DEBtox information
Making sense of ecotoxicity test results

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DEBtox information

DEBtox information


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  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 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.

                DEBnet network of experts

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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: 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.

The DEBtox information site,, since July 2011