This page collects older news
items from the home page.
Website and discussion board
- 17 May 2019: the openGUTS.info
website is now on-line. This site will host the openGUTS
standalone software, but already offers the Matlab
prototype for download.
- 8 Oct. 2015: I have moved debtox.info to another web
hoster due to problems with the services from KPN. There
might still be some glitches; if you run into unexpected
behaviour, please let me know.
- 13 August 2015: the site has a new look and feel! I
moved everything from a php-based web-builder
application to plain html. This makes it easier for me
to maintain, and to move to another webhoster, if
needed. The important old php links should redirect
automatically to the new html pages. Some glitches may
occur .... so please contact me
if you hit an unexpected result.
- 7 August 2015: moved my DEBtox Research activities to
a dedicated website: www.debtox.nl.
This info site will remain the place with information on
models, sorftware, e-books, publications and courses.
- March 2015: the hits counter at the bottom of the page
has now exceeded 100,000 hits!
- 21 June 2012. Check out Roman Ashauer advertising TKTD
modelling in SETACs newsletter over
here.
- 5 May 2012. On the discussion board, I started a forum
on "Ecotox Essays".This forum will present short
opinions and critical comments on an ecotoxicological
topic. I will try to regulary write a contribution, but
I also highly welcome contributions from others! See the
board for further details.
Old events (not complete)
- 17 June 2022: There will be another TKTD Autumn school
in 2023. Tjalling Jager and Roman Ashauer have decided
to step out of the teaching team, but a strong team
remains. More information will be presented or linked on
the course
page.
- Roman Ashauer and myself will be giving a short course
on the openGUTS
software at the upcoming SETAC-Europe
conference in virtual space. This will be a
hands-on course for using the software, so very limited
attention to the backgrounds of the GUTS model itself.
However, you should be able to combine out course with
Sandrine Charles' planned full-day course (which
dedicates its morning session to GUTS theory).
- 18 Sept. 2019: the GUTS course planned for October
2019 has been cancelled due to insufficient
registrations.
- Also at the 2019
SETAC conference in Helsinki, there will be the
spectacular “GUTS to the Max”: Mechanistic Effect Models
Hackathon, organised by Roman Ashauer. More
information.
- For 2019, a new round of the DEB telecourse is planned,
and also a classroom part (1-6 April), followed by
workshops (8-9 April), and the international DEB
symposium (10-12 April). This time, the location will be
Brest, France. More information is provided on the symposium
website. Application to the
DEB2019 school is open and the deadline is
extended to February 15, 2019.
- If you are a young environmental scientist, make sure
to check out the YES
meeting in Ghent, 5-10 February 2019. I will be
teaching a short course on DEBkiss there. Registration
deadline is 18 December 2018.
- Dedicated 2-day GUTS course, geared towards
professionals in risk assessment of pesticides. 16-18
October, Wageningen, the Netherlands. More information.
- As part of the 2019
SETAC conference in Helsinki, Sandrine Charles is
organising a 1-day short course on GUTS (on 26 May
2019). Download
the flyer.
- Sandrine is also organising a more extensive winter
school 6-10 January 2020 (in Lyon, France)
focussing on ecotox effect models.
- 27 August 2018: the EFSA opinion on TKTD models is now
available over
here. This opinion will be pivotal for the
application of GUTS and DEBtox in environmental risk
assessment (in particular for pesticides).
- 26 March 2018: the 2018 round of the TKTD modelling
summer course DynModTox
has been cancelled.
- 24 August 2016. We just finished the third round of
the DynModTox summerschool in Denmark. Some impressions
from the 2016 course over here.
- Wednesday 13 January, at the VU University, Carlos
Teixeira defended his thesis entitled "Application of
Dynamic Energy Budget theory for conservation relevant
modelling of bird life histories." Announcement
(in Dutch).
- On 2 June 2015, James Maino successfully defended his
thesis entitled "The Importance of Body Size: Scaling of
Physiological Traits in Insects" at the VU in Amsterdam.
Announcement over
here.
- On 8 May, Bas Kooijman will deliver his farewell
speech at the VU University, which also marks the end of
the Dept. of Theoretical Biology at this university. See
the announcement
(in Dutch). The trilogy booklet with Bas' inaugaral and
farewell speeches can be downloaded over
here.
- On 28-30 April 2015, there will be the fourth
international DEB symposium in Marseille, France.
Abstract submission is closed.
- As of 1 March 2015, Tjalling Jager has left the VU
University to continue as a self-employed researcher
under the name DEBtox
Research. I will remain associated with the VU as
a guest of the department of Animal Ecology.
February-April 2015, there will be a new round of the
DEB course. Part in tele-mode, and part hands-on in
Marseille, France. More info.
This will be the last course organised by Bas Kooijman,
so don't miss it!
- 14 January, we had the succesful defense
of Alpar Barsi, who's CREAM
project was supervised by Virginie Ducrot and myself.
His thesis can be found here.
- In August 2014, we provided the second summercourse on
dynamic modelling in ecotoxicology. Impressions.
- 18 June 2013. Elke Zimmer and Ben Martin successfully
defended their PhD theses! Congratulations! More info on
Elke's
thesis and Ben's
thesis.
- Cancelled: the 2013 PhD summer course "Dynamic
modelling of toxic effects". More details about the
course over here.
- Mike Newman offers his course on quantitative methods
in ecotoxicology (in the US) from 17-21 June 2013. See brochure.
- Webcast minicourse on DEB principles by Roger Nisbet
31 January till 21 February, see course
description. An excellent starting point for
people doing the DEB
telecourse.
- On 24-26 April 2013, the third international DEB
symposium was held on the island of Texel in the
Netherlands. Details over here.
- In 2012, the first PhD summer course "Dynamic
modelling of toxic effects" was held on 11-18th of
August in Denmark, which focussed on TKTD modelling in
general, and on GUTS and DEBtox in particular.
Impressions from the 2012 course can be found over here.
More details about the course over
here.
Book updates
- 21 November 2022: update of the 'Making sense' e-book.
Also bringing things up to date with the latest
publications. See book info page.
- 21 November 2022: update of the GUTS e-book. Nothing
spectacular, just bringing things up to date with the
latest publications. See book info page.
- 19 September 2022: released a new version of the
DEBkiss e-book. Especially the section on toxicant TK
and effects has been thoroughly reworked. See book
info page.
- 9 May 2019: major update of the "Making sense of
chemical stress" e-book. The book is now up-to-date with
the streamlining of TKTD models that was started with
GUTS. More information.
- 8 December 2018: a new version of the GUTS e-book has
been released at Leanpub. Most
important change is in the statistical treatment. See
version log at the support
page for more details.
- 15 November 2018: a new version of the DEBkiss e-book
has been released at Leanpub.
- 15 August 2018: update to the ring test results for
BYOM. See the guts e-book page.
- 18 January 2018: The long-awaited GUTS e-book is
released in Version 1.0! More
information.
- 24 July 2017: Update of the "Making sense of chemical
stress" e-book. Improved
readability and update with new developments.
- 24 June 2017: Sandrine Charles wrote an excellent
review of my e-book in IEAM. http://dx.doi.org/10.1002/ieam.1931
- 6 December 2016: New version of the DEBkiss book
published. More information.
- 14 August 2015: small update to the technical document, adding a
section on joint confidence regions.
- 11-12 August 2015: the e-books "Making sense of
chemical stress" and "DEBkiss" have both been moved to
the Leanpub publishing framework, and can be downloaded
here and here,
respectively. You can still get them for free, but also
have the possibility to pay me (which will support
future development of this and other books).
- 4 April 2015: small update of the DEBkiss book.
- 11 February 2015: New version of the DEBkiss book.
- 11 February 2015: Small update of the technical background document.
- 15 October 2014: New version 1.1 of the e-book "Making
sense of chemical stress" over here.
Added a chapter with two case studies.
- 15 June 2014. Version 1.1 of the e-book on DEBkiss is
now available over here.
Some minor changes.
- 18 May 2014. Version 1.0 of the e-book on DEBkiss is
now available over here.
Basically an embellished version of our JTB paper.
- 14 June 2013. Version 1.0 of the e-book now available
for download over here. Small
changes relative to Beta 1 version.
- 20 Sept. 2012. The first Beta 1 version of the
technical document for the e-book over
here.
- 9 April 2012. The first Beta 1 version of the free
e-book "Making Sense of Chemical Stress" is available
for download over here.
Software updates
- 22 March 2023: small update of BYOM. Main change is an
extension of the functionality of plotting with
calc_and_plot for use with multiple data sets. See BYOM downloads
page.
- 8 March 2023: new version of the stdDEB-TKTD package.
Repaired a tiny error that could cause problems when
fitting multiple data sets (see release notes for
details). See BYOM downloads page.
- 3 March 2023: new installation file for version 1.1 of
the openGUTS standalone has been released. See openGUTS
download page. This version does not trigger the
(false-positive) trojan warning that was thrown by some
virus scanners with the previous version.
- 13 December 2022: BYOM update to version 6.4. Number
of small changes. Added a function for batch-wise
calculation of EPx, and a function to convert
BYOM-DEBtox2019 MAT files to DeEP
format. Also a small update of the DEBtox2019 package to
demonstrate this new functionality. See BYOM downloads
page.
- 22 August 2022: BYOM update to version 6.3, fixing the
error found a few days ago. See BYOM downloads
page.
- 19 August 2022: Spotted an error in BYOM for the
parameter-sapce explorer. See warning message above
(also placed on the BYOM page).
- 21 April 2022: Small update of the stdDEB-TKTD package
to version Beta 4. See BYOM downloads page.
- 1 April 2022: Small update of BYOM to version 6.1. See
BYOM
downloads page.
- 14 January 2022: Official release of BYOM version 6.0.
See BYOM
downloads page. Also a tiny update of the
DEBtox2019 package, that speeds up the EPx calculations
for some exposure profiles.
- 13 January 2022: First (beta) release of a BYOM
package for standard DEB in ecotoxicology: stdDEB_tktd.
See BYOM
downloads page.
- 6 December 2021: Extension of the reduced GUTS models
for binary mixtures. Package is now available. See BYOM downloads
page.
- 1 December 2021: small update for BYOM to beta 8. See
BYOM
downloads page.
- 29 November 2021: the main packages are now ready for
BYOM v.6.0. See BYOM downloads page.
- 25 November 2021: small update to beta 7 of BYOM,
available for download. The old version 5.2.
still remains available as well for a while.
- 15 November 2021: beta 6 version of BYOM available for
download.
The old version 5.2. remains available as well for a
while, since the old files (and the current packages)
will not work anymore with the new BYOM version (in
general, only small modifications are needed).
- 25 February 2021: new version 1.1 of the openGUTS
software. See the
openGUTS downloads page.
- 28 September 2020: spotted an error in the
no-shrinking equations that are used in the DEBkiss and
DEBtox2019 packages. This error could bias calibrations,
though the simulations were fine. These packages are
thus updated. This error does not affect the
DEBtox_classic package since there is no option to
prevent shrinking in that one. See
the BYOM page.
- 26-27 September 2020: update of the BYOM tox-related
packages. GUTS package: this update is especially a good
idea when using the ODE-solver versions in the
"experimental" folder. DEBtox2019 and DEBtox_classic
packages: more efficient/accurate ODE solving for
time-varying exposure. For all these packages: now
allowing double time points in the exposure definition
(as in openGUTS). See the BYOM page.
- 26 September 2020: update of the BYOM package. This
update is especially a good idea when using the
ODE-solver versions in the "experimental" folder. Also:
now allowing double time points (as in openGUTS). See the BYOM page.
- 24 September 2020: update for BYOM to version 5.2.
Modified the parameter-space explorer to work reasonable
well for 6/7 free parameters (best left to experts).
Further modifications for time-varying exposure, now
allowing double time entries like in openGUTS and
efficiency improved for hard-pulsed exposure (these
changes also require updates for the packages that use
glo.break_time ... working on that!). See the BYOM page.
- 30 August 2020: update for BYOM to version 5.1.
Nothing spectacular, just fixed a few bugs and added a
few bells and whistles. See the
BYOM page.
- 2 June 2020: update for the BYOM package for classic
DEBtox and DEBkiss to match it to BYOM 5.0. See the BYOM page.
- 29 May 2020: update for BYOM to version 5.0. This is a
major update, with much new functionality (incl. the
parameter-space explorer from openGUTS). See the BYOM page. Also an update
of the GUTS and DEBtox2019 packages to make use of the
new functionality!
- 2 Sept. 2019: update for BYOM and a new DEBtox2019
package (replacing DEBkiss-tox). See
the BYOM page.
- 24 May 2019: update for the BYOM DEBkiss-tox package.
This brings the package in line with v.2.0 of the DEBkiss e-book. See the BYOM page.
- 22 May 2019: update for the BYOM dose-response fitting
package for classical ECx estimates at a single time
point. See the BYOM page.
- 23 April 2019: small update of BYOM to v. 4.3. Few
bugs fixed, but main change is explicit licensing
information included. More details on the BYOM page.
- 7 September 2018: small update of BYOM to v. 4.2c and
updated GUTS package v. 2.3. More details on the BYOM page.
- 13 August 2018: a quick update of BYOM to v. 4.2b.
This was needed as I found some errors in conjunction
with GUTS package. See BYOM page
for details.
- 9 August 2018: updates of packages 'dose-response',
'acute Calanus', and 'support marecotox'. The
dose-response package also has a nicer walkthrough.
See BYOM page.
- 7 August 2018: new version of BYOM and the GUTS
package, fixing the issue with the likelihood-region
method. More details on the BYOM
page.
- 28 June 2018: running simulations for GUTS, I am
getting confirmation that the likelihood-region method
(as implemented in BYOM) is yielding exaggerated
confidence intervals on model predictions. More
details on the BYOM page.
- In 2018/2019 we will be producing a user-friendly
software for GUTS. More
information.
- 1 February 2018: New versions of BYOM and the GUTS
package. See the BYOM page.
- 12 May 2017: Spotted a small error in BYOM when
calculatin the intervals on LC50s with the
likelihood-region method. This corrected in a small update to version 4.01.
- 27-28 April 2017: Release of BYOM 4.0 on the BYOM page. This is a major
update, with many new features, but old scripts and
packages will not work anymore! All packages have been
updated; the two GUTS packages have been combined, and
some have been renamed for clarity.
- 6 April 2017: Added the Beta 3 test version of BYOM
4.0 on the BYOM page. Also a
new version of the GUTS package is included.
- 15 February 2017: Added a Beta test version of BYOM
4.0 on the BYOM page. This is
still under testing, but feel free to play with it.
Also, I added some warnings for users of profiling and
slice sampling with BYOM.
- 5 January 2017: New version of the BYOM platform available for
download.
- 7 April 2016. Small update of the BYOM
modelling framework in Matlab.
- 25 and 27 August: another update of BYOM (sorry, found some small
errors again). Additionally, an updated version of the
DEBtox1 package (also demonstrating the improved
population growth rate calculation). Updates of GUTS1
and DEBkiss1 packages. And ... a totally new package:
DEBkiss_tox1, which is DEBkiss
turned into a TKTD model. 29 August: update of the GUTS2
and DEBkiss2 package as well. All packages now have a
walk through.
- 21 August: update of BYOM.
Corrected a few errors and added some new functionality
that will be demonstrated in future packages.
- 30 June 2015: update of BYOM.
Corrected some errors and included a few extra options.
- 21 August: update of BYOM.
Corrected a few errors and added some new functionality
that will be demonstrated in future packages.
- 17 April 2015: update of DEBtoxM
flavours Surv, GUTS and DEBtox. The DEB3 flavour is no
longer offered.
- 3 April 2015: major update of BYOM.
Some alternative optimisation methods are included, plus
the possibility to fit parameters on log-scale. And ...
the possibility to publish the code in Matlab (see the
walkthrough of the BYOM code). Also a new version of the
manual is provided.
- 18 February 2015: update of BYOM
and the GUTS2 package. Main change is to avoid warnings
with newer versions on Matlab (due to different way of
dealing with interpolations), and the option to plot in
black-and-white with different symbols (as in the
DEBtoxM flavours).
- 2 January 2015: tiny 2.02 update for BYOM, and extended the BYOM
manual, and gave a seperate entry on the BYOM download
page.
- 17 December 2014: New version of the BYOM files to version 2.0. Major
change is the possibility to have more than one data set
per stage, and a brand new simulation engine. As of
version 1.5, cleaner and simpler BYOM scripts. New
packages for GUTS, DEBtox and some nice examples for the
simulator! (Version 2.01 also has a small update to the
manual).
- 29 November 2014: New version of the BYOM files. Major change is the
removal of the calculation and plotting from the basic
script into an engine script, which takes away a lot of
complexity from the user.
- 1 May 2014. New version 1.5 of BYOM files posted over here. Also, a new package
general package for DEBkiss.
- 29 Jan. 2013. New version 1.4 of the BYOM package, and
the GUTS and DEBkiss packages over
here.
- 29 Aug. 2012. New version 1.3 of the BYOM package over here.
- 30 June 2012. The flexible modelling platform BYOM is
available over here.
- 19 May 2012. New versions of all flavours posted over here. New versions were
needed because of an error in the calculation of the
likelihood function for replicated graded data (with
different number of individuals per replicate). Further,
changes are made to increase flexibility and ease of
operation.
Recent publications
- 11 November 2022: Paper published on how to use the
standard DEB animal model for TKTD analysis. Share
link (open access). Note that there is also a BYOM
package for this model, which includes scripts to redo
the case study of the paper.
- 5 May 2022: Paper published on applying DEBkiss to
early-life stages of cleaner fish (https://doi.org/10.1016/j.ecolmodel.2022.110005
Open Access). Part of the StartRens
project.
- 11 June 2021: our MultiCop
paper on growth in the copepod Tigriopus brevicornis
has been accepted for publication in J. Sea Res. No DEB
analysis yet, but highly relevant for DEB-based studies
of copepods. Preproof available via the DOI.
- 4 May 2021: discussion paper on the use of
reproduction data in DEB-based models. This is a must
read for all TKTD modellers that work with reproduction
data! A preprint is available at bioRxiv.
Paper has been accepted 7 June for publication in IEAM.
- 27 January 2021: New paper from Sylvain Bart on
mixtures with GUTS in ES&T, see https://doi.org/10.1002/ieam.4333.
- 9 January 2021: Best wishes for the new year! Forget
to announce a new paper on the algorithm used in
openGUTS for calibration and error propagation. It was
accepted in August, but still only available in 'early
view': DOI:
10.1002/ieam.4333
- 11 Dec. 2019: new paper presenting an updated
simplified DEB model for ecotoxicology (based on
DEBkiss, compound parameters). You can download this
paper for free till 29 Jan, 2020 from https://authors.elsevier.com/a/1aCrg15DJ%7ExMQu.
See https://doi.org/10.1016/j.ecolmodel.2019.108904.
- 21 May 2019: new paper on effects of hydrogen peroxide
on shrimps, including GUTS analysis with pulsed
exposure. See https://doi.org/10.1016/j.ecoenv.2019.05.045.
- 27 August 2018: the EFSA opinion on TKTD models is now
available over
here. This opinion will be pivotal for the
application of GUTS and DEBtox in environmental risk
assessment (in particular for pesticides).
- 9 January 2019: new paper on automated high-throughput
measurements of body size (which could really facilitate
DEB(tox) application in the future). Open
access. Note that this is my 100th (co-)authored
paper ;-).
- 8 August 2018: new paper out on modelling
bioenergetics in early life stages of cod: 50-day
free download link.
- 27 March 2018: new paper from the GUTS
project on evaluating the quality of
toxicokinetic-toxicodynamic models. IEAM. https://doi.org/10.1002/ieam.2026
- 1 November 2017: New paper from the GUTS
project: Physiological modes of action across
species and toxicants: the key to predictive
ecotoxicology. Environ. Sci.: Processes Impacts. Open
Access: https://doi.org/10.1039/C7EM00328E
- 14 June 2017: New paper from the EnergyBar
project: Jager T et al. Dynamic links between
lipid storage, toxicokinetics and mortality in a marine
copepod exposed to dimethylnaphthalene. Accepted in
Environ Sci Technol http://dx.doi.org/10.1021/acs.est.7b02212
- 1 January 2017: Our GUTS
paper has just hit 100 citations in Web of Science! DOI
10.1021/es103092a.
- 29 November 2016: New paper from the EnergyBar
project: Jager T et al. (2017). Modelling the
dynamics of growth, development and lipid storage in the
marine copepod Calanus finmarchicus. Marine
Biology 164:1. DOI
10.1007/s00227-016-3030-8 (Open Access!)
- October 2016: The book "Marine Ecotoxicology: current
Knowledge and Future Issues" has just come out. I wrote
a chapter "Dynamic modelling for uptake and effects of
chemicals" in there. The book can obtained from Elsevier
or your favourite bookstore, or via ScienceDirect.
The support page for my chapter can be found over here.
- My paper "Making sense of ecotoxicological test
results: Towards application of process-based models"
has just hit 100 citations in Web of Science. http://dx.doi.org/10.1007/s10646-006-0060-x
- 4 August 2016: Paper from the NETS 2014 conference.
Jager T (2016). Predicting environmental risk: a road
map for the future. J. Toxicol. Environ. Health.
79(13-15):572-584. http://dx.doi.org/10.1080/15287394.2016.1171986
- 4 August 2016: Paper from the NETS 2014 conference.
Hansen BH et al. (2016). Acute toxicity of dispersed
crude oil on the cold-water copepod Calanus
finmarchicus: elusive implications of lipid
content. J. Toxicol. Environ. Health. 79(13-15):549-557.
http://dx.doi.org/10.1080/15287394.2016.1171981
- Ashauer R et al. (2016). Modelling survival: exposure
pattern, species sensitivity and uncertainty. Sci Rep
6:29178 http://dx.doi.org/10.1038/srep29178
- Jager T, Ravagnan E, Dupont S (2016). Near-future
ocean acidification impacts maintenance costs in
sea-urchin larvae: identification of stress factors and
tipping points using a DEB modelling approach. Untill 23
Nov. 2015, it can freely be downloaded using this link:
http://authors.elsevier.com/a/1RpNm51aUK0l2
- Jager T, Altin D, Miljeteig C and Hansen BH (2016).
Stage- and sex-dependent sensitivity to water soluble
fractions of fresh and weathered oil in the marine
copepod Calanus finmarchicus. Environ Toxicol
Chem 35(3):728-735. http://dx.doi.org/10.1002/etc.3237
- Jager T, Ravagnan E (2015). Parameterising a generic
model for the dynamic energy budget of Antarctic krill,
Euphausia superba. Mar Ecol Progr Ser 519:115-128
DOI
10.3354/meps11098.
- Jager T, Salaberria I, Hansen BH (2015). Capturing the
life history of the marine copepod Calanus sinicus
into a generic bioenergetics framework. Ecol Mod
299:114-120. DOI
10.1016/j.ecolmodel.2014.12.011
- Just appeared: the 2014 special issue on DEB research
in the Journal of Sea Research. Find it here.
- Jager T et al. (2014). Dynamic modeling of sub-lethal
mixture toxicity in the nematode Caenorhabditis
elegans. Environ. Sci. Technol. 48:7026-7033 DOI
10.1021/es501306t
- Zimmer et al (2014). Metabolic acceleration in the
pond snail Lymnaea stagnalis? J Sea Res 94:84-91
DOI
10.1016/j.seares.2014.07.006
- Martin et al (2014). Limitations of extrapolating
toxic effects on reproduction to the population level.
Ecol. Appl. 24(8):1972-1983 DOI
10.1890/14-0656.1
- Jager T (2014). Reconsidering sufficient and optimal
test design in acute toxicity testing. Ecotoxicology
23(1):38-44 DOI
10.1007/s10646-013-1149-7
- Barsi et al (2014). Considerations for test design to
accommodate energy-budget models in ecotoxicology: a
case study for acetone in the pond snail Lymnaea
stagnalis. Environ. Toxicol. Chem. 33(7):1466-1475
DOI
10.1002/etc.2399
- Jager et al (2014) Dynamic energy budgets in
population ecotoxicology: applications and outlook.
Ecol. Mod. 280:140-147 DOI
10.1016/j.ecolmodel.2013.06.024
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