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Supporting mechanistic modelling for survival

DEBtox Researc

Old news from home page

  • 7 June 2024: updated the openGUTS manual for the standalone. Added some extra explanation for entering time-varying exposure scenarios, and added a little more explanation here and there. Also updated to reflect the changes for Version 1.2. See download page.
  • 22 April 2024: the GUTS e-book was positively reviewed in IEAM.
  • The Autumn School on TKTD modelling is running again by end of 2024 (Oct/Nov) with an on-line and on-site (in Denmark) part. This is a more general course on TKTD modelling, with most focus on DEBtox models. However, GUTS models will also be treated (especially in the on-line part). Information on (previous and planned runs of) this course. or go directly to the official course page at Copenhagen University.
  • 20 March 2024: release of an update of the openGUTS standalone to v.1.2 so fix an error message for (very) specific data sets and to calculate additional LCx values to support risk assessment for bees following the EFSA guidance. See download page. The Matlab version has also been updated to v.1.2 (it did not suffer from the error in the standalone, but the additional LCx are now, by default, produced).
  • 15 October 2023: added a bit more explanation on the error produced by the standalone for missing observations at the last time point. Also included an example of a data set that causes problems, and how to split up the data set as workaround. See download page.
  • 6 April 2023: new version of the Matlab version of openGUTS. This is a small update that makes openGUTS run error-free under Matlab R2023a. No changes to the calculation engine, only to the calls for plotting. See download page and the version log for details.
  • 3 March 2023: new installation file for version 1.1 of the openGUTS standalone has been released. See download page. This version does not trigger the (false-positive) trojan warning that was thrown by some virus scanners with the previous version. See more detailed explanation in the announcements.
  • Heads up! At SETAC Europe 2023 (30 April), there are two short courses dealing with GUTS: general and bee-specific.
  • 25 February 2021: Version 1.1 of the openGUTS standalone has been released. See download page. Over the next days, the downloads for the manual and source code will be updated as well.
  • 12 February 2021: The paper on the openGUTS algorithm is now available in final format, and included into a volume: DOI: 10.1002/ieam.4333
  • 9 January 2021: Best wishes for the new year! Forgot to provide the link to the new paper on the algorithm used in openGUTS for calibration and error propagation. It is still only available in 'early view': DOI: 10.1002/ieam.4333
  • 29 August 2020: The general statistical framework and the automated optimisation algorithm as developed for openGUTS have been described in detail in a manuscript, including an extensive supporting information. This manuscript has been accepted for publication in IEAM; a link will be provided here when the paper is available on-line.
  • 26 May 2020: update of the Matlab version of openGUTS. This version 1.1 repairs the error that was discovered (the standalone still has this error, so do take a look at the dedicated document for this error). See download page.
  • 20 May 2020: document explaining the error linked to the error warning (on this page above, and on the downloads page). Also updated the 'list of known issues' with this error, and a few more small GUI bugs.
  • 20 May 2020: openGUTS on-line, completely-DIY, short course is now available. See course page.
  • 19 May 2020: error found in the IT calculations. More information and workarounds/repairs coming soon.
  • 10 May 2020: small update to the interpretation document, adding a section with a brief description of the model and its parameters (and what they do). Furthermore some small textual changes and error repair.
  • 21 April 2020: updated the "list with known issues" with a few small bugs and additional items for the wishlist. See download page.
  • We will provide a half-day short course on the openGUTS software at the virtual SETAC Europe in May 2020. See the SETAC web page, and scroll down to "TC11 - Introduction to Effect Modelling with the User-Friendly Software OpenGUTS." We need to see how SETAC will support the short courses on-line, so more information will follow. There will also be a poster on openGUTS at this conference (ID 4.07P.4).
  • 12 December 2019: added the source code and an updated version of the design document. See download page.
  • 10 December 2019: version 1.0 of the standalone is available for download (with manual, but not yet with the source code). Furthermore, a new version of the Matlab version (previously known as the prototype). Also updates of the manuals and for several of the background documents. See download page.
  • 4 November 2019: update for the openGUTS prototype in Matlab, and small update to its manual and design doc. See download page.
  • 18 Sept. 2019: the planned course on openGUTS in October 2019 has been cancelled. Unfortunately, we had insufficient registrations.
  • 30 Aug. 2019: small update to the design and interpretation documents on the download page.
  • 22 July 2019: update of the test document (includes ring test but also additional data sets with difficult properties). See download page.
  • 12 July 2019: another update of the prototype, solving a few minor bugs and adding some nice features (wait bars and error boxes). See download page.
  • 23 May 2019: tiny update of the prototype. It now includes the same set of exposure profiles as used in the EFSA scientific opinion. See download page.
  • 22 May 2019: added a walkthrough through the code of the prototype (made with Matlab's publish option).
  • 21 May 2019: a number of background documents are already downloadable.
  • 17 May 2019: first release of the openGUTS prototype in Matlab. See download page.
  • 14 May 2019: the website is online! Not all pages are completely filled at this point ....

Old announcements from home page

Feb. 2021. New version of the standalone launched (v1.1). The openGUTS standalone has been updated: the error has been fixed and extended batch capabilities have been included.

March 2023. New installation file for the standalone (v1.1). The installation file for the openGUTS standalone has been updated: the version of Feb. 2021 triggered a (false-positive) trojan warning by some virus scanners. We changed the packaged file docto.exe (which creates the reports) to its latest version (v. 1.8), which does not trigger this virus warning. The code for the openGUTS calculations has not changed, and there was no new compilation of the C++ code. The only change is thus a re-packaging with the new docto.exe. Downside is that the line spacing in the produced reports is increased, which does not look so nice. However, that is easily modified manually in the Word version of the report that is produced. If you have successfully installed openGUTS v. 1.1 with the previous installer, there is no need to update your installation.

Oct. 2023. OpenGUTS does not provide LCx at time points needed for EFSA's bee guidance. EFSA's 2023 bee guidance requires GUTS to be used for prediction of LCx (or LDx) after 10 and 27 days. However, these time points are not, by default, generated by openGUTS. This is easily solved in the Matlab version. In the engine folder, there is the function initial_setup.m. In Block 4 of the code (Line 159), the vector SETTINGS_PRED.T_LCx is defined, which represents the time points at which LCx are calculated. This can be modified in any way that you like, e.g., just adding 10 and 27 in there. For the standalone, this requires a new version. We will take up this point with the next update.

The openGUTS project, This site is maintained by Tjalling Jager, email: tjalling (at)