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Informatie over MSc Biomolecular Sciences
Hieronder staan het programma en de vakomschrijvingen van MSc Biomolecular Sciences Klik op de naam van een vak in een schema om naar de omschrijving te gaan.
| » General programme | |||||||
| Periode | Type | Code | Naam | Taal | ECTS | Uren | |
|---|---|---|---|---|---|---|---|
| hele jaar | verplicht | WMBS015-05 | Colloquium | Engels | 5 | ||
| verplicht | WMBS016-05 | Essay | Engels | 5 | |||
| verplicht | WMBS901-40 | Research Project 1 | Engels | 40 | |||
| verplicht | WMBS902-30 | Research Project 2 | Engels | 30 | |||
| semester I a | verplicht | WMBS004-05 | Protein and Enzyme Engineering | Engels | 5 | ||
| Opmerkingen | This on line catalogue is primarily designed to contain descriptions of programmes and course units. Students design their two year individual programme in consultation with their mentor. All possibilities and the rules for an individual programme can be found on the student portal. Although the courses are sorted per half semester it does not give an accurate programme in time. Please consult the schedule for each course unit and the student portal for a year schedule. | ||||||
| » Compulsory courses general programme (3 out of 9) | |||||||
| Periode | Type | Code | Naam | Taal | ECTS | Uren | |
| semester I a | keuzegroep A | WMBS011-05 | Electron Microscopy of Biological Macromolecules | Engels | 5 | ||
| keuzegroep A | WMBS003-05 | Molecular Dynamics | Engels | 5 | |||
| keuzegroep A | WMBS005-05 | Tools and approaches of systems biology | Engels | 5 | |||
| semester I b | keuzegroep A | WMBS006-05 | Advanced Genetic Engineering | Engels | 5 | ||
| keuzegroep A | WMBS007-05 | Advanced membrane biology | Engels | 5 | |||
| keuzegroep A | WMBS008-05 | Advanced Protein Crystallography | Engels | 5 | |||
| keuzegroep A | WMBS009-05 | Advances in Signal Transduction | Engels | 5 | |||
| keuzegroep A | WMBS012-05 | Organelle and Membrane Biogenesis | Engels | 5 | |||
| semester II a | keuzegroep A | WMBS014-05 | Transcriptomics | Engels | 5 | ||
| Opmerkingen | This on line catalogue is primarily designed to contain descriptions of programmes and course units. Students design their two year individual programme in consultation with their mentor. All possibilities and the rules for an individual programme can be found on the student portal. Although the courses are sorted per half semester it does not give an accurate programme in time. Please consult the schedule for each course unit and the student portal for a year schedule. | ||||||
| » Compulsory courses Chemical Biology | |||||||
| Periode | Type | Code | Naam | Taal | ECTS | Uren | |
| semester I b | verplicht | WMBS008-05 | Advanced Protein Crystallography | Engels | 5 | ||
| semester II a | verplicht | WMCH014-05 | Advances in Chemical Biology | Engels | 5 | ||
| verplicht | WMCH021-05 | Synthetic Biology and Systems Chemistry | Engels | 5 | |||
| Opmerkingen | This on line catalogue is primarily designed to contain descriptions of programmes and course units. Students design their two year individual programme in consultation with their mentor. All possibilities and the rules for an individual programme can be found on the student portal. Although the courses are sorted per half semester it does not give an accurate programme in time. Please consult the schedule for each course unit and the student portal for a year schedule. | ||||||
| » Electives/Optional modules | |||||||
| Periode | Type | Code | Naam | Taal | ECTS | Uren | |
| hele jaar | keuze | WMBY019-05 | Animal Experimentation | Engels | 5 | ||
| semester I | keuze | WMSE002-10 | Introduction Science and Policy | Engels | 10 | 40 | |
| keuze | WMMP004-01 | Microbiological Safety | Engels | 1 | 16 | ||
| semester I a | keuze | WMBY005-10 | Biological Modelling and Model Analysis | Engels | 10 | ||
| keuze | WMBM023-05 | Data Science in Biomedicine | Engels | 5 | 40 | ||
| keuze | WMBS011-05 | Electron Microscopy of Biological Macromolecules | Engels | 5 | |||
| keuze | WMEE002-05 | Impact of Energy and Material Systems | Engels | 5 | |||
| keuze | WMSE001-10 | Introduction Science and Business | Engels | 10 | |||
| keuze | WMBY006-05 | Mathematics in the Life Sciences | Engels | 5 | |||
| keuze | WMBM010-05 | Microbiome and Health | Engels | 5 | |||
| keuze | WMBS003-05 | Molecular Dynamics | Engels | 5 | |||
| keuze | WMEV007-10 | Molecular Methods in Ecology and Evolution (2021/2022) | Engels | 10 | |||
| keuze | WMEC005-05 | Research Methods in SEC | Engels | 5 | |||
| keuze | WMBM013-05 | Scientific writing | Engels | 5 | |||
| keuze | WMEE003-05 | Sustainable Use of Ecosystems | Engels | 5 | |||
| keuze | WMBS005-05 | Tools and approaches of systems biology | Engels | 5 | |||
| semester I b | keuze | WMBS006-05 | Advanced Genetic Engineering | Engels | 5 | ||
| keuze | WMBS007-05 | Advanced membrane biology | Engels | 5 | |||
| keuze | WMBS008-05 | Advanced Protein Crystallography | Engels | 5 | |||
| keuze | WMBS009-05 | Advances in Signal Transduction | Engels | 5 | |||
| keuze | WMCH027-05 | Biocatalysis and Green Chemistry | Engels | 5 | |||
| keuze | WMBM017-05 | Molecular Biology of Ageing and Age-related Diseases | Engels | 5 | |||
| keuze | WMBS012-05 | Organelle and Membrane Biogenesis | Engels | 5 | |||
| keuze | WMBY008-05 | Practical Bioinformatics for Biologists | Engels | 5 | 40 | ||
| keuze | WMBY009-05 | Practical Modelling for Biologists | Engels | 5 | 40 | ||
| keuze | WMBY010-05 | Programming C++ for Biologists | Engels | 5 | |||
| keuze | WMBY011-05 | Radioisotopes in Experimental Biology | Engels | 5 | |||
| keuze | WMEE005-05 | Sustainability and Society | Engels | 5 | |||
| keuze | WMEE006-05 | Systems Integration and Sustainability | Engels | 5 | |||
| semester II | keuze | TEM0105 | Basiscursus Master Lerarenopleiding | Nederlands | 5 | variabel | |
| keuze | WMBS013-20 | International Genetically Engineered Machine competition | Engels | 20 | |||
| keuze | TEM0205 | Masterstage 1 Lerarenopleiding | Nederlands | 5 | variabel | ||
| keuze | WMBY013-05 | Meta-analyses in Ecology (22/23) | Engels | 5 | |||
| keuze | WMBY014-05 | Orientation on International Careers | Engels | 5 | |||
| semester II a | keuze | WMCH014-05 | Advances in Chemical Biology | Engels | 5 | ||
| keuze | WMBM024-05 | Applied statistics and modeling | Engels | 5 | |||
| keuze | WMBM025-05 | Big Data & Applications in biomedicine | Engels | 5 | |||
| keuze | WMEV013-06 | Mathematical Models in Ecology and Evolution | Engels | 6 | |||
| keuze | WMEC006-05 | Skills in Science Communication | Engels | 5 | |||
| keuze | WMCH021-05 | Synthetic Biology and Systems Chemistry | Engels | 5 | |||
| keuze | WMBS014-05 | Transcriptomics | Engels | 5 | |||
| semester II b | keuze | WMBY016-05 | Advanced Light Microscopy | Engels | 5 | ||
| keuze | WMBY017-05 | Advanced self-organisation of social systems | Engels | 5 | |||
| keuze | WMBY018-06 | Advanced Statistics | Engels | 6 | |||
| keuze | WMPH047-05 | Biophysical Imaging & Manipulation Techniques | Engels | 5 | |||
| Opmerkingen | This on line catalogue is primarily designed to contain descriptions of programmes and course units. Students design their two year individual programme in consultation with their mentor. All possibilities and the rules for an individual programme can be found on the student portal. Although the courses are sorted per half semester it does not give an accurate programme in time. Please consult the schedule for each course unit and the student portal for a year schedule. | ||||||
| 1 | Advanced Genetic Engineering | WMBS006-05 | |||||||||||||||||||||||||||
| The emphasis will be on the practical aspects of genetic engineering of novel circuitries and on the principles of Synthetic Biology, both in silico and in the lab. In principle, the students will work in pairs on a research project in the practical part. The students will avail of- and study a number of bacterial strains with earlier developed DNA-biobricks (also from iGEM collections). Novel circuitries will be designed and engineered using Gram-positive or Gram-negative organisms as hosts. Modeling efforts will support the design. The engineered circuits will be characterized using various statistics-, bioinformatics and visualization packages, and functionality will be tested experimentally (e.g. by fluorescence microscopy or enzymatic assays). In this course, theory and practicals will be combined to give an in-depth view of current (high-throughput) genetic engineering approaches, gene regulatory mechanisms and -networks related to microbial physiology-Advanced genetic engineering: this includes use of Biobricks, Gibson assembly, use of BACs and YACs, toolboxes, gene integration, complex genetic circuitries (natural and synthetic): bistability, toggle switches, oscillations, feed-back mechanisms. | |||||||||||||||||||||||||||||
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| 2 | 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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| 3 | Advanced membrane biology | WMBS007-05 | |||||||||||||||||||||||||||
| Topics 1. General introduction to optical microscopy and fluorescence spectroscopy, and diffusion in the cell: literature Vangindertael et al 2018; Mika and Poolman 2011. 2. Structural features of membrane proteins: literature Hedin et al, 2011. 3. Evolution of membrane proteins: literature chapters 7.1, 7.3, 7.4, 7.5 from Biochemistry (pp 277-297). 4. Membrane protein biogenesis (protein translocation and thermodynamics of insertion of transmembrane segments into lipid bilayers): literature Schavemaker et al, 2018; Hessa et al, 2005. 5. Expression and quality control of (membrane) proteins: literature Wagner et al, 2006. 6. Membrane solubilization and reconstitution (properties of detergents, lipids): literature Rigaud et al 1995. 7. Electrophysiology and probing of channel activity: literature Chapter I from Bioelectricity (pp1-16). 8. Nucleocytoplasmic transport: literature Rout et al, 2004. | |||||||||||||||||||||||||||||
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| 4 | Advanced Protein Crystallography | WMBS008-05 | |||||||||||||||||||||||||||
| This course will provide insights on the important fundamentals and practices of protein X-ray crystallography. The aims of the course are to learn how protein crystal structures are determined, and to acquire the knowledge and skills necessary for critically analysing a 3D crystal structure. Subjects discussed during the course are: • Protein crystallization and crystal geometry; • Basic diffraction theory; • X-ray instrumentation; • Strategies for phase determination; • Basics of model building and refinement; • Structure validation: quality assessment of a protein crystal structure. Lecture classes are combined with discussion/exercise sessions: students will obtain reading assignments, will have to answer exercises, and are requested to prepare questions and subjects for group discussions. The lecture/discussion/exercise course is complemented with a workshop on the use of the various protein crystallographic computer programs. | |||||||||||||||||||||||||||||
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| 5 | Advanced self-organisation of social systems | WMBY017-05 | |||||||||||||||||||||||||||
| Processes of selforganisation occur at all levels of a system. For instance, in a group of individuals they take place at the level of the cognition of the individual, of its behaviour and of the behaviour of the group. Selforganisation implies that cognitively simple rules at the level of the individual (the so-called micro-level) may lead to complex behaviour at a higher level (the macro-level). The emergence of patterns in a computer model often leads to unexpected new insights. Note that, the other way around, by observing the complex behaviour at a higher level, it is impossible to discover the behavioural rules that operate at a lower level. In this course models of selforganisation of the social phenomena will be treated, such as: swarming by fish and birds, with and without attacks by predators; grouping and foraging behaviour by social insects and primates; nest building by insects, task division in insects; social learning and behaviour of fish and corvids; social structure (despotic and egalitarian), and cultural transmission in primates and humans. Individual-based models will be discussed and taught. The practical work closely follows the contents of the daily lectures. Students will use Excel-spreadsheets and the program Netlogo. In the last part of the course, students work on a modeling project of their own or in pairs. They can work out their own ideas or choose from the projects that are offered. The work is to be rounded off with a presentation. | |||||||||||||||||||||||||||||
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| 6 | 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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| 7 | Advances in Chemical Biology | WMCH014-05 | |||||||||||||||||||||||||||
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| 8 | Advances in Signal Transduction | WMBS009-05 | |||||||||||||||||||||||||||
| In this course, theory and practical work will be combined to acquire knowledge and experimental skills related to signal transduction in eukaryotic cells. In particular attention will be paid to the genetic regulation and biochemistry of proteins involved in signal transduction as well as the use and understanding of the most relevant research methods for studying signal transduction. Emphasis will be on topics that relate to research on eukaryotic cells that is executed within the research institute such as chemotaxis, cell differentiation and immune response. Students will also learn to study and analyse in vivo protein interaction using confocal microscopy combined with biophysical methods. | |||||||||||||||||||||||||||||
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| 9 | Animal Experimentation | WMBY019-05 | |||||||||||||||||||||||||||
| 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. Students will then be prepared to carry out the masterproject, under supervision of and guided by the CCD permit holder. Detailed instructions are found in Nestor, where students have to first fill in an Introduction form to be fully enrolled in the course. This course has a blended classroom format. It consists of a single contact event, whereas theoretical instruction is completely via e-learning, consisting of videos, quizzes, and assignments. Assessment is via essay questions. As the practical part, the students complete an online portfolio in collaboration with their master project instructions, and after approval of the portfolio, they receive project-specific, practical training from their supervisors. The theoretical part consists of 5 modules which guide students through the project steps as follows: (1) Preparations and ethical considerations, (2) Research question, experimental and statistical design, (3) Rules & Regulations, (4) Welfare monitoring, and (5) Scientific Publication. By in-depth reading, 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. The 5 modules contain information on •Ethics and researcher integrity in animal and human experimentation •Rules & Regulations in animal and human experimentation •Research question, experimental and statistical design •Choice of experimental model and subjects, and •Animal experimentation in practice For research involving humans, students must consult with their supervisors. From autumn 2021 onwards, students will require to purchase a small reader with study materials. | |||||||||||||||||||||||||||||
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| 10 | Applied statistics and modeling | WMBM024-05 | |||||||||||||||||||||||||||
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| 11 | Basiscursus Master Lerarenopleiding | TEM0105 | |||||||||||||||||||||||||||
| Bij dit vak doet de student basale kennis en vaardigheden op over het beroep als (vak)docent. Hij volgt daartoe (online) algemene colleges op het terrein van de pedagogiek en didactiek. Daarnaast neemt de student, onder leiding van de vakdidacticus, deel aan fysieke en/of online bijeenkomsten rond vakdidactiek. De student leert hoe een les te plannen en te evalueren, traint in het geven van deellessen, leert wat het betekent om voor een groep pubers te staan en wat hen motiveert en wat het belang is van een veilig leerklimaat. De student krijgt opdrachten mee die uitgevoerd worden in de onderwijspraktijk (Masterstage 1), leert hoe je gegevens verzamelt over die onderwijspraktijk (observaties, interviews, leerlingvragenlijsten) en hoe je die praktijk vanuit de theorie kunt analyseren. De student oriënteert zich daarmee op alles wat hem tijdens het vervolg van de opleiding te wachten staat en bouwt een realistisch beeld op van zijn geschiktheid voor dat vervolg. | |||||||||||||||||||||||||||||
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| 12 | Big Data & Applications in biomedicine | WMBM025-05 | |||||||||||||||||||||||||||
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| 13 | Biocatalysis and Green Chemistry | WMCH027-05 | |||||||||||||||||||||||||||
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| 14 | 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 overview of modelling approaches used in various disciplines of the life sciences. | |||||||||||||||||||||||||||||
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| 15 | Biophysical Imaging & Manipulation Techniques | WMPH047-05 | |||||||||||||||||||||||||||
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| 16 | Colloquium | WMBS015-05 | |||||||||||||||||||||||||||
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| 17 | Data Science in Biomedicine | WMBM023-05 | |||||||||||||||||||||||||||
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| 18 | 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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| 19 | Essay | WMBS016-05 | |||||||||||||||||||||||||||
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| 20 | Impact of Energy and Material Systems | WMEE002-05 | |||||||||||||||||||||||||||
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| 21 | International Genetically Engineered Machine competition | WMBS013-20 | |||||||||||||||||||||||||||
| The iGEM (international Genetically Engineered Machine competition (http://igem.org/Main_Page)) is an international organization that stimulates engineering of novel biological devices. It addresses the question: Can simple biological systems be built from standard interchangeable parts and operated in living cells? The competition already involves more than 340 teams from many major universities and institutes around the world, all trying to actively engineer biological devices by means of Synthetic Biology. The course unit´s content includes formulating and executing an experimental and/ or computational project related to Synthetic Biology and Systems Biology and reaching the goals in Synthetic Biology that are described by the iGEM organization. Students learn to work together in a multidisciplinary team, designing and executing a project, professionally presenting results in public, performing outreach, and obtaining funding. They will have to provide evidence of their contribution to the project on both individual and team level. This includes planning of work meetings and practical laboratory work in the period Feb-Nov and performing research according to work plan from Jul-Aug and also in the proceeding/posterior periods (Feb-Jun and Sep-Nov); occupation can vary between 10-80%. The final results will be presented at the iGEM Jamboree in Oct in Boston, and will have to comply with the iGEM criteria (see iGEM website each year). The course includes two modes of assessment (see also point 7). Official assessment is via an overall assessment, which includes that of an individually written report, presentation(s) during the iGEM seminars and assessment of the student's activities and contributions by at least two supervisors. The outcome of the judgement by international referees at the iGEM jamboree is not part of the assessment, because the iGEM teams are judged by different juries, restricting an objective comparison. | |||||||||||||||||||||||||||||
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| 22 | Introduction Science and Business | WMSE001-10 | |||||||||||||||||||||||||||
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| 23 | Introduction Science and Policy | WMSE002-10 | |||||||||||||||||||||||||||
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| 24 | Masterstage 1 Lerarenopleiding | TEM0205 | |||||||||||||||||||||||||||
| Bij Masterstage 1 loopt de student stage op een school voor voortgezet onderwijs (in de regel twee dagen per week) onder begeleiding van een vakcoach. Hij verricht observaties, interviewt leerlingen, bereidt (deel)lessen voor, geeft ze en bespreekt ze na met de vakcoach. De student verzamelt informatie en feedback over de kwaliteit van het eigen handelen (o.a. door de afname van een leerlingenquête), rapporteert daarover en beschrijft zijn ervaringen in een stageverslag. De student oriënteert zich daarmee op het leraarschap en leert hoe je in de context van de school onderzoekend kunt werken aan het sturen van je ontwikkeling. In de context van de stage voert de student daarnaast opdrachten uit in het kader van de basiscursus lerarenopleiding (TEM0105), die parallel is georganiseerd aan de stage. | |||||||||||||||||||||||||||||
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| 25 | 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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| 26 | 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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| 27 | Meta-analyses in Ecology (22/23) | 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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| 28 | Microbiological Safety | WMMP004-01 | |||||||||||||||||||||||||||
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| 29 | Microbiome and Health | WMBM010-05 | |||||||||||||||||||||||||||
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| 30 | Molecular Biology of Ageing and Age-related Diseases | WMBM017-05 | |||||||||||||||||||||||||||
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| 31 | 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, coarsegrained), 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. self-assembly of lipids in water or sampling the conformational space of proteins. | |||||||||||||||||||||||||||||
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| 32 | Molecular Methods in Ecology and Evolution (2021/2022) | WMEV007-10 | |||||||||||||||||||||||||||
| This course can be followed as 5 ECTS course (following only the first part of the course) or as 10 ECTS course (following both the first and second part of the course). In the first part of the course (5 ECTS), students will learn through a hands-on wet and dry laboratory training a range of methods and their respective laboratory protocols. The first part consists of a mixture of lectures, dry lab (computer) and wet lab practicals. It provides an introduction to molecular techniques that are used in ecological and evolutionary research: DNA extraction; basic principles of PCR, qPCR and primer design; cloning; sequencing approaches; fingerprinting techniques; phylogenetic analyses of sequences; RNA extraction; gene expression analysis; protein quantification and activity. During the second part (5 ECTS), students will apply these molecular techniques to carry out independent research projects, which will be carried out individually or by groups of 2 students and will fit within the ongoing research of GELIFES, using molecular techniques for ecological and evolutionary research. | |||||||||||||||||||||||||||||
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| 33 | Organelle and Membrane Biogenesis | WMBS012-05 | |||||||||||||||||||||||||||
| This course is designed for obtaining insights into the mechanisms of bacterial cell envelope biogenesis and organelle biogenesis in eukaryotes. The course is organized according to the "flip-the-class room" concept. Each student carries out independently a literature study within one of the course subjects. Students are individually guided in this process. The student explores and examines the state-of art "in the field of research, and makes a hypothesis on an open research question that can be tested experimentally. The literature findings, the hypothesis and the possible experimental approach are presented by the students and critically discussed among the students. The practical is a brief introduction into scientific research taking notice of actual research questions and employ the necessary experimental operations. Study: literature The course covers a period of 3 weeks within which twice a one week period for the a theoretical part, consisting of literature research and individual counseling. Each week of the theoretical part is finalized with an oral presentation and active discussion among the students about the topic, issues raised and the chosen experimental approach. The theoretical part concludes with practical work of one week. Assessment form: presentation Implement the literature assignment, initiative and creativity in formulating the research question and associated experimental approach; oral presentation and involvement in subsequent open discussion. | |||||||||||||||||||||||||||||
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| 34 | 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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| 35 | Practical Bioinformatics for Biologists | WMBY008-05 | |||||||||||||||||||||||||||
| Practical Bioinformatics for Biologists (PBfB) introduces students to general computational tools in order to enable to design and execute efficient computations. PBfB presents a broad range of open-source, free and flexible computational tools applicable to geneticists, molecular biologists, ecologists, oceanographers, physiologists, or anyone with an interest or need for bioinformatics in their research. PBfB emphasizes the practical application of bioinformatic methods to solve real-life analyses. PBfB covers data -centered computing in a Unix/Linux environment. PBfB introduces the basics of a 'nix environment, such as; remote installation and execution of software. Students will be familiar with command line tools to explore and analyze data as well as the use of scripting languages such as Python and R to (a) code custom analyses and (b) to design effective pipelines of existing software. The use of databases and retrieval of data from public on-line databases will be introduced. Data visualization techniques will be introduced using the statistical language R. Topics addressed in PBfB will employ practical example from different research fields, e.g., Next Generation Sequencing (NGS) data in genetics and molecular biology, as well as remote sensing and oceanographic data widely used in spatial ecological and evolutionary biology. The course consists of short lectures featuring new concepts and examples as well as practical computer exercises and individual assignments. In the last week, students will conduct a project assignment in small groups implementing the use of skills acquired during the course, aimed at solving real-life analyses. Students will present their pipeline and results to the class in an oral presentation during the last days of the course. | |||||||||||||||||||||||||||||
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| 36 | 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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| 37 | Programming C++ for Biologists | WMBY010-05 | |||||||||||||||||||||||||||
| This course, which is specifically designed for biology students, teaches the participants how to develop software in the programming language C++. Emphasis is given to the implementation of biological models, using individual-based simulations and various numerical methods for dynamical systems analysis. Students are able to tailor the contents of the course to their own level of proficiency. For students with no prior programming experience, the course offers an introduction to the essentials of the C++ programming language, including: • Procedural programming: data types, operators, program flow and functions • The Standard Template Library • Data input, generation of output including statistics like mean and standard deviation • Numerical simulation techniques for biological models More experienced programmers (including those who followed the BSc level course WBBY015-05) can instead focus on advanced topics, such as: • Program design, algorithms and debugging • Pointers and memory allocation • Object-oriented programming • Pseudo-random numbers and stochastic simulations The course consists of two parts: during the first three weeks (5 ECTS), students extend their programming skills by learning a new element of the programming language each day, and practise its application in programming exercises. Students then have the option to apply their newly acquired skills in practice by working on an extended three-week programming project (+5 ECTS). Here, students work on a biological research question of their choice and design and implement a simulation algorithm from scratch. Students preparing for a theoretical MSc project, can use the project to develop a first implementation of the simulation code for their project. Participants also learn how to systematically collect simulation data, and to present their results in an oral presentation, with associated annotated program code and documentation. The course is also available as a self-study course. | |||||||||||||||||||||||||||||
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| 38 | Protein and Enzyme Engineering | WMBS004-05 | |||||||||||||||||||||||||||
| This course aims to provide insight in the scientific basis and applications of protein engineering, especially of enzymes. Enzymes catalyze numerous biochemical reactions, and are highly important for bioprocessing, synthetic biology, biodegradation, as well as for diagnostics and therapeutics in medicine. They are attractive catalysts for the production of bioactive compounds because of their chemo-, regio- and stereoselectivity. Applications of enzymes often require protein engineering aimed at increasing catalytic activity, binding affinity or stability. For this, fundamental insight in structure-function relationships is of key importance. Furthermore, knowledge about methods in structure-based protein engineering and directed evolution contributes to solving many other problems in biomolecular sciences. The course trains students in the scientific background of protein engineering, including directed evolution, as well as the use of protein structures and computational methods. The course includes lectures, tutorials, computer practicals (computational protein design) and (for students lacking the experience) laboratory work to make students familiar with mutagenesis methods. Students are also trained in the ability to examine recent literature to critically present and discuss strategic options and experimental results. There are 2 schemes to follow this course: A) compact (full time), with all parts in three weeks (lectures, tutorials, computer practicals, lab practicals, assignments presentation, assignment report). Best for students full time Biomolecular Sciences or those who have exemption form the lab practicals. This may be too crowded for students who do not have an exemption for the laboratory practical and for students (chemistry, CB) who follow another course in parallel. B) stretched (for chemistry), with most parts (lectures, tutorials, computer practicals, lab practicals) in the first three weeks, but with the assignment presentation and reports scheduled in week 40. | |||||||||||||||||||||||||||||
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| 39 | Radioisotopes in Experimental Biology | WMBY011-05 | |||||||||||||||||||||||||||
| RPO Dispersible Radioactive Materials-D is the minimum expert level which allows you to work with radioisotopes at the university and university hospital (UMCG). It is an official expert level supervised and regulated by the Dutch Government. The University of Groningen is one of the few official recognized institutes were you can obtain certificates of the official radiation expert levels. At the end of the 1st week you will HAVE to pass the RPO DRM-D test to be allowed to participate in the remainder of the course. NOTE: For the course an additional registration is needed apart from Progress for participating in an official RPO DRM-D course. Topics will include: • Radioisotope detection using X-ray film • The (advanced liquid) scintillation counter • In vitro labeling of nucleic acids and proteins • Subcellular localization of biological molecules • Radioisotopes and immunoassay • Pharmacological techniques • Biological effect of radiation The final part of the course consist of chronobiological research question regarding Melatonin using a Radioimmunoessay (RIA). The students will be their own research subjects. The results will be discussed in a concluding tutorial. | |||||||||||||||||||||||||||||
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| 40 | Research Methods in SEC | WMEC005-05 | |||||||||||||||||||||||||||
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| 41 | Research Project 1 | WMBS901-40 | |||||||||||||||||||||||||||
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| 42 | Research Project 2 | WMBS902-30 | |||||||||||||||||||||||||||
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| 43 | Scientific writing | WMBM013-05 | |||||||||||||||||||||||||||
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| 44 | Skills in Science Communication | WMEC006-05 | |||||||||||||||||||||||||||
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| 45 | Sustainability and Society | WMEE005-05 | |||||||||||||||||||||||||||
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| 46 | Sustainable Use of Ecosystems | WMEE003-05 | |||||||||||||||||||||||||||
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| 47 | Synthetic Biology and Systems Chemistry | WMCH021-05 | |||||||||||||||||||||||||||
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| 48 | Systems Integration and Sustainability | WMEE006-05 | |||||||||||||||||||||||||||
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| 49 | 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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| 50 | Transcriptomics | WMBS014-05 | |||||||||||||||||||||||||||
| In this course, theory and practicals are combined to give an in-depth view of transcriptomics research in eukaryotes and prokaryotes. This master course is divided into three parts. The first part focuses on the theoretical background of Next Generation Sequencing (DNA-Seq and RNA-Seq) and on how important the role of RNA is in modern science. The assessment for this part consists of a literature case study on ChIP-Seq in Eukaryotes. The second part consists of 3 - 4 days lab work to practice working with RNA; quality control of the RNA, library preparation for Next Generation Sequencing and running samples on an Illumina sequencer. The projects selected for this part are based on research questions of PhD students and post-doctoral fellows of the department of Molecular Genetics. In principle the experiment has not been done before, which means that the generated data is novel. The last part of the course concerns statistics and data analysis on High-Performance Computing required for transcriptome analyses. Students will analyze and draw conclusions on their own datasets and will link results to biological knowledge by using additional statistical methods. Also, based on their findings, students will be encouraged to propose ideas for further experiments. | |||||||||||||||||||||||||||||
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