Pan-European Biodiversity
Pan-European Biodiversity Use Case
This training handbook covers the Pan-European Use Case developed by BOKU University. It demonstrates how to use the Specleaner package within the AquaINFRA Virtual Environment to detect and remove outliers in species occurrence data.
[!NOTE] 📹 Video Reference Workshop Recording (Source: YouTube AquaINFRA Channel | Duration: ~20 mins)
Table of Contents
| Chapter | Description |
|---|---|
| 1. Introduction | Overview of AquaINFRA and the use case goals. |
| 2. Meet the Researchers | Introduction to the team at BOKU University leading this work. |
| 3. Freshwater Biodiversity | The ecological importance of rivers and the use of bioindicators. |
| 4. Specleaner R Package | Deep dive into ensemble outlier detection methods (Univariate & Multivariate). |
| 5. D2K Package | Overview of the FAIR research package resources and segments. |
| 6. Galaxy Workflow Setup | Step-by-step guide to importing the workflow and Zenodo datasets into Aqua Galaxy. |
| 7. Workflow Structure (Part 1) | Detailed breakdown of Steps 1-4 (Data Acquisition). |
| 8. Workflow Structure (Part 2) | Detailed breakdown of Steps 5-8 (Processing & Detection). |
| 9. Reviewing the Results | Visualizing results in Galaxy and interpreting outlier classifications. |
| 10. Conclusion | Final remarks on accessibility, applicability, and endangered species. |