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
For users of BYOM versions before v.
5.0, 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 has been corrected in version 6.3!
Matlab
R2023a throws errors in BYOM v.6.5 and
earlier.
The newest version of Matlab does not allow
the cell-array format for name-value pairs
anymore, at least not in the way it was used
in BYOM (as well as the openGUTS Matlab
version) for formatting text in figures.
Matlab versions up to 2022b do not have this
problem. (thanks to Amund for spotting
this). This issue is solved with the update
to BYOM v.6.6.
Issues with
moving-time-window EPx calculations in
BYOM v.6.4-6.6.
1) There is an issue with the reporting of
the function calc_epx_window_batch. The
summary table at the end sometimes misses
some endpoints or produces an error. This
happens in rather extreme cases where some
profiles result in an EPx for more endpoints
than others.
2) Found an error in the EPx calculations,
for moving time window EPx calculations (calc_epx_window
and calc_epx_window_batch),
and calling calc_epx with a specific time
window. This leads to erroneous calculations
when the exposure scenario has a low time
resolution, and when reaching the end of the
exposure scenario (where zeros are added to
the profile).
Update: both issues are repared with the
BYOM update to v.6.7.
OpenGUTS v1.1. 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. From 3 March 2023 we
offer a new installer that does not
trigger the (false-positive) trojan
warnings that some users reported.
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.
DeEP tool. 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 calculations. BYOM contains a function to
translate calibration output to a DeEP input file.
There also have been dedicated short courses for
this tool at SETAC-Europe conferences.
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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 (including, 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 will not be in 2023, but is
provisionally planned to run in 2024. More info will
become available here.
- ...
Job opportunities for TKTD/DEB modellers
- The EU-funded doctoral network QTOX is looking for
several PhD students, several on DEB-related topics. More
information (would be 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.
- Postdoc position at Eawag, Switzerland on
computational modelling, including TKTD. More
information. Deadline for application: 14 June
2023.
- ...
Latest news
- 8 June 2023: update of BYOm to v.6.7 to fix some
errors found in EPx calculation with specific or moving
time windows. See BYOM downloads page.
- 27 April 2023: the Summer/Autumn school on TKTD
modelling will not run in 2023, but is postponed to
2024. More info will become available here.
- 17 April 2023: released an update for BYOM to v6.6 to
address the plotting errors in Matlab R2023a. See BYOM downloads
page.
- 6 April 2023: the Matlab version of openGUTS was
updated to v1.1a to run error-free under Matlab R2023a.
See openGUTS
download page.
- 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.
- 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.
Older news over here.
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