rationale behind specific choices.
- Validation Practices: To guarantee that workflows produce reliable results, the guidelines recommend validation practices. These include testing workflows with different datasets and verifying that the outputs remain consistent and accurate.
Introducing the Provenance Scoring System
To encourage adherence to these guidelines and foster continuous improvement, we have introduced a Provenance Scoring System. This system assigns a rating to each workflow based on its compliance with the outlined standards, with the highest possible score being 100 provenance points.
Benefits of the Scoring System: This scoring system should serve as a benchmark for quality, providing developers with a clear understanding of where their workflows excel and where they may need improvement. For users, the score offers a reliable measure of a workflow’s reliability and reproducibility, helping them make informed decisions about which tools to use.
Get Involved
We encourage all developers to review these guidelines and consider how they can be integrated into their current and future projects.
We welcome your feedback on these guidelines as we aim to refine and improve them further.
Please send any comments or suggestions to klemmp@staff.uni-marburg.de.
New Template for your Data Management Plan published
You work with microbiological data and struggle with the data management? We got your back and developed a special “NFDI4Microbiota Edition” Data Management Plan (DMP) Template.
The PDF guides you with simple questions through the data management process. And once you gone through all of the questions, your DMP is finished. Check it out!
You tried the template and got feedback for us? Please get in touch via contact@nfdi4microbiota.de
Training Announcements
There are several interesting training offers currently open for registration, like:
- The NFDI4Microbiota and de.NBI 16S amplicon training course (Oct 8th-10th)
- Microbiota profiling by 16SrRNA gene amplicon sequencing: Data analysis Workshop (Oct 23rd)
- DSMZ Digital Diversity: How to efficiently access the data of BacDive, BRENDA, LPSN, SILVA and more (Nov 11th)
- Research data management: how to start and maintain a project (Nov 12th)
And more courses are planned. In November you can also get an “Introduction on Python”.
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
Exciting workshop initiated crucial dialogue
On September 3rd, 2024, NFDI4Microbiota hosted a digital workshop on long-term data preservation for life sciences, with a focus on maintaining the FAIRness of valuable research data over time. The workshop convened researchers, research data management (RDM) staff, and infrastructure providers to explore key questions around data selection, safety, reusability, and institutional responsibilities.
A highlight of the event was a presentation by the European Bioinformatics Institute (EBI), which outlined the massive scale of data they manage, their role in stewarding the data submission process, and ongoing challenges with metadata completeness that directly impact the long-term reusability of data.
The workshop also featured two hands-on interactive sessions:
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What to Preserve? The Participants discussed the criteria for selecting data to be preserved long-term. The session covered various aspects, including funder and institutional obligations, valuable data and reusability and standards.
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Who Preserves How? This session focused on the roles and responsibilities of institutions in the preservation process. Key discussion points included institutional policies, challenges and gaps and collaborative preservation.
In the end, the workshop initiated a crucial dialogue on aligning preservation strategies, managing institutional resources, and ensuring long-term data reusability in life sciences.
Cooperations
DataPLANT, NFDI4Biodiversity and NFDI4Microbiota intensify their collaboration as the Biodata Group
We signed a Memorandum of Understanding (MoU) with the consortia DataPLANT and NFDI4Biodiversity. 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. Learn more about this new cooperation in the news section of our website.
Recent Publications
Interesting poster on CAMI web portal available
There is an interesting poster on benchmarking metagenomics software with the new CAMI web portal available on our NFDI4Microbiota Zenodo section. Fernando Meyer, Gary Robertson and our co-speaker Alice McHardy created the poster and Fernando presented it at the 32nd Conference on Intelligent Systems for Molecular Biology (ISMB 2024). The poster introduces the new CAMI web portal, which allows users to assess software for common metagenome analyses using the CAMI benchmarking metrics.
The community-led initiative for the Critical Assessment of Metagenome Interpretation (CAMI) promotes standards and good practices agreed upon the community.
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. 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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