| 1 | Advanced Genetic Engineering | WMLS13003 |
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. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. O.P. Kuipers | | Docent(en) | H. Karssensprof. dr. J. Kokprof. dr. O.P. Kuipers A.J. van Heel, MSc. | | Onderwijsvorm | Opdracht (ASM), Practisch werk (PRC), Werkcollege (T), Hoorcollege (LC) | | Toetsvorm | Practisch werk (PR), Presentatie (P), Schriftelijk tentamen (WE) | | ECTS | 5 | | Entreevoorwaarden | Students enrolled in Biomolecular Sciences need to pre subscribe via esc-lifesciences.zernike@rug.nl in June
The course unit assumes a good background in microbiology and genetics courses as presented in the bachelor programme
Moleculaire levenswetenschappen. | | Opmerkingen | Study load:
Lecture 15 hours
Chalktalk 8 hours
Assignment 2 hours
Practical 72 hours
Self-study 43 hours
Total 140 hours
Max 24 students |
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| 2 | Advanced Imaging techniques | MLBI0901 |
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| 3 | Advanced Light Microscopy | WMLS13004 |
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| 4 | Advanced membrane biology | MLBB003 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. B. Poolman | | Docent(en) | prof. dr. B. Poolman | | Onderwijsvorm | Hoorcollege (LC), Practisch werk (PRC), Werkcollege (T) | | Toetsvorm | Practisch werk (PR), Schriftelijk tentamen (WE) | | ECTS | 5 |
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| 5 | Advanced Protein Crystallography | MLBB007 |
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| 6 | Advanced self-organisation of social systems | MLBI0801 |
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| 7 | Advanced Statistics | WMLS19002 |
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| 8 | Advances in Chemical Biology | WMCH13009 |
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| 9 | Advances in Signal Transduction | MLBB002 |
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| 10 | Animal and Human Experimentation | MLAA01 |
This course is in transition to a completely new e-learning format in 2020. 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 or human 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 or METC 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/human 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 6 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, (5) Animal experimentation in practice, and (6) Human 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 and/or humans during their masterproject. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. B. Helm | | Docent(en) | dr. P.R.A. Heckmanprof. dr. B. Helm | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC), Werkcollege (T) | | Toetsvorm | Opdracht (AST), Practisch werk (PR), Schriftelijk tentamen (WE) | | ECTS | 5 | | Entreevoorwaarden | Students need to have completed their Bachelor Degree in Biology, Life Sciences and Technology, Biomedical Sciences, Medicine, or Pharmacy. A supervisor approved planning of a master research projects involving human or animal experimentation is required.
The course is compulsory for master students planning to work with animals during their research project and advised for those
working with humans. Following the course is exclusively possible in combination with a research master project involving animals or
humans | | Opmerkingen | The homework assignment will be judged on: (1) Grammar and spelling, (2) argumentation, (3) creativity, (4) accuracy, (5)
formation of opinions, (6) thinking process on ethical problems, and (7) text structure. A rubric is available to students. The
course is pass / fail, and to pass, each of the above 7 items needs to be passed. If the work is insufficient students need to
redo the asignment.
Participation in the tour and the interactive lecture is obligatory to complete the course |
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| 11 | Biocatalysis and Green Chemistry | MLGBB04 |
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| 12 | Biological Modelling and Model Analysis | WMLS18002 |
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| 13 | Colloquium MBB | WMBB14C001 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Docent(en) | | | ECTS | 5 |
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| 14 | Current Themes Seminar Series (Bio/EE/MB) | MLBIE09 |
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| 15 | Design for Science Education and Communication | WMEC13005 |
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| 16 | Electron Microscopy of Biological Macromolecules | MLGBB03 |
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| 17 | Essay MBB | WMBB14E001 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Docent(en) | | | ECTS | 5 |
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| 18 | History and Philosophy of Science | WMEC17001 |
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| 19 | Impact of Energy and Material Systems | WMEE13001 |
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| 20 | International Genetically Engineered Machine competition | MLBI1003 |
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| 21 | Introduction Science and Business | WNBIBEB08A |
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| 22 | Introduction Science and Policy | WNBIBEB08B |
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| 23 | Mathematical Models in Ecology and Evolution | MLBIE08C |
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| 24 | Mathematics in the Life Sciences | WMLS18001 |
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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| 25 | Meta-analyses in Ecology (20/21) | MLMB01A |
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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| 26 | Microbiological Safety | WMMP15001 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. B.L. Waarts | | Docent(en) | dr. B.L. Waarts | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC) | | Toetsvorm | Meerkeuze toets (MC), Practisch werk (PR) | | ECTS | 1 |
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| 27 | Microbiome and Health | WMBM16001 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | S. El Aidy, PhD. | | Docent(en) | S. El Aidy, PhD. | | Onderwijsvorm | Bijeenkomst (S), Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC) | | Toetsvorm | Practisch werk (PR), Presentatie (P), Verslag (R) | | ECTS | 5 | | Opmerkingen | Capacity: 32. This is a MSc. Biomedical Sciences course unit: see student portal for priority regulations. |
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| 28 | Modern Laser Microscopy | CHMLM05E |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. W.H. Roos | | Docent(en) | prof. dr. W.H. Roos | | Onderwijsvorm | Werkcollege (T), Hoorcollege (LC), Practisch werk (PRC) | | Toetsvorm | Presentatie (P), Schriftelijk tentamen (WE), Verslag (R) | | ECTS | 5 |
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| 29 | Molecular Biology of Ageing and Age-related Diseases | MLBMS08 |
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| 30 | Molecular Dynamics | MLBB005 |
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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| 31 | Molecular Methods in Ecology and Evolution (19/20) | MLBI1201 |
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| 32 | Nature of Scientific Disciplines | WMEC17002 |
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| 33 | Organelle and Membrane Biogenesis | MLBB004 |
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| 34 | Orientation on International Careers | WMLS09002 |
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| 35 | Practical Bioinformatics for Biologists 20/21 | WMLS15005 |
Practical Bioinformatics for Biologists (PBfB) introduces students to use general computational tools to work more effectively on a
daily basis. It pulls together a broad range of free powerful, and flexible tools that are applicable to geneticists, molecular biologists,
ecologists, oceanographers, physiologists, and anyone interested or in need of bioinformatics in their research. It features practical
use of bioinformatic techniques to solve real analysis problems.
PBfB will cover the “nuts and bolts” of data centered computing tasks in a Unix/Linux environment. Basics of using such an
environment, including installing and running software on remote machines will be introduced. Students will become familiar with
command line tools to explore and analyze data, and explore the use of scripting languages such as Python and R to (a) write
custom analysis tools as needed and (b) act as “glue” to make effective pipelines of other tools. Practical use of databases and
how to retrieve data from remote public databases will be introduced. Various data visualization technics, including among other GIS
tools, will be introduced using R statistical language.
Topics address in PBfB will use concrete example taken from various field, for example data from Next Generation Sequencing (NGS) technologies in genetics and molecular biology, as well as remote sensing and oceanographic data widely used in environmental ecological and evolutionary biology.
The course consists of short lectures featuring new concepts and examples interspersed with practical computer exercises and individual assignments. During the last week, students will prepare a project assignment in small groups featuring the use of the skills learned during the course and aiming at solving a concrete example. Students will present and explain their pipeline and results to the group in an oral presentation during the last days of the course. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | M.C. Fontaine, PhD. | | Docent(en) | M.C. Fontaine, PhD. | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC), Werkcollege (T) | | Toetsvorm | Opdracht (AST), Practisch werk (PR) | | ECTS | 5 | | Opmerkingen | Students are expected to bring their own personal laptops for the course. In the case a student would not have a laptop, one can be
provided during the course.
Specific instructions are send a few weeks ahead of the course on how to set-up the computer. Students should follow carefully and
meticulously those instructions |
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| 36 | Practical Modelling for Biologists | WMLS15004 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | prof. dr. J. van de Koppel | | Docent(en) | prof. dr. C.K. Hemelrijkdr. ir. D. van Oevelen | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC) | | Toetsvorm | Presentatie (P), Verslag (R) | | ECTS | 5 | | Entreevoorwaarden | The course unit assumes no prior knowledge but the course ‘Practical Bioinformatics for Biologists’ is advisable. |
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| 37 | Programming C++ for Biologists | WMLS17003 |
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 WBLS16002) 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. The final three weeks of the course (5 ECTS) are devoted to a programming project. Here, students work on a biological research question of their choice and
design and implement a simulation algorithm from scratch. They also learn how to systematically collect simulation data, and to present their results in an oral presentation, with associated annotated program code and documentation.
Students may choose to omit the final project and receive a grade for a 5 ECTS course (MLAA05) after completing the first half of the program, or may work independently on their programming project at a suitable later time. The course is also available as a selfstudy course. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. G.S. van Doorn | | Docent(en) | dr. J. Bakkerdr. G.S. van Doorn | | Onderwijsvorm | Practisch werk (PRC), Hoorcollege (LC), Opdracht (ASM) | | Toetsvorm | Opdracht (AST), Practisch werk (PR), Presentatie (P) | | ECTS | 5 | | Entreevoorwaarden | No specific entry requirements have been formulated for the course, except for elementary computer literacy. | | Opmerkingen | Maximum 25 master students/ 5 PhD students
This course is accessible for students without prior programming experience. Such students will acquire a solid background in procedural programming techniques, and will have the opportunity to develop advanced programming skills based on facultative self-study material. Students who demonstrate to possess elementary programming skills will be offered advanced classes on object-oriented programming.
This is a full-time course. It is not advisable to plan other activities in parallel |
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| 38 | Protein and Enzyme Engineering | MLBB006 |
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| 39 | Radioisotopes in Experimental Biology | MLAA03 |
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| 40 | Research Methods in SEC | WMEC13007 |
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| 41 | Research Project 1 MBB | WMBB14RP1 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Docent(en) | | | ECTS | 40 |
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| 42 | Research Project 2 MBB | WMBB14RP2 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Docent(en) | | | ECTS | 30 | | Entreevoorwaarden | research project 1 should be completed |
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| 43 | Science and the Public | WMEC17003 |
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| 44 | Scientific writing | WMBM12001 |
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| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. G. Krenning | | Docent(en) | dr. G. Krenning | | Onderwijsvorm | Hoorcollege (LC), Opdracht (ASM), Practisch werk (PRC) | | Toetsvorm | Opdracht (AST) | | ECTS | 5 |
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| 45 | Skills in Science Communication | WMEC13004 |
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| 46 | Sustainability and Society | WMEE13003 |
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| 47 | Sustainable Use of Ecosystems | WMEE16000 |
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| 48 | Synthetic Biology and Systems Chemistry | WMCH13002 |
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| 49 | Systems Integration and Sustainability | WMEE13004 |
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| 50 | Tools and approaches of systems biology | MLBB010 |
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| 51 | Transcriptomics | MLBB017A |
| In this course, theory and practical’s are combined to give an in-depth view in the of transcriptomics research on prokaryotes in answering questions in modern molecular genetics and -biology research. The projects selected for this course are based on research questions of PhD students and post-doctoral fellows of the department of Molecular Genetics. In principle the experiment have not been done before, which means that the generated data is novel. This master course is divided into three parts. The first part focuses on the experimental design of a biological experiment, the theoretical background of Next Generation Sequencing (DNASeq and RNA-Seq) and on how transcriptomics data is used in research. Students will grow bacteria according to the experimental design and isolate RNA from the various samples. The second part consists of quality control of the RNA and the library preparation for all samples to will be loaded on a Next Generation Sequencing machine to generate the transcriptomics data. On the basis of lectures on specific software , statistics and High Performance Computing, required for transcriptome analyses, the students will analyze their own datasets. During the third part of the course, the analyzed data will be coupled to biological knowledge by using additional statistical methods and students will draw conclusions from their analyses. Also, based on their findings, the students will be encouraged to propose ideas for further experiments. |
| Faculteit | Science and Engineering | | Voertaal | Engels | | Coordinator | dr. A. de Jong | | Docent(en) | D. Incarnato, PhD.prof. dr. J. Kok | | Onderwijsvorm | Hoorcollege (LC), Practisch werk (PRC), Werkcollege (T) | | Toetsvorm | Practisch werk (PR), Presentatie (P), Verslag (R) | | ECTS | 5 | | Entreevoorwaarden | The course assumes prior knowledge acquired from Microbiology & Genetics research or equivalent. | | Opmerkingen | Course coordinator: dr Anne de Jong, anne.de.jong@rug.nl, 050 363 2047
Location:
Research group Molecular Genetics (GBB), Centre for Life Sciences.
Students in Biomolecular Sciences have priority for this course.
capacity: 18 students |
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| 52 | Wetenschapsvoorlichting en -journalistiek | WNEC1WVJ5 |
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