DEB literature and publications

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DEB theory
Background and Applications

Literature and publications
DEB Research Program
DEB Developments
DEB Applications

Code, manuals, collection

Add-my-Pet wiki style manual
AmP portal and collection
GitHub repositories for DEBtool_M and AmPtool

  • A systematic account of the theory is given in the book DEB3 (Cambridge Univ Press, 3rd edition 2010), which corrected the errata found in the printed version.
  • The notation document contains the rules for notation that are used, as well as the notation itself.
  • Comments to DEB3 is a collection of developments since 2010 and explanations of parts of the book. It is a document which changes frequently.
  • The summary of concepts presents the meaning the various concepts and their function in the theory. It has no formulae or biological observations and follows the section-structure of DEB3.

Below some selected references.

Journal issues on DEB theory

Starting with the most recent:

Editorials of DEB special issues

DEB model introductions

  • Kearney 2020: What is the status of metabolic theory one century after Pütter invented the von Bertalanffy growth curve?
  • Kooijman 2020: The standard Dynamic Energy Budget model has no plausible alternatives
  • Jager 2020: Revisiting simplified DEBtox models for analysing ecotoxicity data
  • Muller et al 2019: Regulation of reproductive processes with dynamic energy budgets
  • Jusup et al 2017: Physics of metabolic organization
  • Sara et al 2014: Thinking beyond organism energy use: a trait-based bioenergetic mechanistic approach for predictions of life history traits in marine organisms
  • Ledder 2014: The basic Dynamic Energy Budget model and some implications
  • Kooijman 2012: Energy budgets
  • Lika and Kooijman 2011: The comparative topology of energy allocation in budget models
  • Sousa et al 2006: The thermodynamics of organisms in the context of Dynamic Energy Budget theory
  • Kooijman 2001: Quantitative aspects of metabolic organization; a discussion of concepts
  • Kooijman 1998: The Dynamic Energy Budget (DEB) model

DEB in evolutionary context

Parameter estimation

  • Lika et al 2020: The use of augmented loss functions for estimating Dynamic Energy Budget parameters
  • Augustine et al 2020: Comparing loss functions and interval estimates for survival data
  • Marques et al 2019: Fitting Multiple Models to Multiple Data Sets
  • Marques et al 2018: The AmP project: Comparing Species on the Basis of Dynamic Energy Budget Parameters
  • Morais et al 2018: Calibration of parameters in Dynamic Energy Budget models using Direct-Search methods
  • Lika et al 2011: The `covariation method' for estimating the parameters of the standard Dynamic Energy Budget model II: Properties of the estimation method and some patterns
  • Lika et al 2011: The `covariation method' for estimating the parameters of the standard Dynamic Energy Budget model I: philosophy and approach
  • Kooijman et al 2008: From food-dependent statistics to metabolic parameters, a practical guide to the use of Dynamic Energy Budget theory
  • Sousa et al 2008: From empirical patterns to theory: A formal metabolic theory of life
  • van der Meer 2006: An introduction to Dynamic Energy Budget (DEB) models with special emphasis on parameter estimation

Patterns in parameter values

  • van der Meer 2020: Production efficiency differences between poikilotherms and homeotherms have little to do with metabolic rate
  • Kooijman et al 2020: The energetic basis of population growth in animal kingdom
  • Kooijman 2020: The comparative energetics of petrels and penguins
  • Augustine et al 2019: Altricial-precocial spectra in animal kingdom
  • Augustine et al 2019: Why big-bodied animal species cannot evolve a waste-to-hurry strategy
  • Lika et al 2019: Body size as emergent property
  • Baas and Kooijman 2015: Sensitivity of animals to chemical compounds links to metabolic rate
  • Kooijman and Lika 2014: Comparative energetics of the 5 fish classes on the basis of Dynamic Energy Budgets
  • Kooijman 2014: Metabolic acceleration in animal ontogeny: an evolutionary perspective
  • Kooijman and Lika 2014: Resource allocation to reproduction in animals
  • Lika et al 2014: Bijection between data and parameter space quantifies the supply-demand spectrum
  • Kooijman 2013: "Waste-to-hurry" Dynamic Energy Budgets explain the need of wasting to fully exploit blooming resources
  • Kooijman et al 2011: Scenarios for acceleration in fish development and the role of metamorphosis
  • Kooijman et al 2007: Scaling relationships based on partition coefficients and body sizes have similarities and interactions
  • Cardoso et al 2006: Body size scaling relationships in bivalves: a comparison of field data with predictions by Dynamic Energy Budgets (DEB theory)
  • van der Veer et al 2006: The estimation of DEB parameters for various Northeast Atlantic bivalve species
  • van der Veer et al 2003: Body size scaling relationships in flatfish as predicted by Dynamic Energy Bugets (DEB theory): implications for recruitment
  • Kooijman 1986: Energy budgets can explain body size relations

Bibliography of DEB papers

  • DEB library on Zotero. The papers include summaries of particular aspects of the theory, formal (axiom-based) and less formal (biology-based), introductions, sub- and supra-organismic levels and applications. Becoming a Zotero member is easy (and has no costs), which gives access to all PDFs.