NFDI4Biodiversity & iDiv Seasonal School on Data Management in Biodiversity and Environmental Science

How to use this repository

This repository provides details on the schedule, on necessary accounts and installations, and links to all available materials used in the course.

About this workshop

The NFDI4Biodiversity & iDiv Seasonal School on Data Management in Biodiversity and Environmental Science is a collaboration between the German Centre for Integrative Biodiversity Research (iDiv) and the NFDI4Biodiversity consortium. This course offers cutting-edge skills and knowledge essential for handling scientific data throughout its life cycle. The intensive five-day program combines direct knowledge transfer with practical lessons to introduce participants to fundamental and advanced tools in research data management (RDM), tailored to enhance their future careers.

Scope

Participants will engage in a simulated scientific project that covers the entire data life cycle (DLC): data collection, integration from databases, quality control, visualization, and data publication. Using the GFBio DMP Tool, attendees will create a Data Management Plan (DMP) and map local plant occurrences with QField. They will also integrate datasets from repositories like PANGAEA, utilize Jupyter and R for data analysis and visualization, and learn how to publish data on platforms such as PANGAEA and GBIF.

Learning objectives

You will learn...

• How to create a data management plan
• How to use Jupyter in combination with R (and Python) as working environment
• Legal aspects of handling data
• How to handle spatial data
• How to integrate data from different sources
• How to publish data

Requirements

You will need a computer where you can install programs, a camera and microphone, and a stable internet connection during the course.

Further, you will need

• basic knowledge of Git on command line or desktop software
  • pull and push from remote
  • recommended:
    • know how to merge
• basic knowledge of Python
  • how to start a Python program from the command line
• basic knowledge of R
  • know how to load packages and use functions
  • loops, variables, input/output
  • recommended:
    • R package data.table
    • tidyverse

Prepare for the workshop

• fill in our pre-workshop survey
• ❗ Find a spot of vegetation close to you that you can visit to collect data during the course 🌳 🌲🌿
• prepare a measuring device for data collection (a ruler, a measuring tape, or a piece of string to be measured with a ruler)
• make sure to adress requirements, i.e. brush-up your Git, Python and R skills
• register for the following services and organisations (find a list of links and resources here)
  • necessary
    • ECMWF CDS
    • GBIF
    • GitHub
    • QFieldCloud
    • Zenodo (alternative: ORCID)
  • recommended
    • ORCID
• install or update the following programs on your local computer (find a list of links and resources here)
  • necessary
    • OpenRefine
    • RightField
    • QField
    • Spreadsheet software (e.g. LibreOffice, Microsoft Excel)
  • recommended
    • Jupyter (local)
    • Git

❗ Please refer to this list of resources if you need help with accounts or installations.

During the workshop

After the workshop

• fill in our post-workshop survey
• find additional resources and details on future workshops on our website https://www.nfdi4biodiversity.org
• find additional resources here xx

Schedule

Day 1

• 08:30 - 09:30 | 🌞 Warm-up
• 09:30 - 10:30 | Lecture 1 - Research Data Management & Data Literacy
• 10:30 - 10:40 | 🍵 Break ☕
• 10:40 - 12:10 | Lecture 2 - FAIR tools & processes to be used
• 12:10 - 13:00 | 🍴 Break
• 13:00 - 15:00 | Practical Session 1 - Create a Data Management Plan (DMP)
• 15:00 - 15:10 | 📌 Wrap-up and outlook

Day 2

• 08:30 - 09:00 | 🌞 Warm-up
• 09:00 - 10:30 | Lecture 3 - Investigating biodiversity data using open-access databases: following FAIR data principles
• 10:30 - 10:40 | 🍵 Break ☕
• 10:40 - 12:10 | Lecture 4 - Legal aspects
• 12:10 - 13:00 | 🍴 Break
• 13:00 - 15:00 | Practical Session 2 - Sampling and handling spatial data using QField
• 15:00 - 15:10 | 📌 Wrap-up and outlook

Day 3

• 08:30 - 09:00 | 🌞 Warm-up
• 09:00 - 10:30 | Lecture 5 - Taxonomic harmonization
• 10:30 - 10:40 | 🍵 Break ☕
• 10:40 - 12:10 | Lecture 6 - Data standards
• 12:10 - 13:00 | 🍴 Break
• 13:00 - 15:00 | Practical Session 3 - Data integration & annotation
• 15:00 - 15:10 | 📌 Wrap-up and outlook

Day 4

• 08:30 - 09:00 | 🌞 Warm-up
• 09:00 - 10:30 | Lecture 7 - Data analysis & visualisation according to FAIR principles
• 10:30 - 10:40 | 🍵 Break ☕
• 10:40 - 12:10 | Lecture 8 - Publishing your workflow, analysis, scripts using Jupyter, Git and software management tools
• 12:10 - 13:00 | 🍴 Break
• 13:00 - 15:00 | Practical Session 4 - Jupyter Hub
• 15:00 - 15:10 | 📌 Wrap-up and outlook

Day 5

• 08:30 - 09:00 | 🌞 Warm-up
• 09:00 - 10:30 | Lecture 9 - Data publication & archiving
• 10:30 - 10:40 | 🍵 Break ☕
• 10:40 - 13:00 | Practical Session 5 - Publishing data
• 13:00 - 13:30 | 🍵 Break ☕
• 13:30 - 14:00 | 📌 Resumée

List of authors/contributors

How to cite

License

Further reading

About NFDI4Biodiversity and iDiv

NFDI4Biodiversity

NFDI4Biodiversity is a consortium of more than 50 partner institutions under the umbrella of the German National Research Data Infrastructure (NFDI) dedicated to mobilising biodiversity and environmental data for collective use. NFDI4Biodiversity offers tools and services for working with data, personal assistance and practice-oriented training events. Together with its partner network, NFDI4Biodiversity provides a wide range of services for the management of biodiversity, ecology and environmental data.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig

iDiv is the only DFG-funded research centre and has a unique structure. It is run by Martin Luther University Halle-Wittenberg (MLU), Friedrich Schiller University Jena (University of Jena) and Leipzig University (UL) – and in cooperation with the Helmholtz Centre for Environmental Research (UFZ). The centre is located in Leipzig.

The science consortium is enhanced through the expertise of the more than 150 active iDiv members, who work on specific aspects of research in various locations and institutions, and also through the collaboration with the following non-university facilities: the Max Planck Institute for Biogeochemistry (MPI BGC), the Max Planck Institute for Chemical Ecology (MPI CE), the Max Planck Institute for Evolutionary Anthropology (MPI EVA), the Leibniz Institute German Collection of Microorganisms and Cell Cultures (DSMZ), the Leibniz Institute of Plant Biochemistry (IPB), the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), and the Leibniz Institute Senckenberg Museum of Natural History (SMNG).