Welcome to the DEBtox information site
Welcome to the DEBtox information page, the
site for people that want to make sense of ecotoxicity data.
This site contains information on mechanistic models for the
analysis of stressor effects on the life-history traits of
individual organisms (and from there to higher and lower
levels of biological organisation). Specifically, this site
is about models based on animal energy budgets (DEBtox and DEBkiss) and survival models
from the GUTS framework.
This website constitutes a node in the international DEBnet
network, together with the associated site of DEBtox Research.
The mission of DEBtox.info is to simplify biology to
get to the essence of what toxicants (and other stresses)
are doing to organisms. Simplification is necessary if we
need to gain understanding. Furthermore, we cannot expect to
test even a small fraction of all possible (combinations of)
toxicants, species and environmental conditions. Once we get
to the essence, it is possible to make educated predictions
of toxicant effects for untested chemicals, untested
species, and under untested conditions.
Here, you can find information, lists of relevant
publications, (links to) free e-books, and freely
downloadable Matlab packages to analyse your data. Use the
major categories on the top left of the screen to navigate
through this site; the corresponding sub-categories will
appear right next to it in the sub-menu.
Messages and warnings
The free and open-source software openGUTS v1.1 is
now available for download!
It is available as a standalone Windows executable
or as Matlab package. It supports the use of GUTS for regulatory
purposes, but will also prove useful for scientific
studies. The dedicated website http://openguts.info/
provides more information. Version 1.1 repairs a
calculation error that was spotted in
openGUTS, which may affect IT
calibrations/predictions for specific types
of exposure scenarios. The Matlab version
has also been updated to v1.1 to repair
this. For more information, see the openGUTS
website.
For users of BYOM
versions before v. 4.3, see the notes and warnings
on the BYOM page (bottom of
page). But, really,
you should update to a newer version ... If you are
working with BYOM, and would like to be notified
immediately in case of errors, new versions, etc., email me and I will
include you in a mailing list. I may also use this
mailing list for other important developments such
as new (versions) of the e-books, and new papers.
This saves you the hassle of checking this website
every week ;-).
Error in BYOM version
4.5-6.2!
I found an error in calc_parspace, in the 'extra
sampling' code block. This section is run when the
profiling step indicates a poor coverage of the
sample: it should resample in the problem areas. Due
to the error, it just duplicated the sample sets
that were selected as starting points, so this step
is useless. This error thus only influences the
results for data sets where the initial sampling
rounds lead to poor results: the additional step
does not improve coverage of the sample. I don't
expect this error to cause serious problems in
optimisation or error propagation. Only in cases
where the sampling is really bad, and in those
cases, it should be clear from the parameter-space
plot that the sample should not be used! So always
check your plots carefully. This
error has been corrected in version 6.3!
Note
that this error is NOT present in openGUTS, even
though the same algorithm is used there (the error
was made in the translation to BYOM).
Changes at Leanpub (keeping my e-books free).
Things changed a bit at Leanpub. My free e-books,
from some point onward, required a paid membership
to Leanpub for free download. While I do want to
support Leanpub, I want several of my e-books to be
really free (and free of access hurdles). And, I am
not sure whether people interested in my books would
also have an interest in the other books offered at
Leanpub. I just noticed this change at Leanpub on 19
Sept. 2022, and immediately changed the settings so
my free e-books are again totally free.
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Upcoming courses and events
- Roman Ashauer and Tjalling Jager gave an on-line short
course on openGUTS
at the 2020 SETAC SciCon. This course is now available
for everyone via Leanpub: https://leanpub.com/c/openguts.
Although you don't get the interaction with the
instructors, this is still a nice way to educate
yourself in quarantine.
- The next DEB school and symposium is offered in the
first half of 2023. Excellent to get you started on
standard DEB and add-my-pet (though not specifically
focussing on TKTD). The free on-line Tele-course DEB2023
runs from 23 March to 4 May 2023 as a MOOC. The 8-day
on-site school is from 5-13 June in Louisiana (US),
followed by the international symposium on 14-16 June.
More info is available here.
- The next TKTD Autumn School on dynamic modelling of
toxic effects is planned for Sept.-Nov. 2023. More info
will become available here.
- The Preditox winter school, 30 January-3 February 2023
in Lyon (France), spends one day on TKTD modelling
(GUTS), among other data analysis tools. More
information.
Job opportunities for TKTD/DEB modellers
- The System Science group at Osnabrück University
(Andreas Focks) is looking for a research associate (30
months). The researcher will participate in the EFSA
project "AMPHIDEB: Development of biologically-based
models in environmental risk assessment to assess the
effects of chemicals and pathogenic fungi on amphibian
and reptile populations." More
information (closing 30 Sept. but announcement is
still available).
- The EU-funded doctoral network QTOX is looking for
several PhD students, several on DEB-related topics. More
information (closing 13 Nov. but announcement is
still available).
- Open position in Winnipeg, Canada to work within the
field of ecotoxicology and in vitro to in vivo
extrapolation. The project is open to student interests
and changes, but the overall goal is to combine
laboratory experiments on the accumulation and effects
of chemical toxicants on cells with DEB-TKTD models in
cells and whole organisms (fish, mammals) to understand
how we can use in vitro data to predict ecological
effects. The position is open to either a MSc or PhD
position. For more information, contact Dr. JP
Desforges.
- ...
Latest news
- 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.
- 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.
- 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.
- 2 November 2022: a new version of the e-book
"Mechanistic modelling essentials" is released. Many
small clarifications and corrections, and a new chapter
on toxicokinetic principles. 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.
- 16 September 2022: added a new BYOM package
DEBkiss_tox. This contains the models formulated in
primary parameters, which were split out of the
DEBtox2019 package (to make that one specific for the
compound-parameter version, which is most commonly
used). 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).
- 4 July 2022: Take a look at the DeEP tool
for EPx predictions with DEBtox2019.
Note that this tool does not perform calibrations or
validations on data sets, but rather makes EPx
predictions for exposure profiles, such as those from
FOCUS.
Older news over here.
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