Basics in Research Data Management
Best practices in research data management are required to yield reliable and reproducible results. We will guide you through the research data life cycle with common gotchas and recommendations in the microbial landscape, including primers on how to plan your research, and structure and document your data. The hands-on includes a live demo of how to create and maintain a data management plan for your project, as required by funders such as the DFG.
What You Will Learn:
· Best practices for managing research data, from planning to documentation.
· How to create and maintain a data management plan using practical tools.
· Common challenges in microbial research data management and how to overcome them.
Target Audience:
Researchers, graduate students, and data managers in microbiology who want to improve their data management skills
Organizers:
Justine Vandendorpe & Clemens Thölken
Date: 4 December 13:15 -14:45 CEST
Workflows for Microbiological Data
This workshop offers a comprehensive dive into the practicalities of workflows in microbiological research. You will start by exploring workflows specifically designed for microbiological data and then learn how to assess these workflows using the CAMI benchmarking portal. The session will also provide hands-on experience with running workflows on the CloWM system, and a live demonstration by EMBL will show you how to execute these workflows efficiently.
What You Will Learn:
· How to implement and assess workflows in microbiological research.
· How to run workflows on the CloWM platform.
· Practical skills in workflow execution and benchmarking for your research.
Target Audience:
Microbiologists, bioinformaticians, and researchers who work with microbiological data and want to enhance their workflow capabilities.
Organizers:
Daniel Podlesney, Hesham Almessady, Fernando Meyer, Daniel Podlesney
Date: 4 December 13:15 -14:45 CEST
First steps towards FAIR (meta)data descriptions, ontology terms and data deposition
Current good science practices require to correctly label the data produced in modern biology. Not only do these labels give context and interpretation during data analysis, but they also allow interoperability between different investigations and potential reanalyses. However, the process of describing your data thoroughly, i.e. adding correct metadata, is not straightforward and can be confusing. This workshop provides guidance on how to describe your datasets in a FAIR manner which ensures that your uploaded data is findable and re-usable by machines and humans for future data analysis and comparable results by you and others. The focus will be on teaching you how to identify metadata standards and selecting the minimal amount of metadata necessary to describe your datasets, as well as how to use FAIR terms/ descriptions based on existing ontologies and controlled vocabulary.
What You Will Learn:
· How to deposit your datasets using FAIR principles at public repositories.
· How to identify and apply minimal metadata standards.
· FAIR descriptions of your datasets – Ontology terms and how to use them
Target Audience:
This workshop is meant to be a beginner-friendly introduction suitable for newbies when it comes to data submission to public repositories and the collection of appropriate biological metadata in microbiome research.
Organizers:
Maja Magel + Charlie Pauvert
Date: 4 December 13:15 -14:45 CEST
Resolving Microbial Strain Identifiers with StrainInfo
Different strain designations and culture collection numbers denoting the same strain are often used interchangeably in literature and databases, which poses a challenge to the communication and comparison of research data. The StrainInfo database (https://straininfo.dsmz.de/) collects and curates culture collection numbers and their relations, connecting links to data describing the same strain. In this workshop we will demonstrate how to navigate the StrainInfo website and show you how to find alternative identifiers and culture details for your strain(s) of interest. You will also learn how you use the API to access StrainInfo data programmatically and integrate it into your workflows. The StrainInfo developers will be present to talk about the history and the future of the database and answer all your questions.
What You Will Learn:
· How to use the StrainInfo database to resolve strain identifiers.
· How to find and compare culture details for your strains.
· How to access and integrate StrainInfo data via API into your workflows.
Target Audience:
Microbiologists, bioinformaticians, and researchers dealing with microbial strain data who need to ensure accuracy and consistency in their work.
Organizers:
Isabel Schober, Lorenz Reimer, Artur Lissin
Date: 5 December 15:00 -17:00 CEST
Use Cases – Contributions from the Community for the Community
Join us for an informative workshop on two of NFDI4Microbiota’s Use Cases, where we will present the progress and established services from the community that support and showcase (meta)data curation efforts in microbiology research. We’ll delve into these collaborative projects that have successfully tested and established tools to enhance research efficiency.
(1) Among these, the VirJenDB will be highlighted—a cloud-based virus database developed in Jena, Germany, that leverages advanced tools like the de.NBI Cloud and CloWM workflow system. VirJenDB is already providing researchers with access to a robust dataset of virus sequences and metadata, with plans for further expansion. This workshop will feature practical demonstrations on using these resources, showcasing how you can integrate them into your research and contribute to ongoing developments and dataset curation efforts. Discover how these tools can elevate your work and explore opportunities for further collaboration.
(2) LC-MS/MS metaproteomics offers detailed insights into the taxonomic and functional composition of microbiomes, with significant applications in health, environmental sciences, and biotechnology. In this workshop, we will explore tools developed within the MetaProt Use Case, which focuses on advancing metaproteomics research, particularly in studying the human gut microbiome and progressing toward routine diagnostics. The focus of the MetaProt use case is the establishment and propagation of metadata standards for complex metaproteomic data, for which MetaProt offers a streamlined solutions. Microbiologists new to metaproteomics can gain initial insights into MetaProteomeAnalyzer, MetaForge and research data management with openBis, tools for metaproteomic analysis and metadata annotation and file conversion that produces a standardized output with enhanced metadata annotation.
What You Will Learn:
· Insights into successful community-driven projects and tools in microbiology.
· How to utilize resources like VirJenDB to enhance your research.
· Getting to know tools for metaprotemics
· Opportunities to collaborate on and contribute to ongoing data curation efforts.
Target Audience:
Microbiologists, bioinformaticians, and data curators interested in using or contributing to community-driven research tools and databases.
Organisers:
Maja Magel, Noriko Cassman, Daniel Krautzner
Date: 5 December 15:00 -17:00 CEST
Data storage within the Research Data Commons
Get an introduction to data organization in ARUNA, our data orchestration engine. Understand, why we want to use ARUNA to structure our data flows. Learn how to store and retrieve data in ARUNA. Understand the importance of hooks and use them to verify and transform your data in ARUNA. Let us show you what future developments, we are planning for ARUNA to support an easy data exchange. And most importantly, let's discuss how we can support your use case with ARUNA.
What You Will Learn:
· How to organize, store, and retrieve data using the ARUNA data orchestration engine.
· The role of ARUNA in structuring data flows and ensuring efficient data exchange.
· Upcoming developments in ARUNA and how they can enhance your research data management.
· How to tailor ARUNA to your specific use cases for seamless data management.
Target Audience:
Microbiologists, bioinformaticians, and data curators interested in data management
Organisers:
Frank Förster, Lukas Brehm, Jannis Hochmuth, Sebastian Beyvers
Date: 5 December 15:00 -17:00 CEST
Lotus2 Amplicon Sequencing: Key Considerations for Sample Design and Data Processing
Amplicon sequencing remains a popular method for exploring microbial communities due to its accessibility, standardized protocols, and suitability for low-biomass samples. In this interactive 2-hour workshop, participants will gain hands-on experience with various amplicon sequencing pipelines, process a small dataset, and analyze the results in R. You'll learn practical skills in both Linux and R, essential for microbial data analysis.
What you'll learn:
- An overview of different amplicon sequencing pipelines and their practical applications.
- How to install and run the LotuS2 pipeline https://lotus2.earlham.ac.uk/ on Linux.
- How to process and analyze microbial data in R.
Target Audience:
Microbiologists and bioinformaticians at every career level
Organisers:
Falk Hildebrand
Date: 5 December 15:00 -17:00 CEST
