Welcome to the DEB laboratory

This electronic laboratory for work on the Dynamic Energy Budget theory is a site that points to material 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_O is a package, written in Octave that was the leading version of DEBtool till 2009, when AmP developed. The need to work with global variables in solvers in Octave was incompatible with the development of AmP. Script-files are included that produce the figures of the DEB-book.
DEBtool_O on GitHub (Octave version, poorly maintained since 2009)
DEBtool_M is a package, written in Matlab, that can be used to study the ecophysiological behaviour of animals, plants, algae, microorganisms and symbioses in a graphical way. Effects of chemicals and population dynamics can be studied. It deals with metabolism and interactions between individuals and species; it also allows to fit DEB models to your data; the Add-my-Pet (AmP) estimation procedure uses DEBtool_M/lib/pet, and all AmP predict files use DEBtool_M/animal/. Script-files are included that produce the figures of the DEB-book.
DEBtool_M on GitHub (Matlab version, intensively maintained)
DEBtool_R is a package, written in R by Goncalo Marques, that can be used to study the ecophysiological behaviour of animals.
DEBtool_R on GitHub (R version, maintenance unknown)
AmPtool is a package, written in Matlab, for visualisation and analysis of the Add-my-Pet (AmP) data base on DEB parameters and implied properties (= traits) of animal species.
AmPtool on GitHub (Matlab version, intensively maintained)
DEBtox Matlab scripts, written by Tjalling Jager, 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.
NicheMapR is a R package written by Mike Kearney and Warren Porter, to link data on microclimate to predicted body temperature of (terrestrial) animals. The aim is to link it also AmP and extend it to the aquatic realm. NicheMapR on GitHub (R version)
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 all large phyla and of all chordate classes) and the Matlab-files that obtain the parameters from data using debtool.
Debber Proposes guesses for DEB parameter values for an arbitrary, but valid, animal species in the Catalog of Life, written by Jorn Bruggeman
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 document changes frequently. 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. It changes from time to time to accomodate these developments.
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:

MOOC Massive Open Online Course with DEB video's, prepared by the Lisbon-node of DEBweb. The focus is on engineering aspects of the standard DEB model.
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