Using openGUTS for survival analysis (The Course)
Using openGUTS for survival analysis
Short course introducing you to TKTD analyses of survival data with the user-friendly openGUTS software
Toxicokinetic-toxicodynamic models are gaining interest for environmental risk assessment of chemicals. The GUTS framework is the leading approach for the endpoint survival (or immobility). GUTS was recently judged by EFSA to be "ready for use" for risk assessment of pesticides in the EU. This short course is a modified version of the course we gave at the 2020 virtual SETAC meeting. It gets you acquainted with the user-friendly openGUTS software (see http://openguts.info), which allows you to analyse survival data over time in a mechanistic manner, and to use that analysis for forward predictions (incl. uncertainty propagation).
This course was originally intended to have a 4-hour workload. However, we now added some quizzes and suggest reading materials to provide you with a better theoretical background. Some background is essential to interpret the model's output (especially for more complex cases). However, we focus on the concepts, and spare you the math (though we will point you to an extensive description, should you be interested). Of course, you can take as much time as you like, or need, on this course, but expect to spend somewhere between 4 and 8 hours. If you are unfamiliar with GUTS and survival modelling, you probably need to take some more time: this course focusses on how to use the openGUTS software, and does not deeply go into the background and model details. Reading material is suggested in the course, in the form of chapters from our dedicated e-book (which can be obtained free of charge). Make sure you read the suggested chapters first.
Unlike the short course at SETAC, the instructors are not available to answer your questions or to provide feedback. However, we appreciate your feedback, especially if you run into software bugs (but don't expect a help desk). We have a series of exercises for you, guiding you through the openGUTS workflow with case studies. Questions are raised for you to think about; many of these questions do not have a simple unique answer. Answers/considerations are available in the course material. These exercises also contain quizzes that you can use to test your understanding, and that is used to decide if you put in the effort to pass the course (and receive a certificate).
Now, we love to teach, but we have little experience in fully on-line courses and are certainly no experts in video recording/editing. So things are a bit rough! Nevertheless, we are confident that this material is useful to quickly find your way in openGUTS and to learn to perform your own survival analyses (and interpret what comes out).
We do charge a small fee for access to this course. Part of this fee is used to keep Leanpub happy (they deserve to earn something for providing this platform), and a part goes to us as instructors (which keeps us happy and motivated to improve this course and to create new ones). If you live in a very-low-income country and this fee is an issue, please contact Tjalling Jager at DEBtox Research. If you like to take this course with a number of your colleagues, also get in touch. We might be able to set up an agreement that includes interactions with one or both of the instructors to answer questions and discuss issues that pop up (at additional cost, of course). Also note that if you feel that the course was not worth the fee you paid you can get a refund under Leanpub's 45-day "100% Happiness Guarantee".
- Note that the standalone openGUTS software works under Windows only. If you are handy with Matlab, you can use the Matlab version of openGUTS, which will work on any platform that supports Matlab. However, that version is less user friendly, so some more effort will be needed from your side.
- The course material assumes that you have MS Word and MS Excel installed. If you do not have Word, you will not be able to create output reports with openGUTS (so you have to work with the screen output). If you do not have Excel, you may have trouble accessing the data sets and/or copying the data into openGUTS. Best contact Tjalling for assistance.
- When using Explorer, the quizzes from this course look garbled and don't seem to function properly. On Firefox, Edge and Chrome they seem to be just fine. So when you encounter problems, please try a different browser.
- Basics of GUTS
- Risk assessment with GUTS
- Installing and working with openGUTS
- Notes on the exercises and quizes
- Doing the exercises
- Quizes to check your answers
- Background of the data sets
- Exercise 1: 24-DCP case study
- Entering data
- Exercise 2: closer look at 24-DCP case study
- Different treatment of background hazard
- Reverse the role of both data sets
- Calibrate on both data sets
- Exercise 3: do the DNOC case study by yourself
Mechanistic modelling is an under-utilised tool in ecotoxicology and stress ecology. It is my passion to promote these models through (applied) scientific projects, providing software solutions, teaching in courses, presentations at conferences, and through writing e-books. The models that I specialise in are so-called toxicokinetic-toxicodynamic (TKTD) models; in particular, models for survival (the GUTS framework) and sublethal effects (based on Dynamic Energy Budget - DEB - theory). These models are based on a rigorous simplification of biological complexity, and have the power to explain (and predict) life-history traits of organisms (e.g., growth, reproduction and survival) over time. Especially when considering exposure to stressors, such dynamic models are indispensable to make sense of the data.
I hold an MSc and PhD in Biology, and have been a professional modeller since 1992, working almost exclusively on DEB- and GUTS-based TKTD modelling since 2002. Currently, I run my own private company 'DEBtox Research'.
What makes man-made chemicals dangerous to the environment? Which species are most vulnerable? How can we improve risk assessment of chemicals? To answer these questions I combine field and laboratory experiments with theory and computation. The models that I specialise in are so-called toxicokinetic-toxicodynamic models and I have been working in this field since 2004.
I hold a PhD in Environmental Science and until 2018 I worked as Associate Professor in the Environment Department at the University of York (UK) as well as Director of Toxicodynamics Ltd. Since 2019 I work as Eco-modelling lead at Syngenta Crop Protection AG, Switzerland. You can find out more at https://www.ecotoxmodels.org/.
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