Welcome to the DEB laboratory

Dynamic Energy Budget (DEB) theory is about the processes of substrate uptake and use by organisms throughout their life cycle. This electronic laboratory for work on the DEB theory is a site where you can download software that may be useful for research and education purposes and access data collections. It aims to facilitate the application of the theory, and to stimulate collaboration.

Like a real laboratory, we have some artwork on the wall and a library.

artwork The three-dimensional state space plot, presented in the artwork, illustrates the asymptotic behaviour of a tri-trophic chain in a chemostat. Click on it and it moves. You want to see a close up?
We also have a poem
DEBlib Collection of papers in which DEB theory plays a substantial role

Code 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Download DEBtool_O from GitHub (Octave version no longer maintained since 2013)
Download DEBtool_M from GitHub (Matlab version).

AmPtool is an extension of DEBtool_M to support the analysis of the AmP data base, and can only be used in combinations with AmPdata.

Download AmPtool from GitHub.

DEBtox Matlab scripts for the simultaneous analysis of multiple endpoints in ecotoxicity tests, written by Tjalling Jager
PlotReader extracts coordinates from plots of data, written by Jorn Bruggeman.

Data bases

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.

DEB Shiny app Illustrates weight, length, food intake and mineral trajectories as well as energy fluxes and weight-respiration/reproduction relationships at constant food and temperature for all the species in the collection. The user can modify the food or temperature level and also explore the effect of the 'covariation rules (= scaling rules) and altering allocation to reproduction (kappa). Please direct any enquiries about this app to Michael Kearney

DEB species explorer A web server that finds a proposal for DEB parameter estimates for any animal species, by averaging parameter values among related species, using the AmP collection.

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

Supporting material for the 3rd edition of the DEB-book, called DEB3:

Summary of concepts Presentation and discussion of DEB concepts, which follows the chapters and sections of the DEB3. It avoids the use of mathematics and also tests against experimental data.
Comments Explanations and extensions of the DEB3; they follow the chapters and sections of this book. It changes frequently
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. It changes regularly.
Errata Errata for the DEB3.
Micro-lectures Collection of some 500 PowerPoint slides with short comments by sound, which follows the chapters and sections of DEB3 (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 DEB3 (241 Mb mpeg-file)
Last update: 2014/04/15
Life-cycles These sheets give a mondern overview of the classification of organisms as background for the many species mentioned in DEB3.

Course material

Current course The DEB2021 course takes place on moodle, starting with DEB MOOC (DEB tele-course) at March 03, 2021. This edition will be fully on line, in view of the covid problems. As usual, it will have a tele-part, a school and a symposium
Exercises & answers Collection of exercises, which follows the chapters of DEB3.
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 are available in the DEB library.
Questions & answers These sites give collections of questions and answers that arose during the DEB tele-courses. The numbering follows the chapters and sections of the DEB-books, editions 2 and 3.
Basic methods in Theoretical biology This document summarises basic methods for work in quantitative biology. Examples illustrate the application of these methods and a ppt some important features.