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_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 combination with AmPdata.
|
| SI | Matlab code that generates figures of selected papers to illustrate the use of DEBtool, AmPtool and AmPdata
|
| AmPtox | A set of examples that show the analysis of results of toxicity tests using parameters from the AmP collection
|
| DEBtox | Matlab scripts for the simultaneous analysis of multiple endpoints in ecotoxicity tests, written by Tjalling Jager
|
| Aquaexcel | A virtual laboratory to support the aquaculture research for a number of fish species; the DEB part is written by Dina Lika.
You first need to register, but this is free of costs and occurs instantaneously.
|
| 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 AmP 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
|
| DEBsea Shiny app | Like the DEB Shiny app, but now for sea water species using satellite data for site-specific surface water temperatures during a specified period.
The user can modify the food 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 micro trait | A genome-informed trait-based DEB modeling package developed for trait-based microbial modeling in Julia.
The DEB approach captures interacting strategies for energy and resource acquisition and allocation,
letting the shape of trade-offs and trait variation at population or community level emerge in response to environmental conditions.
|
| Apecosm | The Apex Predators ECOSystem Model, written in Phyton by Olivier Maury,
aims to represent the spatialized dynamics of open ocean pelagic ecosystems in the global ocean.
Physical forcings (winds, temperature and currents from the OPA circulation model), biogeochemical forcings (primary production and oxygen from the PISCES biogeochemical model)
as well as the effects of fishing are explicitely taken into account in the model.
The model represents the energy flow through the Open Ocean Pelagic Ecosystem (OOPE) with a size-structured energy flux equation in 5 explicit dimensions
(space, time, community and weight).
The epipelagic community is distinguished from the mesopelagic migratory community. The energy input at the basis of the OOPE comes from the PISCES biogeochemical model. The tuna species under interest (yellowfin, skipjack, bigeye, albacore) belongs to the OOPE (i.e. interact trophically with it) but have a finer structure. Tuna population dynamics are indeed represented with a DEB-based (Dynamic Energy Budget) physiologicaly structured advection-diffusion flux equation which transports individuals through a 6 dimensional space (space, time, reserves, structure, gonades). Behaviour of fish is related to their physiological status. A sub-model enables to take into account the small-scale vertical movements of tunas into the larger scale ecosystem dynamics model and drives the interactions between tunas and OOPE.
|
| 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.
Please direct any enquiries about this app to Jorn Bruggeman
|
| pydeb | Pyton package for DEB computations, written by Jorn Bruggeman.
|
| ReadAmP | R-code to import AmPdata into R, written by Jaap van der Meer.
|
| AmP2R | R-code to import AmPdata into R, written by Mike Kearney.
|
| 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 all large phyla and of all 13 chordate classes) and the Matlab-files that obtain the parameters from data using DEBtool.
The data base is available as website and well as Matlab structures
allStat and popStat, with many functions in AmPtool to extract the information.
|
|---|---|
| Phyto_pars | Collection of values for the parameters of the Monod parameters for freshwater phytoplankton species.
Method.
Please direct any enquiries about this app to Jorn Bruggeman
|
| Early-life dispersal traits of coastal fishes | Early-life stages play a key role in the dynamics of bipartite life cycle marine fish populations.
Difficult to monitor, observations of these stages are often scattered in space and time.
While Mediterranean coastlines have been highly surveyed, no effort was made to assemble historical observations.
Here we build an exhaustive compilation of dispersal traits for coastal fish species, considering in-situ observations and growth models.
Our database contains over 110 000 entries collected from 1993 to 2021 in various subregions. All observations are harmonized to inform on dates and geolocations of both spawning and settlement, along with pelagic larval durations. When applicable, missing dates and associated confidence intervals are reconstructed from Dynamic Energy Budget theory. Statistical analyses allow revisiting traits' variability and revealing sampling biases across taxa, space and time, hence providing recommendations for future studies and sampling. Comparison of observed and modelled entries gives hints to improve the feed of observations into models. Overall, this long-term database is a crucial step to investigate how marine fish populations respond to global changes across environmental gradients.
|
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
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
| Upcoming course | The DEB2023 course will take place on moodle, starting with DEB MOOC (DEB tele-course) at March, 2023. 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. |