Welcome to the DEB laboratory

This electronic laboratory for work on the Dynamic Energy Budget theory is a site where you can download software that may be useful for research and education purposes. It aims to facilitate the application of the theory, and to stimulate collaboration.

Like a real laboratory, we have some artwork on the wall. Here, we can let it move ..
artwork The three-dimensional state space plot, presented in the artwork, illustrates the asymptotic behaviour of a tri-trophic chain in a chemostat. You want to see a close up?
We also have a poem

Packages:

DEBtool is a package, written in Matlab and Octave, that can be used to study the ecophysiological behaviour of animals, plants, algae, microorganisms and symbioses in a graphical way. Effects of chemicals can be studied. It deals with metabolism and interactions between individuals and species; it also allows to fit DEB models to your data. Script-files are included that produce the figures of the DEB-book.

Download DEBtool_O (Octave version 3.2.4, 810 kb, 2013/08/22)
Download DEBtool_M (Matlab version 7.14.0 (R2012a), 6.3 Mb, 2016/09/14).

DEBtox Matlab scripts for the simultaneous analysis of multiple endpoints in ecotoxicity tests
DEBibm Implementation of the standard DEB model in DEBibm in NetLogo to simulate population dynamics. Download Background information.
DEBlib library and computational framework for the solution of problems in Dynamic Energy Budget (DEB) theory, dealing with biological systems from the organism to the ecosystem level.
PlotReader extracts coordinates from plots of data, written by Jorn Bruggeman.

Data libraries:

Add_my_pet Collection of data and parameters values of the standard DEB model for a wide variety of species (including representatives of most large phyla and of all 13 chordate classes) and the Matlab-files that obtain the parameters from data using debtool.

Phyto_pars Collection of values for the parameters of the Monod parameters for freshwater phytoplankton species. Method .

Supporting material for the DEB-book:

Errata Errata for the DEB-book. Those for the 2nd edition are no longer maintained. Go to the champion list for error-spotting.
Summary of concepts Presentation and discussion of DEB concepts, which follows the chapters and sections of the DEB-book. It avoids the use of mathematics and also tests against experimental data.
Comments Explanations and extensions of the DEB-book; they follow the chapters and sections of this book. The comments on 2nd edition are no longer maintained.
DEB notation This document explains the notation that is used in DEB theory, in the hope that it helps to standardise it for further development of de theory.
Micro-lectures Collection of some 500 PowerPoint slides with short comments by sound, which follows the chapters and sections of the DEB-book (0.5 Gb). You can also download the ppt-files separately, without sound tracks
ch0.ppt ch1.ppt ch2.ppt ch3.ppt ch4.ppt ch5.ppt
ch6.ppt ch7.ppt ch8.ppt ch9.ppt ch10.ppt ch11.ppt
5 min video-intro to the DEB-book (241 Mb mpeg-file)
Last update: 2014/04/15
Lifecycles These sites give a mondern overview of the classification of organisms as background for the many species mentioned in the DEB-book.

Course material:

Exercises & answers Collection of exercises, which follows the chapters of the DEB-book.
Quizzes & checks These quizzes might help you to check your progress in the understanding of DEB theory. They can be used as part of the DEB tele-course.
Essays & theses The essays were written as part of a DEB tele-course. Theses on DEB theory and its applications.
Questions & answers These sites give collections of questions and answers that arose during the DEB tele-courses. The numbering follow the chapters and sections of the DEB-books, editions 2 and 3.
Basic methods in Theoretical biology This document summarises basic methods that is required for work in quantitative biology. Examples illustrate the application of these methods.


Go to the DEB information page