Development of user-friendly, robust GUTS software

URL	http://cefic-lri.org/projects/eco39-review-ring-test-and-guidance-for-tktd-modelling/ dedicated website: http://openguts.info/
Funding	CEFIC/LRI ECO 39.2
Duration	2018-2019
Project leader	University of York, UK (Dr. Roman Ashauer)

Description

The additional information and insight gained through the application of toxicokinetic-toxicodynamic (TKTD) modelling can strengthen the environmental risk assessment of chemicals in consumer products or plant protection products (PPPs). For the endpoint survival the most suitable and powerful tool is currently the General Unified Threshold model of Survival (GUTS), which consists of two complimentary models: GUTS-SD (stochastic death) and GUTS-IT (individual tolerance). GUTS has been submitted as part of the environmental risk assessment of PPPs, but it can also be used in the context of REACH. In order to ease the use of GUTS and increase trust and acceptability we recently released an extensive e-book (Jager & Ashauer, 2018) and carried out a ring-test of different implementations of GUTS (CEFIC-LRI ECO39).

The results from CEFIC-LRI ECO39 suggest that we need to develop a user-friendly, robust GUTS software that is open-source and freely available. None of the currently available software implementations fulfils these four essential criteria for uptake in the regulatory community (user-friendly, robust, open-source, freely available). Most implementations that are freely available (e.g., Matlab, R, Mathematica, Python) are not user-friendly because they require (basic) programming skills to use, and they are not robust in the sense that too many settings are open to user choice. Those implementations that have a user-friendly GUI (e.g., DELPHI, EasyGUTS) are owned by a company, and not freely downloadable (though EasyGUTS applies open source R scripts), which may impede uptake by regulators.

The software will be named openGUTS, and will follow the workflow as laid down in the 2018 EFSA Scientific Opinion on TKTD models for use in aquatic risk assessment of pesticides. However, the software can be applied for different purposes as well, including derivation of LCx,t values (for constant and time-varying exposure) and survival analysis for scientific purposes.

Objectives:

1.    Develop a user-friendly, robust software for GUTS with basic functionality
2.    Test and benchmark the GUTS software
3.    Produce a basic user manual for the GUTS software
4.    Make source-code and software freely available

Version 1 of the standalone for openGUTS was made available in December 2019 on the dedicated website: http://openguts.info/. The Matlab version that served as the prototype was already available in May 2019 from the same site.

My role

Contribute to the objectives listed above, and developing a Matlab prototype. The coding of the software in C++ will be performed by Dr. Magnus Wang and colleagues (WSC Scientific GmbH).

Output: Software and documentation

The Matlab version (previously the 'prototype') for the software (including a short manual and background documentation) is available for download from the dedicated website: http://openguts.info/. (17 May 2019).
The standalone openGUTS (including a user manual and background documentation) is now also available from the dedicated website: http://openguts.info/.(10 Dec. 2019).
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Output: Publications (as first or co-author)

Output: Presentations (as presenter and as contributor)

User-friendly software for survival modelling with GUTS. Jager T, M Wang and R Ashauer. Poster presentation at the at the 29th SETAC Europe conference in Helsinki, Finland, 26-30 May 2019 (presented by Roman). Abstract. Handout.
OpenGUTS, user-friendly software for survival modelling. Jager T, M Wang and R Ashauer. Poster presentation at the 30th SETAC Europe conference held in virtual space, 3-7 May 2020. Abstract. Handout.

Output: Related publications (as first or co-author)

Jager T (2017). Comment on “Robust Fit of Toxicokinetic–Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests”. Environ, Sci, Technol. 51(14):8200-8201. http://dx.doi.org/10.1021/acs.est.7b02001
Jager T and Ashauer R (2018). Modelling survival under chemical stress. A comprehensive guide to the GUTS framework. Version 1.0. Toxicodynamics Ltd., York, UK. Available from Leanpub: https://leanpub.com/guts_book, More information.
Jager T and Ashauer R (2018). Modelling survival under chemical stress. A comprehensive guide to the GUTS framework. Version 2.0. Toxicodynamics Ltd., York, UK. Available from Leanpub: https://leanpub.com/guts_book, More information.
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Output: Related presentations (as first or co-author)

openGUTS v1.1 - Update of a user-friendly open-source software for GUTS-RED modelling in environmental risk assessment. Singer A, B Rall, D Nickisch, R Ashauer and T Jager. Poster presentation for the 31st SETAC Europe conference in virtual space, 3-6 May 2021. (Note: this update was funded by Syngenta).

Planned course with the software

To bring people up to speed with operating the GUTS software, and interpreting its output, we intend to offer regular courses (not part of this project). More information can be found at: http://openguts.info/courses.html.

Roman Ashauer and myself provided a half-day short course at SETAC-Europe (in virtual space) in May 2020. This was turned into a do-it-yourself on-lince course that is now available at LeanPub.

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