Newsletter August 2023

2023-08-31

Dear Reader,

With our fifth NFDI4Microbiota newsletter, we would like to share news about conferences, Use Cases, training and available online videos.

If you are interested in other topics 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

Upcoming conferences

In September 2023, we will be attending many conferences in order to present our work and to meet our various target communities. Please come by to meet us if you are attending – we look forward to meeting you in person! You can find our contributions to all events below and on our web portal.

NFDI4Microbiota will attend the 2023 Digital-Gipfel (Digital Summit)

The 2023 Digital-Gipfel (Digital Summit) will take place in Jena from November 19th-21st. Various NFDI consortia including the NFDI4Microbiota will come together on the themes of the summit. See more here.

Upcoming hackathon: DataXplorers – Cross-community hackathon

Together with NFDI4Biodiversity and NFDI4Earth, NFDI4Microbiota is organizing a hackathon. The hackathon will start with an online kick-off event on October 23rd and will end with a hybrid final event on December 5th-6th in Frankfurt.**

The main target group are early career researchers (PhD students and postdocs) from the fields of earth system sciences, biodiversity and microbiology – but we also strongly encourage participation from other fields, such as informatics, bio-/media-informatics, and design. More experienced individuals are also welcome to participate.

Challenges will be provided and mentored by partners from the consortia of NFDI4Earth, NFDI4Biodiversity and NFDI4Microbiota. Topics include developing an annotation tool for metaproteomics experiments, building of data cubes and developing machine learning methods for image annotation.

You can register on our hackathon website, where we will also publish the challenge descriptions.

Successful Workshop on “Automating Virus Taxonomy” was held in Jena

The Workshop “Automating Virus Taxonomy”, which took place from July 31st to Aug 2nd in Jena, Germany, was a great success. The hybrid event was co-organized by members of the International Committee for the Taxonomy of Viruses (ICTV), European Virus Bioinformatics Center (EVBC), and the NFDI4Microbiota. About 400 people from 46 countries registered, highlighting the global interest in this important topic.

After the workshop the ICTV Executive Committee discussed this year’s taxonomic proposals and approved most of the additions to the virus taxonomy. For those interested, one can find these under “Taxonomy > Proposals” on the ICTV website.
On the third day of the workshop, a pop-up hackathon and Hands-On Workshop co-organized by Dr. Noriko Cassman (NFDI4Microbiota, FSU Jena) and David Lähnemann (DKFZ Heidelberg/DKTK site Essen-Düsseldorf) took place. About 100 online and 20 onsite participants learned how to write Snakemake workflows and/or created pipelines to automate virus classification.

We are pleased to share the results of the hackathon: two Snakemake workflows for Caudoviricetes classification that follow best coding practices! Take a peek at the mashup-phage and download-and-reannotation-of-phage-genomes workflows on the GitHub repository of the ICTV Virus Bioinformatics Enthusiasts Group. Also available are the Snakemake material and slides.

NFDI4Microbiota Use Cases

NFDI4Microbiota is looking for your input on the Use Cases

We are delighted to invite you to explore our active Use Cases. Whether you are a microbiologist, bioinformatician, or computer scientist, your expertise can be a valuable addition to these projects. Engage with our Use Cases, explore innovative ideas, and contribute to solutions that drive innovation in the field of microbiome research. For each Use Case you will find graphical abstracts, project descriptions, contact details of the project leaders and how to get involved on our web portal. Discover the different topics our Use Cases cover, from metaproteomics and metagenomics to multi-omics data integration:

  • MetaProt: Functional profiling and routine diagnosis of human microbiomes by metaproteomics
  • MetaProv: Provenance and usage of metagenome data
  • MockBench: Systematic assessment in metagenomics using high diversity Mock samples
  • MULTI: Integration of multi-omics data of microbial species
  • Strain-ID: Collecting and matching microbial strain identifiers
  • TAXA: Descriptions of novel taxonomic lineages

Ultimately, the outputs from these projects will help you to be more effective in your daily research. Here are some examples from across the Use Cases where your input is needed and/or how you can benefit from them:
You are a …

  • Microbiologist trying to identify and match culture collection numbers to a given strain: Use the service StrainInfo and provide feedback.

  • Microbiologist with experience in transcriptomics or proteomics analyses: Check out the preliminary guidelines on data processing, analysis, and integration of genomics, transcriptomics, and proteomics data and give feedback.

  • Bioinformaticians curating metagenomes datasets: Provide curated data and metadata from human gut microbiome samples. (Use Case “MetaProt”).

  • Metagenome analyst frustrated with numerical bacteria names lacking functional insights: Use the tool to generate functional descriptions and curate information in a human-readable format.

  • Metagenome researcher looking for sequence data: Find a unified and standardized metadata database from SRA (sequence read archive) metagenomic sequences where you can easily select relevant samples according to your research question.(Use Case “MetaProv”).

  • Bioinformatic software developer interested in evaluating your tools: Specify the application scenario for which your tool is most likely to be used and, consequently, indicate what challenges are to be expected from a typical target microbial community in terms of complexity and diversity. What key parameters should an appropriate evaluation dataset feature? (Use Case “MockBench”).

Metaproteomics Workshop organized by the NFDI4Microbiota Use Case “MetaProt”

Are you interested in metaproteomics and a hands-on training workshop and getting to know the faces behind the NFDI4Microbiota Use Case “MetaProt”?

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

Organizers: Dirk Benndorf, Patrick Hellwig, Kay Schallert, Robert Heyer, Nico Jehmlich
Date: September 18th-22nd, 2023
Location: Otto von Guericke University Magdeburg, Germany
Registration fee: 100 € (including coffee and snacks)
More information: The agenda and registration details are available at mpa@ovgu.de

NFDI4Microbiota Services

Upcoming training and workshops

Supporting the community through education and training is an important goal of our work. Therefore, we provide a comprehensive training program to equip the community with the skills and literacy required for efficient and data-driven microbial research.

Upcoming training courses can be found in our training calendar and below.


Workshop: How to describe biological data? A primer to a FAIR approach for now and the future

Confused about FAIR, ontologies and metadata and how they can help you and your datasets? Begin with our hands-on workshop about description of biological data on October 16th-17th in Aachen and register here by September 20th.

The workshop is intended for:
  • People with knowledge about microbiology
  • Late-stage (wet lab) researchers with datasets that are in preparation to be submitted to repositories
  • Early-stage researchers that will be generating large datasets
  • Researchers having difficulties to apply existing ontologies and metadata fields to their data set
  • Data stewards or broker responsible for submitting data

You will learn how to use terms based on existing ontologies and controlled vocabulary. Your engagement and continuous use of these terms will help to increase future machine-actionable analyses. After the workshop, you will have successfully described your own datasets and prepared the necessary metadata for future deposition of your described datasets.

But beware during this workshop, we will not upload or publish your data, analyze/ re-analyze your data, develop an ontology or set-up an automatic transfer of your metadata to repositories.

Publications

The NFDI4Microbiota Grant Proposal has been published

We are pleased to announce that our DFG grant proposal “NFDI4Microbiota – national research data infrastructure for microbiota research” has been published in the journal Research Ideas and Outcomes (RIO). Here you can find all information about our structure, partners, objectives, work program and strategies.

Reading recommendation: How to make your scientific data accessible, discoverable and useful - Nature

In June 2023, Nature published a Technology Feature article entitled “How to make your scientific data accessible, discoverable and useful” asking data scientists about their best practices for publishing usable, high-quality data. Here, specialists offer seven tips for effectively sharing data. Read the full article here.

Media

NFDI4Microbiota is now part of the LinkedIn network


After having profiles on X (former Twitter) and Mastodon, you can follow us now also on LinkedIn! you can follow us now also on LinkedIn!

We are looking forward to get in touch with you there

Short introduction video of NFDI4Microbiota published

A two-minute introduction video of NFDI4Microbiota is now available online, giving an insight into our vision and mission, and how we aim to democratize the access to microbiota data and high-end computational analyzes

Online video: NFDI4Microbiota lecture talk - Training and education

One focus of our consortium is the democratization of access to data and workflows for the field of microbiology. Training and education, as well as building a knowledge base on topics related to this field, are some of the means to achieve these goals.

This presentation was originally given at the second NFDI4Microbiota annual conference (April 2023). It provides an overview of the overall goals for training and education within NFDI4Microbiota and details on the first steps we have taken to reach these goals. We also introduce the NFDI4Microbiota Knowledge Base as part of our educational efforts.

Online presentation: NFDI4Microbiota - Services to make data FAIR and Open

The presentation “NFDI4Microbiota - Services to make data FAIR and Open” held by Barbara Goetz, member of NFDI4Microbiota, at the fifth Thuringian RDM Days on 20-21 June 2023 has been recorded and is available online. The slides of the presentation can be found here.


Jobs

The members of the NFDI4Microbiota consortium offer specialist positions throughout Germany. The content and funding of all positions are the responsibility of the individual members.

Our partner at the Friedrich Schiller University Jena is looking for a “Postdoctoral researcher (m/f/d) or PhD Candidate (m/f/d) in Frontend development of virus database and community engagement”. The application deadline is November 1st, 2023.

All vacancies are posted on the NFDI4Microbiota website as they become available.

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