DEBtox information
Making sense of ecotoxicity test results



Main menu


Submenu

DEBtox information

DEBtox information

Home

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.



The
                DEBnet network of experts


The Duck of Vaucanson

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. C
orrected 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.

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 most of my e-books to be really free (and free of access hurdles). And, I am not sure whether the people that are interested in my books would also have an interest in the other books offered at Leanpub. I noticed this change at Leanpub on 19 Sept. 2022, and immediately changed the settings so my free e-books are again totally free. I noticed that some of my e-books are also offered on other (rather shady) web sites. Please get them through Leanpub only!

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.
  • A next run of the DEB school and symposium is planned for the first half of 2025. More information will become available here.
  • The next TKTD Autumn School on dynamic modelling of toxic effects is planned to run in 2024. More information will become available (or will be linked) here.
  • For those of you going to SETAC Europe in Seville 5-9 May 2024: don't miss the session on effect modelling in regulatory science, and the special session on ways forward for mechanistic effect modeling in environmental risk assessment.
  • ...

Job opportunities for TKTD/DEB modellers


  • BASF is looking for a quantitative ecotoxicologist, whose responsibilities include mechanistic effect modelling (TKTD is not mentioned explicitly, but may be implied). More information on LinkedIn. (posted 14 Feb. 2024)

Latest news


  • 5 February 2024: minor update of the DEBkiss e-book. See the support page.
  • 5 December 2023: new paper of Romoli et al on-line! In this paper, we compare standard DEB-TKTD with DEBtox (DEBkiss-TKTD) on typical datasets for environmental risk assessment of pesticides. Download from publisher's website. (available open access now!)
  • 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.
Old 'news' over here.


The DEBtox information site, www.debtox.info, since July 2011