This repository contains materials for the MSc course Methods in Biodiversity Analysis, offered through a collaboration between Naturalis, IBL, and CML. The course will take place in weeks 48 through 51 (of 2019, and presumably onwards), mainly in the Sylvius Building (1.5.03) with some practicals in the Van Steenis Building, both on the main (bio)science campus of Leiden.
The goal of the course is to impart data science skills as relevant to biodiversity research. Technical topics to be covered will include research reproducibility (e.g. scripting) and data management (e.g. versioning), while the scientific applications will encompass biodiversity assessment using DNA sequence data (e.g. metabarcoding), geospatial data (e.g. ecological niche modeling) and phenotype/morphology data (e.g. morphometrics).
The course will consist of lectures and hands-on computer practicals that require you to have the following:
- a working laptop, any major operating system is fine
- RStudio (open source edition)
- SQLite browser
- Java
- an account on the Galaxy portal
- an account on EoL
- an installation of Docker desktop (windows, mac, or the windows toolbox or mac toolbox)