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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.

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.

First real error found. 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 2019)



Screenshot
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openGUTS standalone Windows executable

Screenshot prototype small
openGUTS in Matlab

News


  • 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).

For old news items, click here.



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