Using openGUTS for survival analysis (The Course)
Course Info
This course includes 10 attempts.
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".
Warnings
- 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.
Course Material
- Introduction
- 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
- Calibration
- Validation
- Prediction
- 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
Instructors
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/.
Do Well. Do Good.
Authors have earned$11,845,077writing, publishing and selling on Leanpub, earning 80% royalties while saving up to 25 million pounds of CO2 and up to 46,000 trees.
Learn more about writing on Leanpub
The Leanpub 60-day 100% Happiness Guarantee
Within 60 days of purchase you can get a 100% refund on any Leanpub purchase, in two clicks.
See full terms
Free Updates. DRM Free.
If you buy a Leanpub book, you get free updates for as long as the author updates the book! Many authors use Leanpub to publish their books in-progress, while they are writing them. All readers get free updates, regardless of when they bought the book or how much they paid (including free).
Most Leanpub books are available in PDF (for computers) and EPUB (for phones, tablets and Kindle). The formats that a book includes are shown at the top right corner of this page.
Finally, Leanpub books don't have any DRM copy-protection nonsense, so you can easily read them on any supported device.
Learn more about Leanpub's ebook formats and where to read them
Top Books
The Hitchhiker's Guide to DFIR: Experiences From Beginners and Experts
Barry Grundy, Tristram, John Haynes, ApexPredator, Andrew Rathbun, Kevin Pagano, Victor Heiland, Nisarg Suthar, Guus Beckers, and Jason WilkinsA first-of-its-kind crowdsourced Digital Forensics and Incident Response (DFIR) book by the Digital Forensics Discord Server members to share knowledge!
OpenIntro Statistics
David Diez, Christopher Barr, Mine Cetinkaya-Rundel, and OpenIntroA complete foundation for Statistics, also serving as a foundation for Data Science.
Leanpub revenue supports OpenIntro (US-based nonprofit) so we can provide free desk copies to teachers interested in using OpenIntro Statistics in the classroom and expand the project to support free textbooks in other subjects.
More resources: openintro.org.
Ansible for DevOps
Jeff GeerlingAnsible is a simple, but powerful, server and configuration management tool. Learn to use Ansible effectively, whether you manage one server—or thousands.
Maîtriser Apache JMeter
Philippe Mouawad, Bruno Demion (Milamber), and Antonio Gomes RodriguesToute la puissance d'Apache JMeter expliquée par ses commiteurs et utilisateurs experts. De l'intégration continue en passant par le Cloud, vous découvrirez comment intégrer JMeter à vos processus "Agile" et Devops.
If you're looking for the newer english version of this book, go to Master JMeter : From load testing to DevOps
Software Architecture for Developers
Simon BrownA developer-friendly, practical and pragmatic guide to lightweight software architecture, technical leadership and the balance with agility.
Functional Event-Driven Architecture
Gabriel VolpeExplore the event-driven architecture (EDA) in a purely functional way. Learn to design and develop distributed systems that scale. Identify common design patterns in such systems.
Take your functional programming skills to the next level by joining me in developing a distributed system powered by Apache Pulsar and Fs2 streams, all in Scala 3!
R Programming for Data Science
Roger D. PengThis book brings the fundamentals of R programming to you, using the same material developed as part of the industry-leading Johns Hopkins Data Science Specialization. The skills taught in this book will lay the foundation for you to begin your journey learning data science. Printed copies of this book are available through Lulu.
Concurrency with Modern C++
Rainer GrimmC++11 is the first C++ standard that deals with concurrency. The story goes on with C++17, C++20, and will continue with C++23.
I'll give you a detailed insight into the current and the upcoming concurrency in C++. This insight includes the theory and a lot of practice.
Thinking with Types
Sandy MaguireThis book aims to be the comprehensive manual for type-level programming. It's about getting you from here to there---from a competent Haskell programmer to one who convinces the compiler to do their work for them.
Biological Modeling
Phillip CompeauIn this ebook, learn why zebras have stripes, why SARS-CoV-2 spread so quickly around the planet, how to train a computer to classify cellular images, and more!
Top Bundles
- #1
CCIE Service Provider Ultimate Study Bundle
2 Books
Piotr Jablonski, Lukasz Bromirski, and Nick Russo have joined forces to deliver the only CCIE Service Provider training resource you'll ever need. This bundle contains a detailed and challenging collection of workbook labs, plus an extensively detailed technical reference guide. All of us have earned the CCIE Service Provider certification... - #2
Modern C++ Collection
3 Books
Get All about Modern C++C++ Standard Library, including C++20Concurrency with Modern C++, including C++20C++20Each book has about 200 complete code examples. Updates are included. When I update one of the books, you immediately get the updated bundle. You can expect significant updates to each new C++ standard (C++23, C++26, .. ) and also... - #3
Software Architecture
2 Books
"Software Architecture for Developers" is a practical and pragmatic guide to modern, lightweight software architecture, specifically aimed at developers. You'll learn:The essence of software architecture.Why the software architecture role should include coding, coaching and collaboration.The things that you really need to think about before... - #4
Practical FP in Scala + Functional event-driven architecture
2 Books
Practical FP in Scala (A hands-on approach) & Functional event-driven architecture, aka FEDA, (Powered by Scala 3), together as a bundle! The content of PFP in Scala is a requirement to understand FEDA so why not take advantage of this bundle!? - #6
Pattern-Oriented Memory Forensics and Malware Detection
2 Books
This training bundle for security engineers and researchers, malware and memory forensics analysts includes two accelerated training courses for Windows memory dump analysis using WinDbg. It is also useful for technical support and escalation engineers who analyze memory dumps from complex software environments and need to check for possible... - #8
Learn Git, Bash, and Terraform the Hard Way
3 Books
Learn Git, Bash and Terraform using the Hard Way method.These technologies are essential tools in the DevOps armoury. These books walk you through their features and subtleties in a simple, gradual way that reinforces learning rather than baffling you with theory. - #9
Quality Software
11 Books
The Quality Software Bundle is for managers, would-be managers, and any of us who find themselves being managed and confused. This comprehensive bundle covers the entire span of software development approaches, from hacking through waterfall, cascade, prototyping, Iterative enhancement, reusable code, off-the-shelf, to Agile teams. The bundle... - #10
Static Analysis and Automated Refactoring
2 Books
As PHP developers we are living in the "Age of Static Analysis". We can use a tool like PHPStan to learn about potential bugs before we ship our code to production, and we can enforce our team's programming standards using custom PHPStan rules. Recipes for Decoupling by Matthias Noback teaches you in great detail how to do this, while also...