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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.

Error in v1.0. The IT calculations use a shortcut that does not work in all cases. This error will affect IT calibrations 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). It will also affect IT LPx predictions when the exposure scenario is specified with a crude resolution (the hourly resolution of FOCUS profiles will lead to negligible errors). This error is repaired in the update of the Matlab version, to v. 1.1. Download a PDF document explaining this error in detail. (posted 19 May 2020). This error is repaired in the update of the standalone and Matlab version, to v. 1.1.

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.



Screenshot
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openGUTS standalone Windows executable

Screenshot prototype small
openGUTS in Matlab

News


  • 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.

For old news items, click here.



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