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Supporting mechanistic modelling for survival

DEBtox Researc



Welcome to the openGUTS information pages


OpenGUTS is a user-friendly software to perform analyses with GUTS: the General Unified Threshold model for Survival. GUTS is the leading toxicokinetic-toxicodynamic framework for the endpoint survival (and other non-reversible all-or-nothing effects). Version 1.0 was released in December 2019, followed by Version 1.1. in February 2021.

This site hosts the software itself, as a standalone Windows executable, with manuals and background documentation. Since openGUTS is (as the name implies) open source, also the source files can be obtained here. Additionally, you can download the Matlab version, which served as the blueprint for the standalone version. The Matlab version has basically the same functionality, and can be easily adapted or extended to perform customised analyses. Finally, we provide (links to) further information on openGUTS and GUTS.

The main features of the software are:
  1. Open and free: the software is open source and freely downloadable. The fully-functional Matlab version that served as the prototype is also available.
  2. User-friendly: fit models and derive confidence intervals without requiring user interaction (e.g., no need for starting values).
  3. Robust: always find the global optimum and relevant intervals, even for awkward data sets.
  4. Flexible: allow time-varying exposure, missing data, simultaneous fitting on multiple data sets, etc.
  5. Efficient: rapid screening of exposure profiles (e.g., FOCUS output) by batch processing.
  6. Supportive: the software follows the workflow as laid down in the 2018 EFSA opinion on TKTD models.



Screenshot
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openGUTS standalone Windows executable

Screenshot prototype small
openGUTS in Matlab

Announcements



March 2024. Update of the openGUTS standalone to v1.2. The openGUTS standalone has been updated to fix an error message appearing for specific data sets (with a missing data point for survival at the last time point, with time-varying exposure) and to provide additional time points for LCx estimates. EFSA's 2023 bee guidance requires GUTS to be used for prediction of LCx (or LDx) after 10 and 27 (and in some cases 182) days. These time points are now automatically also generated by openGUTS. The Matlab version is updated to v.1.2 as well (to keep the version numbering matched with the standalone, and to show the additional LCx time points by default). See downloads page.

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.

For old announcements, click here.

Important warnings/errors



Summary of errors in older versions (details on the downloads page).

Error in v1.0. The IT calculations used a shortcut that did not work in all cases. This led to errors for time varying exposure, where the exposure scenario includes episodes of linear decrease over time (for constant exposure and block pulses, it will be fine). Repaired in the update of the standalone and Matlab version, to v. 1.1.

Matlab R2023a throws errors (v1.1 and earlier). The newest version of Matlab does not allow the cell-array format for name-value pairs anymore. The update to v1.1a solves this issue (6 April 2023). However, the new version will no longer support Matlab R2014b-R2016a.

OpenGUTS standalone produces error for missing observation at last time point. The openGUTS standalone (v1.0 and v1.1) throws an error when using a data set for survival, with time-varying exposure, in which there are one or more missing values at the last time point. The Matlab version does not have this problem. A workaround is available (see downloads page). Fixed in the update to v.1.2.

News


  • 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.

For old news items, click here.



The openGUTS project, www.openguts.info. This site is maintained by Tjalling Jager, email: tjalling (at) debtox.nl