Practical Modelling for Biologists

Faculteit | Science and Engineering |
Jaar | 2022/23 |
Vakcode | WMBY009-05 |
Vaknaam | Practical Modelling for Biologists |
Niveau(s) | master |
Voertaal | Engels |
Periode | semester I b (16-01-2023 till 05-02-2023) |
ECTS | 5 |
Rooster | rooster.rug.nl |
Uitgebreide vaknaam | Practical Modelling for Biologists | ||||||||||||||||||||||||||||||||||||
Leerdoelen | At the end of the course, the student is able to: 1. Identify whether a scientific or societal problem can be addressed with models; 2. Recognise the types of models used in marine sciences (e.g. models using spatial and non-spatial, e.g. mean-field setting); 3. Develop and code a model in R based on underlying processes and relations concerning the system at study; 4. Analyse the model to study the effect of changing conditions on species interactions and ecosystem functioning; 5. Formulate and evaluate scientific or managerial conclusions from the model analysis. |
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Omschrijving | Mathematical modelling has become an important tool throughout the natural sciences. Especially when the dynamics of natural populations, being molecules within the cell, a population of seals in an estuary, or the global importance of termites are concerned, modelling is an indispensable tool, as it can help in understanding how species interaction can cause unexpected, nonlinear dynamics in ecosystems. Particularly when modelling marine systems, this often involves not only biological interactions, but also interactions with the physical and chemical environment. This course aims to teach how to model species interactions and ecosystem functioning, using marine systems as focus area. It takes a multidisciplinary approach, and introduces the student how to modelling the interactions of organisms with their abiotic environment. The course moreover focuses on computational (i.e. computer calculations) rather than on mathematical (i.e. symbol manipulation) techniques. In the course, the following subjects will be treated: - Resource modelling in (marine) ecosystems - Modelling ecosystem engineering and positive feedback - Spatial modelling: Advection/Diffusion - Self-organization - Modelling water flow: Navier Stokes & shallow water equations - Cellular automata: (wave) disturbance modelling - Individual-based modelling - Animal movement & search The first part of the course will be a series of lectures that provide an introduction into the most important topics within marine modelling. Using practical exercises, the student will get acquainted with the basic modelling techniques, and learn how to use the models to answer ecological and environmental problems. In the last 2 weeks of the course, the students will do a modelling assignment where they independently develop (e.g., not provided by the lecturer) a model to answer a scientific question, as group work. At the last day of the course, the students will report on their work in a presentation. |
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Uren per week | |||||||||||||||||||||||||||||||||||||
Onderwijsvorm |
Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC)
(Self Study (59hrs), LC-1 (15hrs), LC-2 (6hrs), PRC-1 (15hrs), PRC-2 (45hrs); see "remarks" section) |
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Toetsvorm |
Presentatie (P), Verslag (R)
(P-1 (20%), P-2 (60%), AST (20%);Evaluation weight (EW): 20% Practical assignments + 20% Midterm presentation + 60% Group modelling & Presentation (consisting in turn of Coding (20%), interpretation (20%) and Presentation (20%). If the end grade is higher then 5.5, the student passes. The grade is computed as: 1+9*EW) |
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Vaksoort | master | ||||||||||||||||||||||||||||||||||||
Coördinator | prof. dr. J. van de Koppel | ||||||||||||||||||||||||||||||||||||
Docent(en) | dr. ir. D. van Oevelen | ||||||||||||||||||||||||||||||||||||
Verplichte literatuur |
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Entreevoorwaarden | The course unit assumes no prior knowledge, but programming experience is of great benefit. Advisable is to follow the course ‘Practical Bioinformatics for Biologists’. Otherwise, a good preparation would be to follow an online course in programming (not statistics) in R. Consult the course coordinator if you would like advice on preparing yourself for the course. | ||||||||||||||||||||||||||||||||||||
Opmerkingen |
- Be present, with a single possible exception, during the group work; - Be present and contribute to the the mid-term (end of second week) and end (end of third week) presentations. If you do not attend, you will not get the associated points.
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Opgenomen in |
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