DEBtox information

DEBtox information

Website and discussion board

• 17 May 2019: the openGUTS.info website is now on-line. This site will host the openGUTS standalone software, but already offers the Matlab prototype for download.
• 8 Oct. 2015: I have moved debtox.info to another web hoster due to problems with the services from KPN. There might still be some glitches; if you run into unexpected behaviour, please let me know.
  
• 13 August 2015: the site has a new look and feel! I moved everything from a php-based web-builder application to plain html. This makes it easier for me to maintain, and to move to another webhoster, if needed. The important old php links should redirect automatically to the new html pages. Some glitches may occur .... so please contact me if you hit an unexpected result.
• 7 August 2015: moved my DEBtox Research activities to a dedicated website: www.debtox.nl. This info site will remain the place with information on models, sorftware, e-books, publications and courses.
• March 2015: the hits counter at the bottom of the page has now exceeded 100,000 hits!
• 21 June 2012. Check out Roman Ashauer advertising TKTD modelling in SETACs newsletter over here.
• 5 May 2012. On the discussion board, I started a forum on "Ecotox Essays".This forum will present short opinions and critical comments on an ecotoxicological topic. I will try to regulary write a contribution, but I also highly welcome contributions from others! See the board for further details.

Old events (not complete)

• 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 June 2022: There will be another TKTD Autumn school in 2023. Tjalling Jager and Roman Ashauer have decided to step out of the teaching team, but a strong team remains. More information will be presented or linked on the course page.
• Roman Ashauer and myself will be giving a short course on the openGUTS software at the upcoming SETAC-Europe conference in virtual space. This will be a hands-on course for using the software, so very limited attention to the backgrounds of the GUTS model itself. However, you should be able to combine out course with Sandrine Charles' planned full-day course (which dedicates its morning session to GUTS theory).
  
• 18 Sept. 2019: the GUTS course planned for October 2019 has been cancelled due to insufficient registrations.
• Also at the 2019 SETAC conference in Helsinki, there will be the spectacular “GUTS to the Max”: Mechanistic Effect Models Hackathon, organised by Roman Ashauer. More information.
• For 2019, a new round of the DEB telecourse is planned, and also a classroom part (1-6 April), followed by workshops (8-9 April), and the international DEB symposium (10-12 April). This time, the location will be Brest, France. More information is provided on the symposium website. Application to the DEB2019 school is open and the deadline is extended to February 15, 2019.
• If you are a young environmental scientist, make sure to check out the YES meeting in Ghent, 5-10 February 2019. I will be teaching a short course on DEBkiss there. Registration deadline is 18 December 2018.
• Dedicated 2-day GUTS course, geared towards professionals in risk assessment of pesticides. 16-18 October, Wageningen, the Netherlands. More information.
  
• As part of the 2019 SETAC conference in Helsinki, Sandrine Charles is organising a 1-day short course on GUTS (on 26 May 2019). Download the flyer.
  
• Sandrine is also organising a more extensive winter school 6-10 January 2020 (in Lyon, France) focussing on ecotox effect models.
• 27 August 2018: the EFSA opinion on TKTD models is now available over here. This opinion will be pivotal for the application of GUTS and DEBtox in environmental risk assessment (in particular for pesticides).
• 26 March 2018: the 2018 round of the TKTD modelling summer course DynModTox has been cancelled.
• 24 August 2016. We just finished the third round of the DynModTox summerschool in Denmark. Some impressions from the 2016 course over here.
  
• Wednesday 13 January, at the VU University, Carlos Teixeira defended his thesis entitled "Application of Dynamic Energy Budget theory for conservation relevant modelling of bird life histories." Announcement (in Dutch).
• On 2 June 2015, James Maino successfully defended his thesis entitled "The Importance of Body Size: Scaling of Physiological Traits in Insects" at the VU in Amsterdam. Announcement over here.
• On 8 May, Bas Kooijman will deliver his farewell speech at the VU University, which also marks the end of the Dept. of Theoretical Biology at this university. See the announcement (in Dutch). The trilogy booklet with Bas' inaugaral and farewell speeches can be downloaded over here.
• On 28-30 April 2015, there will be the fourth international DEB symposium in Marseille, France. Abstract submission is closed.
• As of 1 March 2015, Tjalling Jager has left the VU University to continue as a self-employed researcher under the name DEBtox Research. I will remain associated with the VU as a guest of the department of Animal Ecology. February-April 2015, there will be a new round of the DEB course. Part in tele-mode, and part hands-on in Marseille, France. More info. This will be the last course organised by Bas Kooijman, so don't miss it!
• 14 January, we had the succesful defense of Alpar Barsi, who's CREAM project was supervised by Virginie Ducrot and myself. His thesis can be found here.
• In August 2014, we provided the second summercourse on dynamic modelling in ecotoxicology. Impressions.
• 18 June 2013. Elke Zimmer and Ben Martin successfully defended their PhD theses! Congratulations! More info on Elke's thesis and Ben's thesis.
• Cancelled: the 2013 PhD summer course "Dynamic modelling of toxic effects". More details about the course over here.
• Mike Newman offers his course on quantitative methods in ecotoxicology (in the US) from 17-21 June 2013. See brochure.
• Webcast minicourse on DEB principles by Roger Nisbet 31 January till 21 February, see course description. An excellent starting point for people doing the DEB telecourse.
• On 24-26 April 2013, the third international DEB symposium was held on the island of Texel in the Netherlands. Details over here.
• In 2012, the first PhD summer course "Dynamic modelling of toxic effects" was held on 11-18th of August in Denmark, which focussed on TKTD modelling in general, and on GUTS and DEBtox in particular. Impressions from the 2012 course can be found over here. More details about the course over here.

Book updates

• 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.
• 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.
• 9 May 2019: major update of the "Making sense of chemical stress" e-book. The book is now up-to-date with the streamlining of TKTD models that was started with GUTS. More information.
• 8 December 2018: a new version of the GUTS e-book has been released at Leanpub. Most important change is in the statistical treatment. See version log at the support page for more details.
• 15 November 2018: a new version of the DEBkiss e-book has been released at Leanpub.
• 15 August 2018: update to the ring test results for BYOM. See the guts e-book page.
• 18 January 2018: The long-awaited GUTS e-book is released in Version 1.0! More information.
• 24 July 2017: Update of the "Making sense of chemical stress" e-book. Improved readability and update with new developments.
• 24 June 2017: Sandrine Charles wrote an excellent review of my e-book in IEAM. http://dx.doi.org/10.1002/ieam.1931 
• 6 December 2016: New version of the DEBkiss book published. More information.
• 14 August 2015: small update to the technical document, adding a section on joint confidence regions.
• 11-12 August 2015: the e-books "Making sense of chemical stress" and "DEBkiss" have both been moved to the Leanpub publishing framework, and can be downloaded here and here, respectively. You can still get them for free, but also have the possibility to pay me (which will support future development of this and other books).
• 4 April 2015: small update of the DEBkiss book.
• 11 February 2015: New version of the DEBkiss book.
• 11 February 2015: Small update of the technical background document.
• 15 October 2014: New version 1.1 of the e-book "Making sense of chemical stress" over here. Added a chapter with two case studies.
• 15 June 2014. Version 1.1 of the e-book on DEBkiss is now available over here. Some minor changes.
• 18 May 2014. Version 1.0 of the e-book on DEBkiss is now available over here. Basically an embellished version of our JTB paper.
• 14 June 2013. Version 1.0 of the e-book now available for download over here. Small changes relative to Beta 1 version.
• 20 Sept. 2012. The first Beta 1 version of the technical document for the e-book over here.
• 9 April 2012. The first Beta 1 version of the free e-book "Making Sense of Chemical Stress" is available for download over here.

Software updates

• 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.
• 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.
• 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).
• 21 April 2022: Small update of the stdDEB-TKTD package to version Beta 4. See BYOM downloads page.
• 1 April 2022: Small update of BYOM to version 6.1. See BYOM downloads page.
• 14 January 2022: Official release of BYOM version 6.0. See BYOM downloads page. Also a tiny update of the DEBtox2019 package, that speeds up the EPx calculations for some exposure profiles.
• 13 January 2022: First (beta) release of a BYOM package for standard DEB in ecotoxicology: stdDEB_tktd. See BYOM downloads page.
• 6 December 2021: Extension of the reduced GUTS models for binary mixtures. Package is now available. See BYOM downloads page.
• 1 December 2021: small update for BYOM to beta 8. See BYOM downloads page.
• 29 November 2021: the main packages are now ready for BYOM v.6.0. See BYOM downloads page.
• 25 November 2021: small update to beta 7 of BYOM, available for download. The old version 5.2. still remains available as well for a while.
• 15 November 2021: beta 6 version of BYOM available for download. The old version 5.2. remains available as well for a while, since the old files (and the current packages) will not work anymore with the new BYOM version (in general, only small modifications are needed).
• 25 February 2021: new version 1.1 of the openGUTS software. See the openGUTS downloads page.
• 28 September 2020: spotted an error in the no-shrinking equations that are used in the DEBkiss and DEBtox2019 packages. This error could bias calibrations, though the simulations were fine. These packages are thus updated. This error does not affect the DEBtox_classic package since there is no option to prevent shrinking in that one. See the BYOM page.
• 26-27 September 2020: update of the BYOM tox-related packages. GUTS package: this update is especially a good idea when using the ODE-solver versions in the "experimental" folder. DEBtox2019 and DEBtox_classic packages: more efficient/accurate ODE solving for time-varying exposure. For all these packages: now allowing double time points in the exposure definition (as in openGUTS). See the BYOM page.
• 26 September 2020: update of the BYOM package. This update is especially a good idea when using the ODE-solver versions in the "experimental" folder. Also: now allowing double time points (as in openGUTS). See the BYOM page.
• 24 September 2020: update for BYOM to version 5.2. Modified the parameter-space explorer to work reasonable well for 6/7 free parameters (best left to experts). Further modifications for time-varying exposure, now allowing double time entries like in openGUTS and efficiency improved for hard-pulsed exposure (these changes also require updates for the packages that use glo.break_time ... working on that!). See the BYOM page.
• 30 August 2020: update for BYOM to version 5.1. Nothing spectacular, just fixed a few bugs and added a few bells and whistles. See the BYOM page.
• 2 June 2020: update for the BYOM package for classic DEBtox and DEBkiss to match it to BYOM 5.0. See the BYOM page.
• 29 May 2020: update for BYOM to version 5.0. This is a major update, with much new functionality (incl. the parameter-space explorer from openGUTS). See the BYOM page. Also an update of the GUTS and DEBtox2019 packages to make use of the new functionality!
  
• 2 Sept. 2019: update for BYOM and a new DEBtox2019 package (replacing DEBkiss-tox). See the BYOM page.
• 24 May 2019: update for the BYOM DEBkiss-tox package. This brings the package in line with v.2.0 of the DEBkiss e-book. See the BYOM page.
• 22 May 2019: update for the BYOM dose-response fitting package for classical ECx estimates at a single time point. See the BYOM page.
• 23 April 2019: small update of BYOM to v. 4.3. Few bugs fixed, but main change is explicit licensing information included. More details on the BYOM page.
• 7 September 2018: small update of BYOM to v. 4.2c and updated GUTS package v. 2.3. More details on the BYOM page.
• 13 August 2018: a quick update of BYOM to v. 4.2b. This was needed as I found some errors in conjunction with GUTS package. See BYOM page for details.
• 9 August 2018: updates of packages 'dose-response', 'acute Calanus', and 'support marecotox'. The dose-response package also has a nicer walkthrough. See BYOM page.
• 7 August 2018: new version of BYOM and the GUTS package, fixing the issue with the likelihood-region method. More details on the BYOM page.
• 28 June 2018: running simulations for GUTS, I am getting confirmation that the likelihood-region method (as implemented in BYOM) is yielding exaggerated confidence intervals on  model predictions. More details on the BYOM page.
• In 2018/2019 we will be producing a user-friendly software for GUTS. More information.
• 1 February 2018: New versions of BYOM and the GUTS package. See the BYOM page.
• 12 May 2017: Spotted a small error in BYOM when calculatin the intervals on LC50s with the likelihood-region method. This corrected in a small update to version 4.01.
• 27-28 April 2017: Release of BYOM 4.0 on the BYOM page. This is a major update, with many new features, but old scripts and packages will not work anymore! All packages have been updated; the two GUTS packages have been combined, and some have been renamed for clarity.
• 6 April 2017: Added the Beta 3 test version of BYOM 4.0 on the BYOM page. Also a new version of the GUTS package is included.
• 15 February 2017: Added a Beta test version of BYOM 4.0 on the BYOM page. This is still under testing, but feel free to play with it. Also, I added some warnings for users of profiling and slice sampling with BYOM.
• 5 January 2017: New version of the BYOM platform available for download.
• 7 April 2016. Small update of the BYOM modelling framework in Matlab.
• 25 and 27 August: another update of BYOM (sorry, found some small errors again). Additionally, an updated version of the DEBtox1 package (also demonstrating the improved population growth rate calculation). Updates of GUTS1 and DEBkiss1 packages. And ... a totally new package: DEBkiss_tox1, which is DEBkiss turned into a TKTD model. 29 August: update of the GUTS2 and DEBkiss2 package as well. All packages now have a walk through.
• 21 August: update of BYOM. Corrected a few errors and added some new functionality that will be demonstrated in future packages.
• 30 June 2015: update of BYOM. Corrected some errors and included a few extra options.
• 21 August: update of BYOM. Corrected a few errors and added some new functionality that will be demonstrated in future packages.
• 17 April 2015: update of DEBtoxM flavours Surv, GUTS and DEBtox. The DEB3 flavour is no longer offered.
• 3 April 2015: major update of BYOM. Some alternative optimisation methods are included, plus the possibility to fit parameters on log-scale. And ... the possibility to publish the code in Matlab (see the walkthrough of the BYOM code). Also a new version of the manual is provided.
• 18 February 2015: update of BYOM and the GUTS2 package. Main change is to avoid warnings with newer versions on Matlab (due to different way of dealing with interpolations), and the option to plot in black-and-white with different symbols (as in the DEBtoxM flavours).
• 2 January 2015: tiny 2.02 update for BYOM, and extended the BYOM manual, and gave a seperate entry on the BYOM download page.
• 17 December 2014: New version of the BYOM files to version 2.0. Major change is the possibility to have more than one data set per stage, and a brand new simulation engine. As of version 1.5, cleaner and simpler BYOM scripts. New packages for GUTS, DEBtox and some nice examples for the simulator! (Version 2.01 also has a small update to the manual).
• 29 November 2014: New version of the BYOM files. Major change is the removal of the calculation and plotting from the basic script into an engine script, which takes away a lot of complexity from the user.
• 1 May 2014. New version 1.5 of BYOM files posted over here. Also, a new package general package for DEBkiss.
• 29 Jan. 2013. New version 1.4 of the BYOM package, and the GUTS and DEBkiss packages over here.
• 29 Aug. 2012. New version 1.3 of the BYOM package over here.
• 30 June 2012. The flexible modelling platform BYOM is available over here.
• 19 May 2012. New versions of all flavours posted over here. New versions were needed because of an error in the calculation of the likelihood function for replicated graded data (with different number of individuals per replicate). Further, changes are made to increase flexibility and ease of operation.

Recent publications

• 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.
• 5 May 2022: Paper published on applying DEBkiss to early-life stages of cleaner fish (https://doi.org/10.1016/j.ecolmodel.2022.110005 Open Access). Part of the StartRens project.
• 11 June 2021: our MultiCop paper on growth in the copepod Tigriopus brevicornis has been accepted for publication in J. Sea Res. No DEB analysis yet, but highly relevant for DEB-based studies of copepods. Preproof available via the DOI.
• 4 May 2021: discussion paper on the use of reproduction data in DEB-based models. This is a must read for all TKTD modellers that work with reproduction data! A preprint is available at bioRxiv. Paper has been accepted 7 June for publication in IEAM.
• 27 January 2021: New paper from Sylvain Bart on mixtures with GUTS in ES&T, see https://doi.org/10.1002/ieam.4333.
• 9 January 2021: Best wishes for the new year! Forget to announce a new paper on the algorithm used in openGUTS for calibration and error propagation. It was accepted in August, but still only available in 'early view': DOI: 10.1002/ieam.4333
• 11 Dec. 2019: new paper presenting an updated simplified DEB model for ecotoxicology (based on DEBkiss, compound parameters). You can download this paper for free till 29 Jan, 2020 from https://authors.elsevier.com/a/1aCrg15DJ%7ExMQu. See https://doi.org/10.1016/j.ecolmodel.2019.108904.
  
• 21 May 2019: new paper on effects of hydrogen peroxide on shrimps, including GUTS analysis with pulsed exposure. See https://doi.org/10.1016/j.ecoenv.2019.05.045.
• 27 August 2018: the EFSA opinion on TKTD models is now available over here. This opinion will be pivotal for the application of GUTS and DEBtox in environmental risk assessment (in particular for pesticides).
• 9 January 2019: new paper on automated high-throughput measurements of body size (which could really facilitate DEB(tox) application in the future). Open access. Note that this is my 100th (co-)authored paper ;-).
• 8 August 2018: new paper out on modelling bioenergetics in early life stages of cod: 50-day free download link.
• 27 March 2018: new paper from the GUTS project on evaluating the quality of toxicokinetic-toxicodynamic models. IEAM. https://doi.org/10.1002/ieam.2026 
• 1 November 2017: New paper from the GUTS project: Physiological modes of action across species and toxicants: the key to predictive ecotoxicology. Environ. Sci.: Processes Impacts. Open Access: https://doi.org/10.1039/C7EM00328E 
• 14 June 2017: New paper from the EnergyBar project: Jager T et al. Dynamic links between lipid storage, toxicokinetics and mortality in a marine copepod exposed to dimethylnaphthalene. Accepted in Environ Sci Technol http://dx.doi.org/10.1021/acs.est.7b02212
  
• 1 January 2017: Our GUTS paper has just hit 100 citations in Web of Science! DOI 10.1021/es103092a.
• 29 November 2016: New paper from the EnergyBar project: Jager T et al. (2017). Modelling the dynamics of growth, development and lipid storage in the marine copepod Calanus finmarchicus. Marine Biology 164:1. DOI 10.1007/s00227-016-3030-8 (Open Access!)
• October 2016: The book "Marine Ecotoxicology: current Knowledge and Future Issues" has just come out. I wrote a chapter "Dynamic modelling for uptake and effects of chemicals" in there. The book can obtained from Elsevier or your favourite bookstore, or via ScienceDirect. The support page for my chapter can be found over here.
• My paper "Making sense of ecotoxicological test results: Towards application of process-based models" has just hit 100 citations in Web of Science. http://dx.doi.org/10.1007/s10646-006-0060-x 
• 4 August 2016: Paper from the NETS 2014 conference. Jager T (2016). Predicting environmental risk: a road map for the future. J. Toxicol. Environ. Health. 79(13-15):572-584. http://dx.doi.org/10.1080/15287394.2016.1171986 
  
• 4 August 2016: Paper from the NETS 2014 conference. Hansen BH et al. (2016). Acute toxicity of dispersed crude oil on the cold-water copepod Calanus finmarchicus: elusive implications of lipid content. J. Toxicol. Environ. Health. 79(13-15):549-557. http://dx.doi.org/10.1080/15287394.2016.1171981 
  
• Ashauer R et al. (2016). Modelling survival: exposure pattern, species sensitivity and uncertainty. Sci Rep 6:29178 http://dx.doi.org/10.1038/srep29178
• Jager T, Ravagnan E, Dupont S (2016). Near-future ocean acidification impacts maintenance costs in sea-urchin larvae: identification of stress factors and tipping points using a DEB modelling approach. Untill 23 Nov. 2015, it can freely be downloaded using this link: http://authors.elsevier.com/a/1RpNm51aUK0l2
• Jager T, Altin D, Miljeteig C and Hansen BH (2016). Stage- and sex-dependent sensitivity to water soluble fractions of fresh and weathered oil in the marine copepod Calanus finmarchicus. Environ Toxicol Chem 35(3):728-735. http://dx.doi.org/10.1002/etc.3237
• Jager T, Ravagnan E (2015). Parameterising a generic model for the dynamic energy budget of Antarctic krill, Euphausia superba. Mar Ecol Progr Ser 519:115-128 DOI 10.3354/meps11098.
• Jager T, Salaberria I, Hansen BH (2015). Capturing the life history of the marine copepod Calanus sinicus into a generic bioenergetics framework. Ecol Mod 299:114-120. DOI 10.1016/j.ecolmodel.2014.12.011 
  
• Just appeared: the 2014 special issue on DEB research in the Journal of Sea Research. Find it here.
• Jager T et al. (2014). Dynamic modeling of sub-lethal mixture toxicity in the nematode Caenorhabditis elegans. Environ. Sci. Technol. 48:7026-7033 DOI 10.1021/es501306t
• Zimmer et al (2014). Metabolic acceleration in the pond snail Lymnaea stagnalis? J Sea Res 94:84-91 DOI 10.1016/j.seares.2014.07.006
• Martin et al (2014). Limitations of extrapolating toxic effects on reproduction to the population level. Ecol. Appl. 24(8):1972-1983 DOI 10.1890/14-0656.1
• Jager T (2014). Reconsidering sufficient and optimal test design in acute toxicity testing. Ecotoxicology 23(1):38-44 DOI 10.1007/s10646-013-1149-7 
  
• Barsi et al (2014). Considerations for test design to accommodate energy-budget models in ecotoxicology: a case study for acetone in the pond snail Lymnaea stagnalis. Environ. Toxicol. Chem. 33(7):1466-1475 DOI 10.1002/etc.2399
• Jager et al (2014) Dynamic energy budgets in population ecotoxicology: applications and outlook. Ecol. Mod. 280:140-147 DOI 10.1016/j.ecolmodel.2013.06.024

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