Information about "Making sense ..."
This page contains information
about the e-book "Making sense of chemical stress" on the
application of Dynamic Energy Budget theory in ecotoxicology
and stress ecology. This book forms a gentle introduction in
the concepts behind DEB theory, and how to apply them in
practice. Therefore, the book is completely "math-free". For
those that like to see the equations and derivations: check
out the downloads below under "Technical background for the
e-book". The first version of this book was made available
April 9, 2012.
The book is offered through the Leanpub publishing
framework. It can still be downloaded for free, but you also
have the option to pay for it. Please consider this option,
for it will allow me to dedicate time and effort to updating
of this e-book, writing new ones, and maintaining/developing
the supporting software.
Note about version 2.0 of
the e-book.
With the development of GUTS, and especially the e-book update
of 8 Dec. 2018, Roman Ashauer and myself have established a
highly consistent outline for TKTD models. This outline
places the concept of 'damage' in a central position. We
strongly feel that it is now time to use the same general
outline for DEB-based models as well. This was already
included in the update of the DEBkiss e-book, but now also in
this e-book (however, not yet in the associated technical
document).
Technical background for the e-book
When I started with this e-book, I
also started working on a technical background document
containing model derivations, model equations, and model
extensions. However, as time progressed, I failed to keep
this document up to date with the latest developments. The
document I prepared is now severely outdated (the bulk was
written in 2012). Most strikingly: it still links effects to
internal concentrations, whereas we should now always
consider a 'damage' state variable. Furthermore it focusses
on the scaled standard model, which is not so much
used anymore (e.g., the AmP project applies the non-scaled
model), and it focusses on the 'classical DEBtox'
formulation (as published by Jager & Zimmer in 2012,
which is now replaced by 'DEBtox2019').
In short: I do not recommend the technical document anymore;
for the up-to-date DEB-TKTD models, it is best to use the
supporting information (SI) of the papers in which they are
presented. However, the technical document does contain some
additional ideas (e.g., extended TK modules, more modes of
action) and a more extensive treatment of the statistics for
model fitting. Therefore, I still keep it available for
download.
- Download the technical document
(version Beta 1.2 of 14 August 2015, PDF 1.3 Mb, see
warnings above!). Check the version log for changes
relative to the previous version.
- For simplified DEBtox models, I suggest focussing on my
2020 paper (download accepted
version) and its extensive SI
for the equations and derivations. Also the DEBkiss
e-book contains a lot of background on this model,
as well as derivations of simplified models and possible
model extensions.
- For DEB-TKTD with the full standard DEB animal model,
I advice our paper, published open
access in 2023 and the extensive SI
with all model equations.
I may decide to update the technical document at some
point (or write a new one), when I can find plenty of time.
But I don't expect this to happen soon.
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How do I refer to the book?
Please refer to the Leanpub page (https://leanpub.com/debtox_book)
with the version of the PDF. For more specific citations,
you could refer to the published papers in the open
literature, such as:
- Jager T, Heugens EHW, Kooijman SALM (2006). Making
sense of ecotoxicological test results: towards
application of process-based models. Ecotoxicology
15:305-314. DOI
10.1007/s10646-006-0060-x (general DEBtox
principles)
- Jager T, Vandenbrouck T, Baas J, De Coen WM, Kooijman
SALM (2010). A biology-based approach for mixture
toxicity of multiple endpoints over the life cycle.
Ecotoxicology 19:351-361. DOI
10.1007/s10646-009-0417-z (toxicants in full DEB
model)
- Jager T, Albert C, Preuss T, Ashauer R (2011). General
Unified Threshold model of Survival - a
toxicokinetic-toxicodynamic framework for ecotoxicology.
Environ Sci Technol 45:2529-2540. DOI
10.1021/es103092a (effects on survival only)
- Jager T, Zimmer EI (2012). Simplified Dynamic Energy
Budget model for analysing ecotoxicity data. Ecol Mod.
225:74-81 DOI
10.1016/j.ecolmodel.2011.11.012 (simplified DEBtox
model with statistical framework)
- Jager T, Martin BT, Zimmer EI (2013). DEBkiss or the
quest for the simplest generic model of animal life
history. Journal of Theoretical Biology 328:9-18. DOI
10.1016/j.jtbi.2013.03.011 (simplified DEBkiss
model)
- Jager T (2020). Revisiting simplified DEBtox models
for analysing ecotoxicity data. Ecol Modell 416:108904.
https://doi.org/10.1016/j.ecolmodel.2019.108904
(based on DEBkiss)
- Jager T, Goussen B, Gergs A (2023). Using the standard
DEB animal model for toxicokinetic-toxicodynamic
analysis. Ecol Modell 475:110187. https://doi.org/10.1016/j.ecolmodel.2022.110187
(based on standard DEB)
Where can I find software to do 'DEBtox' analysis?
Matlab-based software packages for
DEB-based analyses are offered as part of the BYOM platform
on this web site. This is not user-friendly
software, so you need expertise with Matlab, experience with
BYOM, and knowledge of DEB-TKTD models to use them properly.
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