Workshops 20 April

The workshops will be organised at Sciencepark 904,  Amsterdam


9.00 – 9.30 Registration and coffee Hall Building D*
9.30 – 13.00 Workshop  Annotation of behaviour Gis-studio
Workshop  Space Use / Homerange F2.04
13.00 – 14.00 Lunch Eetcafe: Oerknal
14.00 – 17.30 Workshop  Classification of behaviour Gis-studio
Workshop  Uva-BiTS services F2.04
Workshop  Catching and tagging G3.02


* Through main entrance Sciencepark 904


Workshop annotation of behaviour

Willem Bouten1  and  Thomas Lameris2

Institute for Biodiversity and Ecosystem Dynamics ,University of Amsterdam, Amsterdam, The Netherlands

2 Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands

Tri-axial accelerometers measure body orientation and body dynamics. These measurements thus provide an opportunity to determine behaviour of birds to calculate time budgets, energy expenditure or food intake. With UvA-BiTS we generally measure 1-10 seconds of accelerometer at 20 Hz after every GPS measurement. Annotating the data with behaviour is a first step needed to train/calibrate models that can then automatically classify the data. We will discuss the types of behaviour that we recognize in the data and how these can be used to answer research questions. Behind the computer we will annotate data using synchronised movies and measurements. We will also try to annotate measurements on the basis of expert knowledge if there are no movies or visual observations available.
This workshop can be followed separately but even better in combination with the afternoon’s workshop on classification of behaviour.


Workshop space-use / homerange

Emiel van Loon1

Institute for Biodiversity and Ecosystem Dynamics ,University of Amsterdam, Amsterdam, The Netherlands

The goal of workshop is to familiarize you with the most important techniques to determine space-use by animals on the basis of tracking data. We will first apply common methods to estimate areas of frequent use (like convex polygon, kernel density and Brownian bridge methods) and learn about the assumptions, strengths and weaknesses underlying these. Subsequently, we will apply techniques to assess habitat preferences using different designs. The work is structured around exercises in R, using several characteristic data sets. For each type of analysis there are exercises for those who have a basic understanding of the techniques and limited R-skills but also material for those who are more experienced.


Workshop classification of behaviour.

Willem Bouten1  and Thomas Lameris2

Institute for Biodiversity and Ecosystem Dynamics ,University of Amsterdam, Amsterdam, The Netherlands

2 Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands

In this workshop we will present and discuss the workflow of behaviour classification based on accelerometer data. Existing annotated data will be used to  discuss which data features are needed to recognize behaviours and to discriminate between them. We will discuss split data sets, training and testing of models and the application of the classification model. You will be introduced to and you will work with the UvA-BiTS tool box for machine learning. We will use an UvA-BiTS visualization tool to evaluate the classified data. Finally we will discuss the lessons learned, opportunities and limitations of behavioural studies based on GPS and accelerometer.
This workshop can be followed separately but even better as a follow up to the morning workshop on annotation of behaviour. The combination of the two should give you a good start to analyze your own data.


Getting to grips with UvA-BiTS web services

Wouter Vansteelant1

1Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, the Netherlands

 The Virtual Lab of the UvA Bird Tracking System (UvA-BiTS) offers a wide range of web services with which researchers can store, manage, process and visualize their tracking data. These features make UvA-BiTS one the most advanced animal tracking systems in the world. However, getting to grips with all these services can be challenging, especially new users with little or no background in database management and computational techniques. Moreover, even experienced users may not be aware of all the goodness the Virtual Lab has to offer.

This workshop offers allows any user, beginner or experienced, to explore all the main features of the Virtual Lab. We will focus on the ‘Dashboard’ and ‘Project Admin’ tools in conjunction with the ‘Database’. This exercise will help you understand the architecture of the database, and thus to link metadata about your research project, your birds and devices with your tracking data. In addition, we will explore how to retrieve data from the database, and how to visualize bird movements using the KMZ-generator and the Flight Simulator.


Catching and tagging birds

Kees Camhuysen1

1 Royal Netherlands Institute for Sea Research and Utrecht University(NIOZ), Texel, The Netherlands

Catching and tagging birds (manuscript preparation) – after 8 years of tagging a large variety of species with UvA-BiTS GPS loggers, usually with harnesses, it is about time to report experiences and the effects of tagging on our study species. We aim at a peer-reviewed publication in which hands-on experiences are reported for contrasting species. We will discuss the scope of this paper (papers?), we will call for short presentations reporting techniques & experiences with tagging and discuss the information we would wish to report, subdivide tasks and draft a manuscript that will be completed after the workshop.