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Informatie over MSc Courses for Exchange Students: Biology
Hieronder staan het programma en de vakomschrijvingen van MSc Courses for Exchange Students: Biology Klik op de naam van een vak in een schema om naar de omschrijving te gaan.
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| Periode | Type | Code | Naam | Taal | ECTS | Uren | |
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| hele jaar | WMBY019-05 | Animal Experimentation | Engels | 5 | |||
| semester I | WMSE002-10 | Introduction Science and Policy | Engels | 10 | 40 | ||
| semester I a | WMBY005-10 | Biological Modelling and Model Analysis | Engels | 10 | |||
| WMSE001-10 | Introduction Science and Business | Engels | 10 | ||||
| WMBY006-05 | Mathematics in the Life Sciences | Engels | 5 | ||||
| WMBS003-05 | Molecular Dynamics | Engels | 5 | ||||
| WMBS005-05 | Tools and approaches of systems biology | Engels | 5 | ||||
| keuze | WMBY007-05 | Skills and Scopes in Biology | Engels | 5 | |||
| semester I b | Ecology of sustainable farming (21/22) | Engels | 5 | ||||
| WMEV010-05 | Flyway Ecology (20/21) | Engels | 5 | ||||
| WMBY009-05 | Practical Modelling for Biologists | Engels | 5 | 40 | |||
| keuze | WMBS007-05 | Advanced membrane biology | Engels | 5 | |||
| keuze | WMBS011-05 | Electron Microscopy of Biological Macromolecules | Engels | 5 | |||
| semester II | WMBY013-05 | Meta-analyses in Ecology (20/21) | Engels | 5 | |||
| WMBY014-05 | Orientation on International Careers | Engels | 5 | ||||
| semester II a | WMEV013-06 | Mathematical Models in Ecology and Evolution | Engels | 6 | |||
| WMMB009-05 | Polar Ecosystems | Engels | 5 | ||||
| keuze | WMMB008-05 | Marine Ecosystem Service and Global Change | Engels | 5 | |||
| semester II b | WMBY016-05 | Advanced Light Microscopy | Engels | 5 | |||
| WMBY018-06 | Advanced Statistics | Engels | 6 | ||||
| Opmerkingen | o TERMS: In the Netherlands, the academic years are not only divided into semesters, but also in ‘terms’. Each semester consists of 2 terms. The 1st semester entails a term 1a and 1b (Term 1a is the 1st half of the 1st semester. Term 1b, the 2nd half of the 1st semester). Term 2a (or IIa) stands for the 1st half of the 2nd semester and 2b (or IIb) for the 2nd half of the 2nd semester. | ||||||
| 1 | Advanced Light Microscopy | WMBY016-05 | |||||||||||||||||||||||||||
| In this course students learn various aspects of modern advanced light and fluorescence microscopy techniques. The course includes basic knowledge on light microscopy, several aspects of fluorescence microscopy, including the principles of fluorescence, properties of fluorescent dyes and proteins, wide field-, confocal-, SIM-, TIRF- and spinning disc microscopy, advanced fluorescence microscopy techniques such as FRET,FLIM and FCS as well as super resolution microscopy. Additional topics include live cell imaging, image processing and analysis and artifacts in fluorescence microscopy. The course consists of a theoretical part (lectures), practicals and a short research project. Assessment is via the preparation and presentation of a poster that contains the results of the research project and a written examination | |||||||||||||||||||||||||||||
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| 2 | Advanced membrane biology | WMBS007-05 | |||||||||||||||||||||||||||
| 1. Structural features of membrane proteins (building on the lectures of JS Lolkema; incl. topology prediction and manipulation): literature Hedin et al, 2011 and Dalbey et al, 2011. 2. Membrane protein biogenesis (protein translocation and thermodynamics of insertion of transmembrane segments into lipid bilayers): literature Dalbey et al, 2011 and Hessa et al, 2005 3. Expression and quality control of (membrane) proteins: literature Wagner et al, 2006. 4. Membrane solubilization and reconstitution (properties of detergents, lipids): literature Rigaud et al 1995. 5. Electrophysiology and probing of channel activity: literature Chapter I from Bioelectricity (pp1-16) and Sakmann & Neher 1984. 6. Fluorescence microscopy and probing of the structure and dynamics of biological membranes: literature Mika and Poolman, 2011. 7. Nucleocytoplasmic transport: literature Rout et al, 2004. | |||||||||||||||||||||||||||||
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| 3 | Advanced Statistics | WMBY018-06 | |||||||||||||||||||||||||||
| Content: Introduction to R and review of basic statistics. Further topics: general linear models (ANOVA, ANCOVA, multiple regression); generalized least squares; mixed models; generalized linear models; generalized linear mixed models; Bayesian analysis and MCMC; animal models; multivariate analysis. During the last week of the course analysis and presentation of own data set. Description: This course teaches advanced statistical analysis almost from the ground up. The only requirement is some familiarity with basic statistical concepts and methods, such as taught in most introductory statistics courses. Some experience with R is useful but not crucial. During the first three days, basic methods and R will be reviewed to refresh your memory. During the next three weeks, cutting-edge techniques such as GLMMs, power analyses and Bayesian MCMC models will discussed and practiced. Each day will start with a review of the exercises of the previous day, followed by lectures and new computer labs. Mathematics will be kept to a minimum, and in addition to developing analytical skills, the course also puts much emphasis on producing effective and great-looking graphs (mostly using the ggplot2 package). The last week of the course will be dedicated to analyzing your own data, unleashing the newly learned techniques. If you have no data yet, alternative suitable data will be found elsewhere or simply created de novo with simulation models. Your methods, results and conclusions will be documented in a report which will be graded. | |||||||||||||||||||||||||||||
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| 4 | Animal Experimentation | WMBY019-05 | |||||||||||||||||||||||||||
| This course is in transition to a completely new e-learning format. Please be prepared for possible change during the academic year. The learning objectives, content and judgement will be very similar, but the format is changed to learning via videos, quizzes, and assignments. Enrolling in this course is only finalized once you will have completed following your first instruction in NESTOR. Thereafter, selected course participants will work within a google classroom environment, where more detailed information will be provided. The aim of the course is to prepare students starting a master research project in which they participate in animal experimentation, with respect to methodological, practical and ethical aspects. At the end the students are prepared to carry out the masterproject, under supervision of and guided by the CCD permit holder. The course has a blended classroom format with a limited contact hours. The students complete an online portfolio after practical instructions in their master project, and conduct the theoretical part as a homework assignment. They will also participate in a tour through the animal facility to learn about practical procedures while performing their study and the people involved, and attend a contact hour with an interactive lecture when topics can be discussed. The theoretical part consists of 5 modules containing information on (1) Ethics and researcher integrity in animal and human experimentation, (2) Rules & Regulations in animal and human experimentation, (3) Research question, experimental and statistical design, (4) Choice of experimental model and subjects, and (5) Animal experimentation in practice. By in-depth reading of scientific papers, looking up content on the internet and by self-reflection, students will learn about scientific, practical and societal aspects of working with animals during their master project. For research involving humans, students must consult with their supervisors. | |||||||||||||||||||||||||||||
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| 5 | Biological Modelling and Model Analysis | WMBY005-10 | |||||||||||||||||||||||||||
| In this course, students are made familiar with all phases of the modelling cycle: the translation of biological questions into formal models; the simplification of models to manageable complexity; the analysis of models with the help of mathematical, numerical and simulation techniques; the presentation of the qualitative and quantitative conclusions obtained from the model analysis; the estimation of model parameters and model validation; model comparison and selection of the best-supported model on the basis of empirical data; the refinement of models on the basis of the interplay between modelling and model-based data analysis. Throughout the course, students will apply modelling and model analysis to research questions from various disciplines (e.g., systems biology, neurobiology, bioinformatics, phylogenetics, behavioural and social sciences, community ecology, evolutionary biology). The emphasis of the course will not only be on the technical aspects, but also (and perhaps even more) on the biological conclusions that can be drawn from a modelling approach. The course is taught by theoreticians working in different areas of biology, who are using a broad variety of modelling techniques. In this way, students gain an overview of the theoretical research done in the life sciences at the University of Groningen, as well as an understanding of the strength and weaknesses of different modelling strategies for addressing particular kinds of research questions. Half of the course consists of a structured program of lectures and computer practicals covering all aspects of the modelling cycle. Along the way, students will develop their own modelling project (from model building, analysis, interpretation and validation to communication of the results). The other half of the course provides an in-depth overview of modelling approaches used in various disciplines of the life sciences. For each topic, students submit one of the exercises for evaluation. | |||||||||||||||||||||||||||||
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| 6 | Electron Microscopy of Biological Macromolecules | WMBS011-05 | |||||||||||||||||||||||||||
| This 3-week course is an introduction to electron microscopy (EM), ranging from a general theoretical and practical understanding of the technique to news advances and applications in the field. It is meant for students with an interest in structural biology. The focus is on learning how to operate a transmission electron microscope, including EM sample preparation (2-weeks). In the last week, students will conduct image processing of a single particle cryo-electron microscopy data set to determine a high-resolution protein structure (1 week). Students are expected to obtain a better understanding of the advantages and disadvantages, the possibilities and limitation of the technique and were it is employed. Recent breakthroughs in cryo-electron microscopy (cryo-EM) have revolutionize the field entirely making it often the method of choice for high resolution structure determination of proteins, which was acknowledged by the Nobel Prize in Chemistry in 2017. | |||||||||||||||||||||||||||||
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| 7 | Flyway Ecology (20/21) | WMEV010-05 | |||||||||||||||||||||||||||
| In three weeks students are introduced in the field of flyway ecology and shown the boundaries of our knowledge in this field. To experience those boundaries and to be inspired to create research ideas that will cross those boundaries, students and docents will closely work together to understand and synthesize theory and methodology. Avian migration will be placed in the context of (a) seasonal connections and (b) global connections of ecosystems. The course materials will encompass global research programmes on these phenomena. The course will be a mixed of lectures, workshops and reading/presentation assignments. The first week of the course mostly consists of classroom lectures. The second week involves a retreat to immerse the students in an inspiring setting, with 4-5 docents where classroom lectures will be alternated with workshops on methodological advances. In the third week the students will write a research proposal in the field of flyway ecology, which includes a literature search. The classroom lectures will cover migration theory on the level of the individual and on the level of ecosystems, including: annual cycles; seasonal changes in body composition (fuelling the flights); extreme migrations; weather and wind effects on migration; stopover habitats and food resources; controlling mechanisms of migration schedules; sex and age differences in migration; responses to anthropogenic change; demography and population regulation; population consequences of mass mortalities during migration; phenotypic flexibility and facilities for rapid change; the evolution of migration systems. The workshops will cover practical themes and methodological applications such as tracking free-living animals, estimating annual and seasonal survival, measuring the ecological context of variation in survival, migrants as integrative sentinels, the societal impact of flyway ecology, and applications in nature conservation. | |||||||||||||||||||||||||||||
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| 8 | Introduction Science and Business | WMSE001-10 | |||||||||||||||||||||||||||
| This module will take place in two phases. 1. Theory Science and Business 2. Group project Science and Business In the first three weeks you will follow an intensive program in which you get acquainted with important business concepts. After that you will train the skills to solve business cases and to write and present a feasible science advise to company owners. Most assignments will be done in groups and teams. For more information see www.rug.nl/fwn/sbp | |||||||||||||||||||||||||||||
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| 9 | Introduction Science and Policy | WMSE002-10 | |||||||||||||||||||||||||||
| This module will take place in two phases. 1. Theory Science and Policy 2. Group project Science and Policy In the first three weeks you will follow an intensive program in which you get acquainted with important policy concepts. After that you will train the skills to solve policy cases and to write and present a feasible science advise to governmental organisations. Most assignments will be done in groups and teams. For more information see www.rug.nl/fwn/sbp | |||||||||||||||||||||||||||||
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| 10 | Marine Ecosystem Service and Global Change | WMMB008-05 | |||||||||||||||||||||||||||
| Global population growth stimulates pressures of humanity to use marine resources in the deep seas, coastal areas and delta? Marine resources that are exploited or have the potential to be exploited are called ecosystem services. Simultaneously, global change processes impose threats to the ecosystems that provide these valuable services. This course provides fundamental knowledge and understanding of i) the concept of ecosystem services, ii) which services are provided by different marine ecosystems and how do these relate to ecosystem functions, iii) mechanisms behind the main anthropogenic and global change stressors that threaten ecosystem functions/services, iv) opportunities to benefit from ecosystem services under conditions of global change. Students will acquire practical skills in studying global change processes and quantifying ecosystem services. Students will develop a critical reflective attitude on how to deal with coastal management for example in balancing preserving and unlocking ecosystem functions and services and determining climate related and non-climate related drivers. The course includes classroom lectures, presenting assignments, practicals in unique research facilities at NIOZ, such as the SeaweedCentre and wave-flume and a field trip. The lectures will consist of 4 blocks. The first block, the concept of ecosystem services (ES) will be introduced, highlighting the importance of ES for marine ecosystems. The second block focuses on the functioning of marine ecosystems that provide important ES, ranging from the deep sea to shallow coastal areas including delta?. The third block provides fundamental knowledge on the threats to marine ecosystems, e.g. ocean acidification, eutrophication. In the fourth block, threats are linked to challenges and opportunities, e.g. (over-)fishing and deep-sea mining) in benefitting from marine ecosystem services. | |||||||||||||||||||||||||||||
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| 11 | Mathematical Models in Ecology and Evolution | WMEV013-06 | |||||||||||||||||||||||||||
| Mathematical models have become an indispensable tool in ecology and evolutionary biology, to the point that aspiring scientists in these fields must have a working knowledge of basic mathematical modeling techniques. This course teaches such techniques practically from scratch, without requiring much background knowledge except elementary high school algebra and a little calculus. If successful, it will allow the students to understand papers that contain models, to develop new models to explore their own ideas, and to generate and use models for analysis and interpretation of data. Students are required to study one book chapter per week on their own and to do several exercises for hands-on experience. Some exercises are of the pencil-and-paper variety, but others require the help of the computer-aided mathematical tools such as Maple, Mathematica or R, which the student will learn how to use during the course. One afternoon per week, participants meet with a teacher for demonstration and discussion. The meetings usually start with a discussion of the chapter content where difficulties will be explained on the blackboard or with computer + beamer. For each of the suggested book-exercises, one of the participants is appointed as “volunteer” to demonstrate her or his solutions in the classroom, followed by discussion. Depending on the students’ background knowledge, sometimes during these meetings a “remedial” lecture of one or two hours is given about particular mathematical (e.g. linear algebra) or technical (e.g. Mathematica) subjects. | |||||||||||||||||||||||||||||
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| 12 | Mathematics in the Life Sciences | WMBY006-05 | |||||||||||||||||||||||||||
| The course will: - train basic mathematical skills, such as differentiation and integration; - introduce students to important mathematical concepts and methods, such as complex numbers, linear algebra, multivariate analysis, and linearization techniques; - provide insight into the use and interpretation of dynamical models in the life sciences; - expose students to important classes of example models in the life sciences; - teach students how to investigate dynamical models with analytical and numerical methods; - expose students to more advanced concepts and methods, such as chaotic attractors and bifurcation analysis; - teach students how to solve mathematical problems with the help of technical computing software (Mathematica). The first week of the course will focus on mathematical key concepts (such as differentiation, integration, Taylor expansion) and on the analysis of one-dimensional dynamical systems (single ordinary differential equations (ODEs) and single recurrence equations). Students will learn how to solve these systems either analytically or numerically, both with pencil and paper and with a programme like Mathematica, and to perform an equilibrium and stability analysis. Students will also be exposed to bifurcation analysis, catastrophes, and chaotic attractors. In the second week, complex numbers and concepts of linear algebra (eigenvalues and eigenvectors) will be introduced. Students will learn the basics of multivariate analysis, including multivariate optimization (Hessian). These techniques will allow them to analyse simple stochastic systems, like Markov processes. Students also learn how to analyse 2nd_ order ODEs and recurrence equations. The third week is devoted to systems of ODEs and recurrence equations. Students learn how to solve linear systems analytically, how to solve non-linear systems numerically, and how to conduct a qualitative analysis of a multidimensional dynamical system (equilibrium and stability analysis). | |||||||||||||||||||||||||||||
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| 13 | Meta-analyses in Ecology (20/21) | WMBY013-05 | |||||||||||||||||||||||||||
| Generalization of ecological research by the synthesis of experiments and data from the literature has proven to be an important modern complement to empirical ecological research. Instead of focusing on an indefinite number of idiosyncratic exceptions meta-analysis emphasizes general insights and promotes common ecological understanding. Understanding the function of biodiversity is an emerging ecological topic related to ecosystem functioning. It facilitates predicting consequences of biodiversity loss for ecosystem services by the global biodiversity crisis. The course will: 1) give an overview on the importance of species diversity and species functional traits for the function of important community properties. 2) teach to use different tools in ecological meta-analysis. 3) perform a meta-analysis, including tests of own hypothesis, either using provided datasets of experiments testing the function of biodiversity for ecosystem performance (B~F experiments), or using own data collected from recent literature. The course is given together with the University of Oldenburg, and is arranged around three workshops. The first workshop (in Wilhelmshaven, Germany) contains theoretical sections on biodiversity. The second workshop is on tools used to extract, handle and analyze large data sets using meta-analyses. There will be a strong focus on recent literature and the students are expected to analyze this literature for new exciting questions. In the third workshop (in Groningen, The Netherlands) the results will be presented at a mini-symposium. The course is run over ca. 8 weeks during which the main effort will be to produce your own ecological meta-analysis! Thus, the course can be run in parallel with other master projects | |||||||||||||||||||||||||||||
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| 14 | Molecular Dynamics | WMBS003-05 | |||||||||||||||||||||||||||
| Together with experiment and theory, computational modeling is one of the three pillars of modern science. In chemistry as well as in life sciences, modeling of the interactions between molecules is essential to understand the emerging behavior of complex systems. In particular the Molecular Dynamics (MD) simulation technique provides a detailed view of the behavior of molecules in space and time, at a resolution that cannot be attained by any single experimental technique. In a series of lectures, the underlying theory (statistical thermodynamics), the diversity of molecular models (atomistic, coarse-grained), and numerical techniques (integration of Newton's equations of motion) used in MD simulations will be discussed. Applications of the technique will be shown, with a focus on simulation of biomolecular processes. An important part of the course is hands-on experience using the GROMACS modeling software in a series of tutorials and practicals covering the basics of the techniques and selected applications, e.g. selfassembly of lipids in water or sampling the conformational space of proteins. | |||||||||||||||||||||||||||||
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| 15 | Orientation on International Careers | WMBY014-05 | |||||||||||||||||||||||||||
| Research topics will be provided by participating companies or organizations. Research topics are typically centered on biotechnology and bioprocessing, ecology, population science or pharmaceutical science. Students are expected to investigate the literature and other sources on the assigned topic, and will work in interdisciplinary teams to combine their findings in written and oral reports. The students will be mentored by a supervisor, with whom they discuss their findings, prepare a written report and oral presentation, and receive a grade from. The completed work will be followed up with the Study Tour along the participating companies organised by GLV-idun where a site visit is combined with a presentation of the company on aims and acquisition of scientific staff. During the visit each groups will also present their findings to their participating companies and hand over the written report. | |||||||||||||||||||||||||||||
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| 16 | Polar Ecosystems | WMMB009-05 | |||||||||||||||||||||||||||
| The course is based on a series of lectures (22) and a reading assignment. Lectures will be given by internal (ESRIG, Arctic Centre) as well as external polar experts. Topics covered are polar climatology, marine and terrestrial polar habitats, key species, effects of climate change from species to ecosystem level, and other human impacts. The second part of the course consists of a reading assignment, followed by presentations. A set of key scientific papers will be handed out to small groups of students (max 3 per group), covering as much scientific disciplines as possible. The students will need to understand, reproduce, summarize, evaluate and discuss the result and implications of the papers during a symposium, where the reading assignments will be presented. The course will be evaluated by a written examination, passing this exam is mandatory. Examination material includes material from the lectures as well as a selection of key scientific papers. | |||||||||||||||||||||||||||||
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| 17 | Practical Modelling for Biologists | WMBY009-05 | |||||||||||||||||||||||||||
| 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 indispensible 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. In the course, the following subjects will be treated: -Marine resource modelling -Modelling ecosystem engineering and positive feedback -Spatial modelling: Advection/Diffusion -Simple 1D depth models -Self organization -Modelling water flow: Navier Stokes & shallow water equations -Cellular automata: (wave) disturbance modelling -Individual-based modelling -Movement & search of animals. The course will consist of three parts. The first part will be a series of lectures that will 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 poster presentation. The course is part of the Marine Biology Master’s curriculum, and therefore strongly builds on examples from the Marine realm. The techniques that are taught are general, and the course is therefore open to all biology students. | |||||||||||||||||||||||||||||
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| 18 | Skills and Scopes in Biology | WMBY007-05 | |||||||||||||||||||||||||||
| The MSc Biology allows students to either specialize in one discipline or they combine multiple domains. One aim of this introductory course is that every participating student the program before the end of this course selecting courses and research projects within either the Research or the Science, Business & Policy profile. The course also aims to support a choice for a study mentor during the course. Students will explore their discipline(s) of interest in depth, by conducting literature search on current trends and topics. In this task, they will not only focus on academic literature, but also on how this topic is embedded in the broader context of society. Major parts of this introductory course are shared with the introductory course of Biomedical Sciences (Biomedical Sciences: Professional Perspectives). In this shared part, students get acquainted, through lectures and tutorial assignments, to the concepts of scientific integrity and code of conduct in the scientific disciplines of their interest, and apply these to their topic. Through acquisition tools & career management workshops, students identify what they have to offer to society, consider in what direction they aim to develop their career, learn how to apply for a job and how to write a CV. Students will integrate all assignments in a final portfolio that will map out the route to their ideal career. Through the final portfolio, students will recognize the competencies and skills required for the job. Finally, by recognizing the skills, they have already and discovering further skills to acquire, students can make a well-informed choice from the available modules and internships available in the various disciplines such as Ecology & Evolution, Marine Biology, Biomolecular Science or Biomedical Sciences. | |||||||||||||||||||||||||||||
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| 19 | Tools and approaches of systems biology | WMBS005-05 | |||||||||||||||||||||||||||
| In the course, students should become familiar with the modern tools and approaches of systems biology. Specifically, the course will introduce (i) the principles of the powerful omics measurement technologies, (ii) the computational concepts used to extract information from these large data sets, and (iii) how mathematical models can be used to investigate complex biological systems. These concepts and approaches will be illustrated with examples from metabolism-related research such that the students also gain further knowledge in this particular field of biology. The course consists of three parts: 1) lectures, focusing on overview of tools with examples from recent literature; 2) practical work in which students perform computational analyses and develop their own mathematical models; 3) assignments in which students prepare short presentations on questions related to recent literature | |||||||||||||||||||||||||||||
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