9th International Tele-course on DEB: description
This is a 5-week tele-course on "Dynamic Energy Budget theory for metabolic organisation", otherwise known as DEB theory, where biology, chemistry, physics and mathematics all come together. The course focuses on chapters 1-4 of the "DEB-book", by S.A.L.M. Kooijman, which covers the principles of the theory and univariate DEB models. Each week, we will study a section of the book.
The spring 2017 tele-course is now over. Interested to follow a DEB course ?
A specially edited version of the first four chapters of the book will be provided online at the start of the course (free of charge). The emphasis should be on the concepts, not on the technical details.
The tele-course is primarily meant for graduate students, but advanced undergraduates as well as scientists are also welcome. The course will be of interest for persons with a background in biology, mathematics, engineering, chemistry or physics with an interest in the logic behind the quantitative aspects of the metabolic organisation of living systems.
A summary of concepts is already available, that follows all the sections of the book, while avoiding technicalities and biological details. It is recommended to first read a chapter of this summary before reading the corresponding chapter of the DEB book.
It is not essential that you understand each step in the mathematical derivations of the formulae. Continue to read if you do not understand a particular formula. Ask your group members for help. Pose questions on the discussion forum. This also applies for biological and chemical questions.
We want to stimulate a critical attitude. Please do not take anything for granted and ask yourself:
- Do I understand this?
- Do I agree with this?
- Where is the origin of my disagreement?
Discussions and formulation of questionsDiscussions with group or course members can serve a number of functions. Apart from being entertaining, it can help you to understand a problem. Please do not be shy, or afraid that you might look stupid. Subjects like the one of the course requires a large number of skills to deal with them effectively. No one masters all the required skills. The art of science is more about asking the right questions, than about looking for the proper answers. This is why the course puts emphasis on the careful formulation of questions. We will form local groups, that come together (possibly via Skype or google hangouts) once a week to discuss orally, and to complement the discussions on the discussion board. If you wish to form a group or alternatively are looking for a group then please contact Starrlight Augustine.
Discussion forumEach week, participants have the responsibility of each posting at least one well formulated question in the Discussion forum. Participants should also post summary of key findings and qustions raised during the local discusion groups.
Quizz and ExcericesEach week, there will be a set of quizz and exercises. The quizzes are meant to provide an active understanding of the underlying concepts. The excercices help get a numerical feel for the behaviour of the models that result from the theory. The freely downloadable matlab and octave package DEBtool has been written to minimize the effort to do the exercises. The package has script-files for each of the >100 figures of the DEB book. If you run the file, DEBtool produces a figure that is close to the corresponding figure in the book, and you can see in the file how the data are set, which functions are used, how the parameters are estimated, etc, with a lot of comments between de code.
Essays and data-collectionParticipants who only follow the tele-part are supposed to complete the course with an essay on (an application of) DEB theory that will be made available for all, and will be discussed by the participants who do follow the practical part.
Participants who will also follow the practical part are supposed to
- write a "discussion topic" (about half a page). The partipant will present the topic to the others during a "Group discussion" session. The topic preferably relates to potential DEB applications in your own research, where you can pose questions about problems that you expect to meet in such applications. We want to stimulate a critical attitude and the essay might argue against the DEB theory and discuss alternatives.
- prepare a my_data-file for a species of their choice, which will be used to estimate DEB-parameters, and will be added to the add-my-pet collection. So we only ask to collect data (e.g. from the literature) prior to your travel; the parameter estimation will be done on Texel, with help of experienced people in this art
Suggestions and commentsWe like to stimulate a constructive attitude, and welcome very much any suggestions and comments for improvement of the course, the book and/or DEBtool. We cannot garantee that all suggestions will be implemented in the future, but they will be considered carefully).
The nature of the suggestions and comments can be very diverse.
The huge subject of the DEB theory does not allow a complete overview of the relevant literature.
It is easy to miss important results that have been published, and pointing to those references can be of great help, especially if you indicate why you think that they matter.
The suggestions can also be on the numerical procedures used by DEBtool, for instance, if you know of better alternatives.
This tele-course is supported by the Norwegian Science council in connection with the MARINFORSK project (NFR 255295) "FRamework for integrating Eco-physiological and Ecotoxicological data into marine ecosystem-based management tools".