Practical Modelling for Biologists

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.
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.
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)
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)
Vaksoort	master
Coördinator	prof. dr. J. van de Koppel
Docent(en)	dr. ir. D. van Oevelen
Verplichte literatuur	Titel Auteur ISBN Prijs A Practical Guide to Ecological Modelling (2009) (non-obligatory) Soetaert and Herman 978-90-481-7936-7 ca. €  70,00
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	ATTENDANCE: The students are expected to - make the practical assignments on Wednesday, Thursday and Friday in the first week; - 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. Students from the Marine Biology Master are advised to follow this course if they have an interest in gaining experience in modelling in marine systems and professions. The course is also open to students and PhD students from other fields, and the techniques that are learned are generally applicable in the field of ecology. Capacity: 15 students
Opgenomen in	Opleiding Jaar Periode Type MSc Biology: Modelling in the Life Sciences  (Electives/Optional modules) - semester I b keuze MSc Biology: Research  (Compulsory master courses) - semester I b keuze MSc Biology: Science, Business and Policy  (Compulsory master courses) - semester I b keuze MSc Biomolecular Sciences  (Electives/Optional modules) - semester I b keuze MSc Courses for Exchange Students: Biology - semester I b MSc Ecology and Evolution: Ecology and Conservation  (Electives/optional modules) - semester I b keuze MSc Ecology and Evolution: Evolutionary Biology  (Electives/optional modules) - semester I b keuze MSc Marine Biology: Research  (Compulsory master courses) - semester I b keuze