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 want 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.
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Errors 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 have updated
long ago! 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 ;-).
Summary of more recent errors in BYOM. For more
detail, check the BYOM
page.
Error
in BYOM version 4.5-6.2. I
found an error in calc_parspace, in the 'extra
sampling' code block. Corrected
in BYOM v.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. Solved with the
update to BYOM v.6.6.
Issues with
moving-time-window EPx calculations in
BYOM v.6.4-6.6. Issues
with the reporting of the function
calc_epx_window_batch. Error in the EPx
calculations, leading
to erroneous calculations when the exposure
scenario has a low time resolution. Both
issues repaired with the update to BYOM
v.6.7.
Other announcements
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. Note that the
DeEP site hosts an on-line calculation tool, but
also a downloadable setup file for a standalone
application.
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 at home.
- The 2023 DEB school and symposium is over. More info
is available here. A
next run can be expected in the first half of 2025.
- The next TKTD Autumn School on dynamic modelling of
toxic effects will not be in 2023, but is
planned to run in 2024. More info will become available
(or will be linked) here.
- The next PrediTox school is held on 15-19 January 2024
in Lyon, France (there is also a virtual session
planned). On the programme is dose-response modelling as
well as TKTD modelling with GUTS. More
information.
- ...
Job opportunities for TKTD/DEB modellers
- PhD position at Wageningen University (The
Netherlands): Understanding Species Sensitivity to
Chemicals. More
information.
Latest news
- 22 September 2023: new version of the DEBtox_classic
package for BYOM. Small changes to make the calculations
more efficient, and allowing for time-to-death data. See
version log for all changes. See BYOM downloads
page. Note that using time-to-death data also requires
updating to BYOM v.6.8.
- 21 September 2023: new version of the GUTS package for
BYOM. Small changes to make the calculations more
efficient, and allowing for time-to-death data. See
version log for all changes. See BYOM downloads
page. Note that using time-to-death data also requires
updating to BYOM v.6.8.
- 18 September 2023: small update of BYOM. Added an
option to use time-to-death data, small functionality
improvements for EPx calculations, preparations for the
DEBtox_mix package. Also added the experimental
DEBtox_mix package for DEBtox2019-based analysis of
binary mixture data. See BYOM downloads page.
- 18 September 2023: removed the menu entry for the
DEBtoxM software. The last update was in 2015, and I do
not maintain nor use this software anymore. The web page
still exists here, so old links will still
resolve.
- 7 August 2023: released a new version of the "Making
sense ..." e-book. The most important change is a
complete overhaul of the case studies to reflect the
latest thinking and methods for DEB-based TKTD analysis.
More
information.
- 20 July 2023: released a new version of the GUTS
e-book, adding a.o. a new case study with openGUTS. More
information.
- 14 June 2023: released a new version of the
'Mechanistic modelling essentials' e-book. More
information.
- 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.
Old 'news' over here.
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