Swedish Biodiversity Data Infrastructure
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Below you find an overview of our educational online modules in Biodiversity Informatics. Many of these modules are thematically linked and can be used to stepwise build up your expertise in a certain topic.
This online course will focus on automated ways of retrieving and processing biodiversity data from public databases. You will mostly work in the R programming environment and be introduced to common R-packages and functions to retrieve publication-quality (DOI-assigned) species occurrence data from the Global Biodiversity Information Facility (GBIF). Further you...
This online course will focus on automated ways of retrieving and processing biodiversity data from public databases. You will mostly work in the R programming environment and be introduced to common R-packages and functions to retrieve publication-quality (DOI-assigned) species occurrence data from the Global Biodiversity Information Facility (GBIF). Further you will exercise the most important steps of data cleaning and filtering, including taxonomic filtering to account for the variation of species name synonyms and misspellings using the package taxise. The tutorial will also include common approaches to download occurrences of a larger taxonomic group, such as a family or order. Finally you will try some fancy plotting options to best display the retrieved biodiversity data, including plotting on interactive maps. We encourage you to bring your own scientific questions, and if possible run this course together in a small group – this will make the exercises more interesting and comprehensible.
This online course will introduce you to several applications related to the reading, processing and plotting of spatial data within the R environment (incl. maps, species ranges, etc.). It’s preferable if you have basic knowledge of the R programming language. You will play with several R-packages related to processing spatial...
This online course will introduce you to several applications related to the reading, processing and plotting of spatial data within the R environment (incl. maps, species ranges, etc.). It’s preferable if you have basic knowledge of the R programming language. You will play with several R-packages related to processing spatial data and work with both vector and raster data, learning how to convert between the two. Further you will run exercises related to plotting species diversity and individual species range maps. This course is intended to familiarize you with the most common spatial data operations and transformation in biodiversity research and provide a toolkit for further exploring big data in ecology and evolutionary research. We encourage you to bring your own data and problems, and if possible run this course together in a small group – this will make the exercises more interesting and comprehensible.
This online course helps you to tackle common challenges that arise with any kind of spatial coordinate data in biology. Knowledge of the tools introduced in this workshop is essential when presenting spatial biological data (e.g. a map of sampling sites) in presentations or publications. More specifically you will be...
This online course helps you to tackle common challenges that arise with any kind of spatial coordinate data in biology. Knowledge of the tools introduced in this workshop is essential when presenting spatial biological data (e.g. a map of sampling sites) in presentations or publications. More specifically you will be introduced to strategies to deal with the non-independence of spatial data points also known as spatial autocorrelation. Further the course addresses challenges arising in global analyses from the simple fact that the earth is round. You will also touch upon some of the globally available environmental predictors often applied in spatial analyses and their potential challenges. To run this course you should have basic knowledge of the R programming language and more specifically with spatial operations in R. We therefore encourage you to run the basic spatial R course (SBDI-03) first. We also encourage you to bring your own data and questions, and if possible run this course together in a small group – this will make the exercises more fun and comprehensible.
This module is intended as a Python introduction course, not assuming any prior knowledge of the programming language. It is however useful and desired for participants to have had prior exposure to a different programming language (such as R, bash, Perl, etc.). During this half-day module, you will cover the...
This module is intended as a Python introduction course, not assuming any prior knowledge of the programming language. It is however useful and desired for participants to have had prior exposure to a different programming language (such as R, bash, Perl, etc.). During this half-day module, you will cover the basic python syntax, starting with the basic objects such as strings, lists, dictionaries and arrays. You will learn how to import packages into python, enabling a variety of third-party functions, with a focus on common applications in biology (packages related to sequence data, and reading of data frames). There is potential for a follow up this tutorial with other tutorials (e.g. Advanced Python for biologists).
This is the sequel to the module “Basic Python for biologists”. In this course you will expand your basic Python skills and learn how to write our own Python program with a basic command line user-interaction. During this course you will also run through a mini machine learning exercise. By...
This is the sequel to the module “Basic Python for biologists”. In this course you will expand your basic Python skills and learn how to write our own Python program with a basic command line user-interaction. During this course you will also run through a mini machine learning exercise. By the end of the course you will have the necessary knowledge to produce personalized tools for common applications in biodiversity research (e.g. processing of ecological data, DNA sequence data, etc). Even though the focus will be on biodiversity data, the course is equally suitable for you if your background is in any of the life-sciences, since the tools and the syntax introduced in this course are universally applicable to any kind of data. We encourage you to bring your own data and problems, which will make the exercises more…spicy.
This course will give you a basic introduction to the R environment and show you how to run some very basic analysis of biodiversity data. You will combine biogeographic information with basic sequence analysis. The tutorials in this course explain how to get familiar with R studio, plot maps and...
This course will give you a basic introduction to the R environment and show you how to run some very basic analysis of biodiversity data. You will combine biogeographic information with basic sequence analysis. The tutorials in this course explain how to get familiar with R studio, plot maps and build phylogenetic trees and then combine this information. This module is intended for beginners and 1st – 2nd year biology students. Before the exercises you should read the three papers in the “literature” folder. They will explain the scientific questions that can be addressed with an example. We encourage you to run this course in a small group – this will make the exercises more fun and also more comprehensible. After you complete the exercises you should discuss your findings with your peers and reflect on the provided papers in a group discussion.
This course will introduce you to a series of R packages that together form a complete phylogenetic analysis pipeline. The tutorials outline all necessary steps for a phylogenetic inference and also demonstrates the steps for advancing and scaling up the method. In this course you will be introduced to the...
This course will introduce you to a series of R packages that together form a complete phylogenetic analysis pipeline. The tutorials outline all necessary steps for a phylogenetic inference and also demonstrates the steps for advancing and scaling up the method. In this course you will be introduced to the four existing supersmartR packages: phylotaR, restez, outsider, gaius. You will furthermore run simple exercises to create phylogenetic pipelines, develop your own customised analysis pipeline, improve your R programming skills, and become aware of the different phylogenetic and computing options. We encourage you to bring your own data and questions, and if possible run this course together in a small group – this will make the exercises more fun and comprehensible.
This course enables participants to plan and implement biodiversity data mobilization efforts effectively using accepted community standards. Its aim is to increase the volume, richness and quality of the data published through the GBIF network. This course is comprised of video instruction paired with quizzes and practical exercises.
Topics...
This course enables participants to plan and implement biodiversity data mobilization efforts effectively using accepted community standards. Its aim is to increase the volume, richness and quality of the data published through the GBIF network. This course is comprised of video instruction paired with quizzes and practical exercises.
Topics include:
Here you find a library of past webinars and workshop recordings. You can also browse the SBDI YouTube channel for more movies and webinars.
So, what is SBDI? In this short webinar, the acting director of the Swedish Biodiversity Data Infrastructure Fredrik Ronquist will give you a quick overview of SBDI, its services and partner networks.
How can we help you? In this short webinar our Support coordinator Matthias Obst will give you an overview of how the SBDI Support center works and how SBDI interacts with the scientific user community.
How does SBDI link to genetic data? In this webinar our molecular genetics expert Anders Andersson gives you a short overview of the genetic data services in SBDI. He also outlines the plan for further expenading these services.
Looking for a pipeline to process and publish your metabarcoding data? In this webinar our molecular genetics expert Daniel Lundin gives a demonstration of SBDI’s metabarcoding workflow.
In this webinar our molecular genetics expert Maria Pager introduces you to SBDI’s portal for access and publication of genetic data.
Are you planning to analyze data from marine biological monitoring programs? In this webinar our marine data experts Lisa Sundqvist and Malin Werner explain how you can access marine data and time series in SBDI.
Are you planning to analyze data and time series from terrestrial vegetation monitoring programs? In this webinar our forest data expert Anna-Lena Axelsson explains what data SBDI can offer and how you can access these.
SBDI is linked to biological monitoring programs for birds, butterflies and mammals. In this webinar our data expert Annelie Maria Jönsson explains how to access data from these programs.
Are you planing to set up your own monitoring program? In this webinar our database expert Aleksandra Magdziarek explains how to use the BioCollect tool to create a customized database for your own systematic monitoring project and publish the collected data through SBDI.
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