Search result: Catalogue data in Spring Semester 2018
Biotechnology Master  More information at www.master-biotech.ethz.ch | ||||||
 Master Studies (Programme Regulations 2017) | ||||||
| Core Courses Students need to acquire a total of 8 ECTS in lectures in this category. The list of core courses is a closed list, no other course can be added to this category. | ||||||
| Practical Training Students need to acquire a total of 14 ECTS in lab courses. All listed lab courses are mandatory. | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
|---|---|---|---|---|---|---|
| 636-0207-00L | Lab Course: Cellular Engineering Stem Cells  Only for Biotechnology MSc, Programme Regulations 2017. Attention: This lab course was offered in previous semesters with the number: 626-0806-00L "Laboratory Course Stem Cell Purification, Culture and Manipulation”. Students that already passed course 626-0806-00L cannot receive credits for course 636-0207-00L. | O | 2 credits | 6P | T. Schroeder | |
| Abstract | Mammalian stem cells of different organs are purified, cultured, differentiated, analyzed and manipulated. Plasmids and viral vectors will be cloned, produced and transfected / transduced to manipulate stem cells. Computational and analytical molecular biology methods, FACS and imaging and lectures complement the program. | |||||
| Learning objective | Independent planning and conducting of experiments with mammalian stem cells including all steps from culturing different cell lines to DNA transfection / transduction and expression analysis by different analytical methods. Documenting and writing a report on conducted experiments and results. | |||||
| Content | Practical course on purification of primary mammalian stem cells, culture of primary stem cells and stem cell lines, characterization, manipulation and differentiation of stem cells. Construction of plasmids or viral vectors for gene expression, DNA transfer by transfection and transduction, analysis of gene expression by fluorescent proteins, PCR, fluorescence-activated cell sorting (FACS), imaging. Documentation of experiments in a laboratory journal, writing of a report on the experiments and results. | |||||
| 636-0206-00L | Lab Course: Cellular Engineering Mammalian Cells Only for Biotechnology MSc, Programme Regulations 2017 Attention: This lab course was offered in previous semesters with the number: 626-0802-00L "Practical Course in Mammalian Cell Biotechnology”. Students that already passed course 626-0802-00L cannot receive credits for course 636-0206-00L. | O | 2 credits | 6P | M. Fussenegger, M. Folcher | |
| Abstract | Mammalian cells will be transfected and transduced for the production of biopharmaceuticals, for drug discovery as well as for the design of synthetic biology-inspired programmable gene circuits. A wide array of analytical techniques, lectures, and excursions to biotech companies will complement the practical part. | |||||
| Learning objective | Independent planning and conducting of experiments with mammalian cells including all steps from culturing different cell lines to DNA transfection/transduction and expression analysis using a wide array of analytical methods. | |||||
| Content | A practical course on characterization and cultivation of mammalian cells, DNA transfer by transfection, construction of synthetic gene networks, analysis of gene expression by enzymatic and immunological methods and fluorescent proteins, bioprocessing, mammalian cell-based assays for drug discovery and diagnostics. Excursions to Biotech/Pharma companies. | |||||
| Lecture notes | Will be distributed on first day of the practical course | |||||
| 636-0204-00L | Lab Course: Microbial Biotechnology Only for Biotechnology MSc, Programme Regulations 2017. | O | 2 credits | 5P | M. Held | |
| Abstract | Students will learn the foundations of monoseptic working practice and create and screen microbial libraries for identification of strains expressing different fluorescent protein (XFP) levels | |||||
| Learning objective | Students will learn the foundations of monoseptic working practice and create and screen microbial libraries for identification of strains expressing different fluorescent protein (XFP) levels | |||||
| Content | Block A: Handling and preparation and of microbial libraries D1: Introduction to microbiological cultures and monoseptic working techniques. D2: Plasmid-based expression systems and variation of XFP synthesis levels via site-directed RBS mutagenesis. Block B: Library screening D3: In vivo screening for XFP expression levels. D4: Analysis of XFP levels via SDS-PAGE analysis. RBS-sequencing. Block C: Hit recovery and validation D5: In silico analysis of RBS variants. D6: Cellular XFP content for selected variants at different culture conditions. Block D: Data analysis and presentation D7: Protein expression analysis. Q&A for reports and presentations. D8: Final presentations and wrap-up. | |||||
| Lecture notes | Material will be provided during the course. | |||||
| Literature | (1) Reetz MT, Kahakeaw D, and Lohmer R. "Addressing the numbers problem in directed evolution." ChemBioChem 2008 (2) Jeschek M, Gerngross D, and Panke S. “Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.” Nat. Commun. 2016 (3) Salis HM. “The ribosome binding site calculator.” Methods Enzymol. 2011 (4) Nienhaus G, Nienhaus K, and Wiedenmann J. "Structure–Function Relationships in Fluorescent Marker Proteins of the Green Fluorescent Protein Family." Fluorescent Proteins I. Springer Berlin Heidelberg, 2011 General introduction to microbiology: (5) Schlegel HG, and Zaborosch C. “General Microbiology.” Cambridge University Press 1993 (6) Pirt JS. “Principles of microbe and cell cultivation.” Blackwell Scientific Publications 1975 | |||||
| 636-0205-00L | Lab Course: Mammalian Gene Circuits Only for Biotechnology MSc, Programme Regulations 2017. | O | 2 credits | 5P | Y. Benenson | |
| Abstract | The students are trained in basic techniques in construction and characterization of synthetic gene circuits in mammalian cells. Experimental circuits are built with both the input and the output conjugated to fluorescent reporters, allowing characterization at the single cell level. | |||||
| Learning objective | The objective of the course is to construct a genetic sensor for a molecular regulatory input such as microRNA or a transcription factor and characterize the input/output relationship of this sensor with the help of fluorescent reporters, fluorescent microscopy and fluorescent-activated cell sorting. The emphasis is on single-cell characterization. | |||||
| Content | The course will take place over 4 weeks, with 2 days per week spent on lab work. The 4 weeks will be dedicated to the following activities Week 1: Introduction to the course; supervised construct design and detailed planning. Cloning of the constructs: part 1. Week 2: Cloning of the constructs, purification and characterization of DNA constructs Week 3: Cell culture transfection, microscopy and flow cytometry characterization Week 4: Data analysis and preparation of the final report; possibility to repeat failed experiments. | |||||
| Lecture notes | Preparatory materials will be provided before the start of the course. | |||||
| Literature | Will be provided before the course | |||||
| Advanced Courses Students need to aquire a total of 24 ECTS in this category. The list of advanced courses is a closed list, no other course can be added to this category. | ||||||
| Biomelecular-Orientated | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0109-00L | Stem Cells: Biology and Therapeutic Manipulation Attention: This course was offered in previous semesters with the number: 636-0013-00L "Stem Cells: Biology and Therapeutic Manipulation". Students that already passed course 636-0013-00L cannot receive credits for course 636-0109-00L. | W | 4 credits | 3G | T. Schroeder | |
| Abstract | Stem cells are central in tissue regeneration and repair, and hold great potential for therapy. We will discuss the role of stem cells in health and disease, and possibilities to manipulate their behavior for therapeutic application. Basic molecular and cell biology, engineering and novel technologies relevant for stem cell research and therapy will be discussed. | |||||
| Learning objective | Understanding of current knowledge, and lack thereof, in stem cell biology, regenerative medicine and required technologies. Theoretical preparation for practical laboratory experimentation with stem cells. | |||||
| Content | We will use different diseases to discuss how to potentially model, diagnose or heal them by stem cell based therapies. This will be used as a guiding framework to discuss relevant concepts and technologies in cell and molecular biology, engineering, imaging, bioinformatics, tissue engineering, that are required to manipulate stem cells for therapeutic application. Topics will include: - Embryonic and adult stem cells and their niches - Induced stem cells by directed reprogramming - Relevant basic cell biology and developmental biology - Relevant molecular biology - Cell culture systems - Cell fates and their molecular control by transcription factors and signalling pathways - Cell reprogramming - Disease modelling - Tissue engineering - Bioimaging, Bioinformatics - Single cell technologies | |||||
| 636-0110-00L | ImmunoEngineering Attention: This course was offered in previous semesters with the number: 636-0010-00L "Biomolecular Engineering and Immunotechnology". Students that already passed course 636-0010-00L cannot receive credits for course 636-0110-00L. | W | 4 credits | 3V | S. Reddy | |
| Abstract | Immunoengineering is an emerging area of research that uses technology and engineering principles to understand and manipulate the immune system. This is a highly interdisciplinary field and thus the instructor will present an integrated view that will include basic immunology, systems immunology, and synthetic immunology. | |||||
| Learning objective | The objective of this course is to introduce the students to the basic principles and applications of Immunoengineering. There will be an emphasis directed towards applications directly relevant in immunotherapy and biotechnology. This course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course. | |||||
| Content | Immunoengineering will be divided into three primary sections: i) basic principles in immunology; ii) systems immunology; iii) synthetic immunology. I. Basic principles in immunology will cover the foundational concepts of innate and adaptive immunity. Topics include immunogenetics, pattern recognition receptors, lymphocyte receptors, humoral and T cell responses. II. Systems immunology uses quantitative multiscale measurements and computational biology to describe and understand the complexity of the immune system. In this section we will cover high-throughput methods that are used to understand and profile immune responses. III. Synthetic immunology is based on using methods in molecular and cellular engineering to control immune cell function and behavior. In this section students will learn about how immune receptors and cells are being engineered for applications such as cancer immunotherapy and precision and personalized medicine. | |||||
| Literature | Reading material from Janeway's Immunobiology will be distributed, so students do not need to worry about purchasing or obtaining it. Supporting reading material from research articles will be provided to students. | |||||
| Prerequisites / Notice | This course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course. | |||||
| 636-0114-00L | Microsensors and Microsystems Attention: This course was offered in previous semesters with the number: 636-0004-00 "Microsensors and Microsystems". Students that already passed course 636-0004-00 cannot receive credits for course 636-0114-00. Prerequisites: Physics I and Physics II highly recommended. This class builds on the contents of course 636-0103-00L, "Microtechnology", which are assumed to be known | W | 4 credits | 3G | A. Hierlemann | |
| Abstract | Students are introduced to microsensor and microsystem technology, the different materials and associated micromachining and fabrication techniques. They become acquainted with fundamentals of different transducers and their applications. | |||||
| Learning objective | Students are introduced to microsensor and microsystem technology. The students will get to know the different materials (silicon, glass, plastics) and the respective micromachining and fabrication techniques. They will become acquainted with the fundamentals of the different transducers including mechanical, thermal, magnetic, chemical, optical, and biosensors. They also will get to know strategies to integrate components into microsystems. | |||||
| Content | Introduction to microensors and microsystems # Brief introduction to semiconductors # Silicon and glass micromachining # Wafer bonding # Plastic materials and their micromachining # Fundamentals of different transducers # Mechanical sensors # Thermal sensors # Magnetic sensors # Optical devices # Chemical and biosensors # Microfluidics # BioMEMS | |||||
| Lecture notes | Handouts in English | |||||
| Literature | - S.M. Sze, "Semiconductor Devices, Physics and Technology", 2nd edition, Wiley, 2002 - W. Menz, J. Mohr, O. Paul, “Microsystem Technology”, Wiley-VCH, 2001 - G. T. A. Kovacs, “Micromachined Transducers Sourcebook”, McGraw-Hill, 1998 - M. J. Madou, “Fundamentals of Microfabrication", 2nd ed., CRC Press, 2002 - S.A. Campbell, "The Science and Engineering of Microelectronic Fabrication", 2nd edition, Oxford University Press, 2001 | |||||
| Prerequisites / Notice | Lab URL: www.bel.ethz.ch | |||||
| 636-0113-00L | Genome Engineering | W | 4 credits | 3V | R. Platt | |
| Abstract | This course is an introduction to genome engineering and an examination of recent advancements and future challenges. It covers the discovery and development of gene editing technologies and their applications in basic and applied research. The focus is on gaining an in-depth molecular and cellular understanding of the technologies and also insight into how these tools can be used and further deve | |||||
| Learning objective | The objective of this course is to learn how gene editing technologies function at the molecular and cellular level, and how they are leveraged to understand the role of genetic elements in biological processes. Students will be introduced to the history and motivation behind the discovery and development of transformative genome engineering technologies, and also gain insight into the ethical, safety, and regulatory facets shaping the field. | |||||
| Content | The course content is comprised of lectures, discussions of important literature in the field, and a project. Lectures in Genome Engineering will be technology-focused and incorporate: 1) historical context to motivate the need for developing the technology, 2) development of the technology from concept to robust tool, 3) methods to discover, characterize, and evaluate the technology, and 4) applications of the technology in basic and applied research. Discussions of important literature in the field will be conducted in class, one course meeting following a lecture covering the topic material and assignment of the reading. The project will be team-based and entail devising a solution to a critical need in the field. Main topics: --Discovery and development of genome editing technologies --The prokaryotic adaptive immune system CRISPR-Cas --Genome engineering methods for generating genetically engineered model systems --Genotype-phenotype linkage via genetic screens --Massively paralleled perturbation and phenotyping --Gene editing tools as genetic recording devices --Gene editing tools as diagnostics and therapeutics --Ethics, safety, and regulatory facets of genome engineering | |||||
| Lecture notes | Handout during the course. | |||||
| Literature | Peer-reviewed scientific publications will be assigned to complement lecture content. | |||||
| 636-0022-00L | Design of Experiments | W | 4 credits | 3G | H.‑M. Kaltenbach | |
| Abstract | The course introduces 'classical' statistical design of experiments, particularly designs for blocking, full and fractional factorial designs with confounding, and response surface methods. Topics covered include (restricted) randomization and blocking, sample size and power calculations, confounding, and basics of analysis-of-variance methods for analysis including random effects and nesting. | |||||
| Learning objective | Students will learn about the statistical basics of designing and analyzing experiments with multiple qualitative and/or quantitative variables. Students will be able to construct designs for efficiently identifying important influence factors in their experiments, use sequential designs for optimizing experimental conditions, and correctly handle analyses with nested sampling or involving multiple comparisons. | |||||
| Content | The course introduces the basics of statistical design of experiments. We will start by discussing the role of randomization for the validity of inferences, see how replication (i.e., sample size) affects the precision of estimates that can be made, how we deal with nested replication (for example, taking several measurements on the same animal), and how we correctly handle multiple comparisons based on the same data. We will then discuss how restrictions of randomization lead to blocked designs, which serve to improve precision of comparisons between experimental conditions. Such designs are also important to avoid confounding of the experimental effect of interest with other effects of no interest, e.g., to handle batch effects that are common in biological experimentation. Next, we learn how to design efficient experiments with multiple factors of interest. In contrast to a one-variable-at-a time approach, factorial designs allow investigation of multiple factors simultaneously, and under some assumptions on the interplay of the factors, we may even get away with only a fraction of all possible factor combinations while still getting all the information we need. We then discuss optimizing the combination of factors with respect to some response function, such as optimizing the composition of a medium solution to achieve maximum growth rate. Response surface methods offer an efficient and systematic way of finding optimal conditions with low effort through sequential experimentation; they are also common in industrial (engineering) applications. Throughout the course, we will touch on several additional topics without getting into much detail, such as designs that are 'optimal' for either inference or prediction, and designs where experimental conditions are nested (e.g., split-plot designs). The course assumes familiarity with the content of a typical introductory course in statistics: distributions and random variables, estimators and confidence intervals, hypothesis testing using p-values and false positives/negatives, and basics of linear regression or analysis of variance. | |||||
| Lecture notes | Course material will be made available at: http://www.csb.ethz.ch/education/lectures.html | |||||
| Literature | Main text: Gary W. Oehlert: A first course in design and analysis of experiments, Freeman (http://users.stat.umn.edu/~gary/Book.html) Additional texts: D. R. Cox: Planning of Experiments, Wiley G. Casella: Statistical Design, Springer H. R. Lindman: Analysis of variance in complex experimental designs, Freeman (now Springer) | |||||
| 636-0115-00L | Biochemical Engineering | W | 4 credits | 3G | S. Panke, W. Minas | |
| Abstract | The course covers the fundamentals of implementing biotechnological reactions and cultivations into reactors and major methods of product purification. | |||||
| Learning objective | The objective is to instruct students in the key concepts that are required for efficient application of biotechnological systems (enzymes and cells) for the production of chemicals and proteins. | |||||
| Content | Enzyme kinetics – mass transfer in heterogeneous systems – enzyme reactors – residence time distributions - upstream processing of fermentation processes – ideal reactors – macrokinetics - gas transfer – membrane processes – chromatography | |||||
| Lecture notes | Handouts and text book references will be provided over the course. | |||||
| Literature | Eg Pauline Doran, Bioprocess Engineering, Clark & Blanch, Biochemical Engineering, Harrison and Todd, Bioseparation Science and Engineering | |||||
| 636-0112-00L | Analytical Methods and Lab-on-Chip Technology for Biology and Molecular Diagnostics | W | 4 credits | 3G | P. S. Dittrich | |
| Abstract | Analytical methods are the key for a comprehensive understanding of biological systems. This course introduces modern bioanalytical concepts and methods that are applied in the life sciences. Techniques for sample preparation, fluid handling, and detection, including microfluidics, microarray technology, immunological methods, sensors and biosensors, and various spectroscopic detection techniques | |||||
| Learning objective | Students will learn the basic principles, potential and limitations of analytical methods and lab-on-chip technology. | |||||
| Content | Analytical methods are the key for a comprehensive understanding of biological systems. This course introduces into modern bioanalytical concepts and methods that are applied in the life sciences. The lecture includes discussions of highly topical studies. Topics will include: Targets: Biomolecules, biomarkers, signalling factors – what and where to measure Detection: Fluorescence spectroscopy, related techniques and label-free detection methods Basic principles of microfluidics/lab-on-chip technology Applied microfluidics: Single-cell analysis, medical applications and point-of-care diagnostic Microarray technology Immunological methods Sensors and biosensors | |||||
| Lecture notes | Handouts during the course . | |||||
| 636-0111-00L | Synthetic Biology I Attention: This course was offered in previous semesters with the number: 636-0002-00L "Synthetic Biology I". Students that already passed course 636-0002-00L cannot receive credits for course 636-0111-00L. | W | 4 credits | 3G | S. Panke, J. Stelling | |
| Abstract | Theoretical & practical introduction into the design of dynamic biological systems at different levels of abstraction, ranging from biological fundamentals of systems design (introduction to bacterial gene regulation, elements of transcriptional & translational control, advanced genetic engineering) to engineering design principles (standards, abstractions) mathematical modelling & systems desig | |||||
| Learning objective | After the course, students will be able to theoretically master the biological and engineering fundamentals required for biological design to be able to participate in the international iGEM competition (see www.syntheticbiology.ethz.ch). | |||||
| Content | The overall goal of the course is to familiarize the students with the potential, the requirements and the problems of designing dynamic biological elements that are of central importance for manipulating biological systems, primarily (but not exclusively) prokaryotic systems. Next, the students will be taken through a number of successful examples of biological design, such as toggle switches, pulse generators, and oscillating systems, and apply the biological and engineering fundamentals to these examples, so that they get hands-on experience on how to integrate the various disciplines on their way to designing biological systems. | |||||
| Lecture notes | Handouts during classes. | |||||
| Literature | Mark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press Uri Alon, An Introduction to Systems Biology, Chapman & Hall | |||||
| Prerequisites / Notice | 1) Though we do not place a formal requirement for previous participation in particular courses, we expect all participants to be familiar with a certain level of biology and of mathematics. Specifically, there will be material for self study available on http://www.bsse.ethz.ch/bpl/education/index as of mid January, and everybody is expected to be fully familiar with this material BEFORE THE CLASS BEGINS to be able to follow the different lectures. Please contact sven.panke@bsse.ethz.ch for access to material 2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (www.syntheticbiology.ethz.ch, http://www.igem.org). This competition is also the contents of the course Synthetic Biology II. http://www.bsse.ethz.ch/bpl/education/index | |||||
| 636-0116-00L | Nanomachines of the Cell (Part II): Engineering and Application Attention: This course was offered in previous semesters with the number: 636-0008-00L "Nanomachines of the Cell II". Students that already passed course 636-0008-00 cannot receive credits for course 636-0116-00. Prerequisites: Students should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering. | W | 4 credits | 3G | D. J. Müller | |
| Abstract | This second part of the lecture series "Nanomachines of the Cell" extends what has been learned in the first module. "Engineering and application" will be thus a consolidation of the concepts of functional biomolecular units of the cell as nanoscopic machines. The specific aim is to be able to use these cellular machines in more complex biotechnological processes as nanoscale functional elements. | |||||
| Learning objective | Gain of an interdisciplinary research and development competence which qualifies for scientific work (master`s or doctoral thesis) as well as for work in the research and development department of a biotechnological company. The module is of general use in nano- and biotechnological courses of study focusing modern biomolecular technologies. | |||||
| Content | Assembly of fibrillar structures. Filamentous structures inside and outside the cell. Principles of polymerisation dynamics: Nucleation, polarity, equilibrium and non-equilibrium driven polymerization, treadmilling, energy consumption, asymmetric building blocks, ... Self-assembly processes in polymer chemistry and physics. Self-assembly processes into two- and three-dimensions. Filaments of the cell: F-actin, intermediate filaments, microtubuli, and collagen. Filaments of the cell fulfil several functions: Structural integrity and functionalization of the environment. How does the cell control these functions? Example: The collagen family. Molecular and supramolecular structure of collagens. On the importance of motifs on the molecular packing mechanism of collagen. Occurrence of collagens and functional roles. Diseases related to collagen malfunction. Properties of collagen: Flexibility, elasticity, strength, persistence length, conformations, binding sites, signal transduction, ... Proteins that functionalize collagens. Can we use these proteins as a biomolecular toolbox to build up three-dimensional functional scaffolds? Directing and controlling the self-assembly of collagen type I. Learning which factors determine the supramolecular structure of self-assembled collagen. Using this knowledge to guide the self-assembly of collagen into nanoscopic scaffolds. Creating intelligent collagen scaffolds to guide cellular functions. Ways to functionalize collagen matrices for their use in biotechnology and tissue engineering. The great challenges: How can we create three-dimensional collagen scaffolds? DNA origami. Using DNA to build artificial three-dimensional structures at nanometer precision. From smilies to mechanical building blocks to three-dimensional containers almost every three-dimensional structure can be build. Self-assembly process of DNA. 'Programming the DNA': How to engineer the DNA sequence to promote it's self-assembly into a three-dimensional structure. How to engineer the DNA sequence to promote the self-assembly of the DNA into a precise three-dimensional nanoscopic arrangement. Engineering lessons: How to functionalize three-dimensional DNA containers so that they have a different fluorescent protein on each corner? How to functionalize a functionalize three-dimensional DNA container so that it frees its cargo on response to an external stimuli? How to functionalize a three-dimensional DNA container so that a cell can opens it and extract the cargo? Where may DNA origami be in 10 years? Comparative approaches using peptides to design origami. Microtubuli. Occurrence, structure, function, and properties. Cell mechanics, motility and dynamic. Mitosis. Cargo transport by motor proteins. Assembly mechanisms, tubulin subunits, nucleation, polarity, kinetics, concentration dependent growth, GTP dependency, dynamic instability, capping, ..). Designing three-dimensional structures using microtubuli. Creating a racing track: Motility assays. Designing and microstructuring of supports as circuits for molecular shuttles. Biofunctionalization of the circuits. Transporting molecular cargo along circuits. Engineering molecular devices to switch the transport 'on' and 'off'. Motor proteins. Introduction: Translational motors, rotary motors, chemical driven motors, light-driven motors, unidirectional and bidirectional motors, reversibility, molecular ratchets, future visions. Example of rotary motors: F-ATP synthase and flagella motor. F-ATP synthase was introduced in (Nanomachines of the cell Part I). Common and different engineering principles of the F-ATP synthase and the flagella motor. Structure, function, energy source, and rotational modes. Controlled assembly of a complex machinery such as the flagella motor. Are there ways to exchange the building blocks of the motor and to 'tune' it? Motor proteins of the cytoskeleton. iViruses. Prediction, design und engineering of cellular machines. | |||||
| Lecture notes | Hand out will be given to students at lecture. | |||||
| Literature | lberts et al: Molecular Biology of the cell Biochemistry (5th edition), Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; ISBN 0-7167-4684-0, Freeman Principles of Biochemistry, Nelson & Cox; ISBN: 1-57259-153-6, Worth Publishers, New York Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania Intermolecular & Surface Forces, Israelachvili; ISBN: 0-12-375181-0, Academic Press, London Proteins: Biochemistry and Biotechnolgy, Walsh; ISBN: 0-471-899070, Wiley & Sons, New York Textbook of Biochemistry with Clinical Correlations, Devlin; ISBN: 0-471-411361, Wiley & Sons, New York Molecular Virology, Modrow et al.; ISBN: 3-8274-1086-X, Spektrum Verlag, Heidelberg | |||||
| Prerequisites / Notice | Students should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering. The module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher. | |||||
| System-Orientated | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0109-00L | Stem Cells: Biology and Therapeutic Manipulation Attention: This course was offered in previous semesters with the number: 636-0013-00L "Stem Cells: Biology and Therapeutic Manipulation". Students that already passed course 636-0013-00L cannot receive credits for course 636-0109-00L. | W | 4 credits | 3G | T. Schroeder | |
| Abstract | Stem cells are central in tissue regeneration and repair, and hold great potential for therapy. We will discuss the role of stem cells in health and disease, and possibilities to manipulate their behavior for therapeutic application. Basic molecular and cell biology, engineering and novel technologies relevant for stem cell research and therapy will be discussed. | |||||
| Learning objective | Understanding of current knowledge, and lack thereof, in stem cell biology, regenerative medicine and required technologies. Theoretical preparation for practical laboratory experimentation with stem cells. | |||||
| Content | We will use different diseases to discuss how to potentially model, diagnose or heal them by stem cell based therapies. This will be used as a guiding framework to discuss relevant concepts and technologies in cell and molecular biology, engineering, imaging, bioinformatics, tissue engineering, that are required to manipulate stem cells for therapeutic application. Topics will include: - Embryonic and adult stem cells and their niches - Induced stem cells by directed reprogramming - Relevant basic cell biology and developmental biology - Relevant molecular biology - Cell culture systems - Cell fates and their molecular control by transcription factors and signalling pathways - Cell reprogramming - Disease modelling - Tissue engineering - Bioimaging, Bioinformatics - Single cell technologies | |||||
| 636-0110-00L | ImmunoEngineering Attention: This course was offered in previous semesters with the number: 636-0010-00L "Biomolecular Engineering and Immunotechnology". Students that already passed course 636-0010-00L cannot receive credits for course 636-0110-00L. | W | 4 credits | 3V | S. Reddy | |
| Abstract | Immunoengineering is an emerging area of research that uses technology and engineering principles to understand and manipulate the immune system. This is a highly interdisciplinary field and thus the instructor will present an integrated view that will include basic immunology, systems immunology, and synthetic immunology. | |||||
| Learning objective | The objective of this course is to introduce the students to the basic principles and applications of Immunoengineering. There will be an emphasis directed towards applications directly relevant in immunotherapy and biotechnology. This course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course. | |||||
| Content | Immunoengineering will be divided into three primary sections: i) basic principles in immunology; ii) systems immunology; iii) synthetic immunology. I. Basic principles in immunology will cover the foundational concepts of innate and adaptive immunity. Topics include immunogenetics, pattern recognition receptors, lymphocyte receptors, humoral and T cell responses. II. Systems immunology uses quantitative multiscale measurements and computational biology to describe and understand the complexity of the immune system. In this section we will cover high-throughput methods that are used to understand and profile immune responses. III. Synthetic immunology is based on using methods in molecular and cellular engineering to control immune cell function and behavior. In this section students will learn about how immune receptors and cells are being engineered for applications such as cancer immunotherapy and precision and personalized medicine. | |||||
| Literature | Reading material from Janeway's Immunobiology will be distributed, so students do not need to worry about purchasing or obtaining it. Supporting reading material from research articles will be provided to students. | |||||
| Prerequisites / Notice | This course requires prerequisite knowledge of molecular biology, biochemistry, cell biology, and genetics; these subjects will only be reviewed briefly during the course. | |||||
| 636-0114-00L | Microsensors and Microsystems Attention: This course was offered in previous semesters with the number: 636-0004-00 "Microsensors and Microsystems". Students that already passed course 636-0004-00 cannot receive credits for course 636-0114-00. Prerequisites: Physics I and Physics II highly recommended. This class builds on the contents of course 636-0103-00L, "Microtechnology", which are assumed to be known | W | 4 credits | 3G | A. Hierlemann | |
| Abstract | Students are introduced to microsensor and microsystem technology, the different materials and associated micromachining and fabrication techniques. They become acquainted with fundamentals of different transducers and their applications. | |||||
| Learning objective | Students are introduced to microsensor and microsystem technology. The students will get to know the different materials (silicon, glass, plastics) and the respective micromachining and fabrication techniques. They will become acquainted with the fundamentals of the different transducers including mechanical, thermal, magnetic, chemical, optical, and biosensors. They also will get to know strategies to integrate components into microsystems. | |||||
| Content | Introduction to microensors and microsystems # Brief introduction to semiconductors # Silicon and glass micromachining # Wafer bonding # Plastic materials and their micromachining # Fundamentals of different transducers # Mechanical sensors # Thermal sensors # Magnetic sensors # Optical devices # Chemical and biosensors # Microfluidics # BioMEMS | |||||
| Lecture notes | Handouts in English | |||||
| Literature | - S.M. Sze, "Semiconductor Devices, Physics and Technology", 2nd edition, Wiley, 2002 - W. Menz, J. Mohr, O. Paul, “Microsystem Technology”, Wiley-VCH, 2001 - G. T. A. Kovacs, “Micromachined Transducers Sourcebook”, McGraw-Hill, 1998 - M. J. Madou, “Fundamentals of Microfabrication", 2nd ed., CRC Press, 2002 - S.A. Campbell, "The Science and Engineering of Microelectronic Fabrication", 2nd edition, Oxford University Press, 2001 | |||||
| Prerequisites / Notice | Lab URL: www.bel.ethz.ch | |||||
| 636-0113-00L | Genome Engineering | W | 4 credits | 3V | R. Platt | |
| Abstract | This course is an introduction to genome engineering and an examination of recent advancements and future challenges. It covers the discovery and development of gene editing technologies and their applications in basic and applied research. The focus is on gaining an in-depth molecular and cellular understanding of the technologies and also insight into how these tools can be used and further deve | |||||
| Learning objective | The objective of this course is to learn how gene editing technologies function at the molecular and cellular level, and how they are leveraged to understand the role of genetic elements in biological processes. Students will be introduced to the history and motivation behind the discovery and development of transformative genome engineering technologies, and also gain insight into the ethical, safety, and regulatory facets shaping the field. | |||||
| Content | The course content is comprised of lectures, discussions of important literature in the field, and a project. Lectures in Genome Engineering will be technology-focused and incorporate: 1) historical context to motivate the need for developing the technology, 2) development of the technology from concept to robust tool, 3) methods to discover, characterize, and evaluate the technology, and 4) applications of the technology in basic and applied research. Discussions of important literature in the field will be conducted in class, one course meeting following a lecture covering the topic material and assignment of the reading. The project will be team-based and entail devising a solution to a critical need in the field. Main topics: --Discovery and development of genome editing technologies --The prokaryotic adaptive immune system CRISPR-Cas --Genome engineering methods for generating genetically engineered model systems --Genotype-phenotype linkage via genetic screens --Massively paralleled perturbation and phenotyping --Gene editing tools as genetic recording devices --Gene editing tools as diagnostics and therapeutics --Ethics, safety, and regulatory facets of genome engineering | |||||
| Lecture notes | Handout during the course. | |||||
| Literature | Peer-reviewed scientific publications will be assigned to complement lecture content. | |||||
| 636-0022-00L | Design of Experiments | W | 4 credits | 3G | H.‑M. Kaltenbach | |
| Abstract | The course introduces 'classical' statistical design of experiments, particularly designs for blocking, full and fractional factorial designs with confounding, and response surface methods. Topics covered include (restricted) randomization and blocking, sample size and power calculations, confounding, and basics of analysis-of-variance methods for analysis including random effects and nesting. | |||||
| Learning objective | Students will learn about the statistical basics of designing and analyzing experiments with multiple qualitative and/or quantitative variables. Students will be able to construct designs for efficiently identifying important influence factors in their experiments, use sequential designs for optimizing experimental conditions, and correctly handle analyses with nested sampling or involving multiple comparisons. | |||||
| Content | The course introduces the basics of statistical design of experiments. We will start by discussing the role of randomization for the validity of inferences, see how replication (i.e., sample size) affects the precision of estimates that can be made, how we deal with nested replication (for example, taking several measurements on the same animal), and how we correctly handle multiple comparisons based on the same data. We will then discuss how restrictions of randomization lead to blocked designs, which serve to improve precision of comparisons between experimental conditions. Such designs are also important to avoid confounding of the experimental effect of interest with other effects of no interest, e.g., to handle batch effects that are common in biological experimentation. Next, we learn how to design efficient experiments with multiple factors of interest. In contrast to a one-variable-at-a time approach, factorial designs allow investigation of multiple factors simultaneously, and under some assumptions on the interplay of the factors, we may even get away with only a fraction of all possible factor combinations while still getting all the information we need. We then discuss optimizing the combination of factors with respect to some response function, such as optimizing the composition of a medium solution to achieve maximum growth rate. Response surface methods offer an efficient and systematic way of finding optimal conditions with low effort through sequential experimentation; they are also common in industrial (engineering) applications. Throughout the course, we will touch on several additional topics without getting into much detail, such as designs that are 'optimal' for either inference or prediction, and designs where experimental conditions are nested (e.g., split-plot designs). The course assumes familiarity with the content of a typical introductory course in statistics: distributions and random variables, estimators and confidence intervals, hypothesis testing using p-values and false positives/negatives, and basics of linear regression or analysis of variance. | |||||
| Lecture notes | Course material will be made available at: http://www.csb.ethz.ch/education/lectures.html | |||||
| Literature | Main text: Gary W. Oehlert: A first course in design and analysis of experiments, Freeman (http://users.stat.umn.edu/~gary/Book.html) Additional texts: D. R. Cox: Planning of Experiments, Wiley G. Casella: Statistical Design, Springer H. R. Lindman: Analysis of variance in complex experimental designs, Freeman (now Springer) | |||||
| 636-0115-00L | Biochemical Engineering | W | 4 credits | 3G | S. Panke, W. Minas | |
| Abstract | The course covers the fundamentals of implementing biotechnological reactions and cultivations into reactors and major methods of product purification. | |||||
| Learning objective | The objective is to instruct students in the key concepts that are required for efficient application of biotechnological systems (enzymes and cells) for the production of chemicals and proteins. | |||||
| Content | Enzyme kinetics – mass transfer in heterogeneous systems – enzyme reactors – residence time distributions - upstream processing of fermentation processes – ideal reactors – macrokinetics - gas transfer – membrane processes – chromatography | |||||
| Lecture notes | Handouts and text book references will be provided over the course. | |||||
| Literature | Eg Pauline Doran, Bioprocess Engineering, Clark & Blanch, Biochemical Engineering, Harrison and Todd, Bioseparation Science and Engineering | |||||
| 636-0112-00L | Analytical Methods and Lab-on-Chip Technology for Biology and Molecular Diagnostics | W | 4 credits | 3G | P. S. Dittrich | |
| Abstract | Analytical methods are the key for a comprehensive understanding of biological systems. This course introduces modern bioanalytical concepts and methods that are applied in the life sciences. Techniques for sample preparation, fluid handling, and detection, including microfluidics, microarray technology, immunological methods, sensors and biosensors, and various spectroscopic detection techniques | |||||
| Learning objective | Students will learn the basic principles, potential and limitations of analytical methods and lab-on-chip technology. | |||||
| Content | Analytical methods are the key for a comprehensive understanding of biological systems. This course introduces into modern bioanalytical concepts and methods that are applied in the life sciences. The lecture includes discussions of highly topical studies. Topics will include: Targets: Biomolecules, biomarkers, signalling factors – what and where to measure Detection: Fluorescence spectroscopy, related techniques and label-free detection methods Basic principles of microfluidics/lab-on-chip technology Applied microfluidics: Single-cell analysis, medical applications and point-of-care diagnostic Microarray technology Immunological methods Sensors and biosensors | |||||
| Lecture notes | Handouts during the course . | |||||
| 636-0111-00L | Synthetic Biology I Attention: This course was offered in previous semesters with the number: 636-0002-00L "Synthetic Biology I". Students that already passed course 636-0002-00L cannot receive credits for course 636-0111-00L. | W | 4 credits | 3G | S. Panke, J. Stelling | |
| Abstract | Theoretical & practical introduction into the design of dynamic biological systems at different levels of abstraction, ranging from biological fundamentals of systems design (introduction to bacterial gene regulation, elements of transcriptional & translational control, advanced genetic engineering) to engineering design principles (standards, abstractions) mathematical modelling & systems desig | |||||
| Learning objective | After the course, students will be able to theoretically master the biological and engineering fundamentals required for biological design to be able to participate in the international iGEM competition (see www.syntheticbiology.ethz.ch). | |||||
| Content | The overall goal of the course is to familiarize the students with the potential, the requirements and the problems of designing dynamic biological elements that are of central importance for manipulating biological systems, primarily (but not exclusively) prokaryotic systems. Next, the students will be taken through a number of successful examples of biological design, such as toggle switches, pulse generators, and oscillating systems, and apply the biological and engineering fundamentals to these examples, so that they get hands-on experience on how to integrate the various disciplines on their way to designing biological systems. | |||||
| Lecture notes | Handouts during classes. | |||||
| Literature | Mark Ptashne, A Genetic Switch (3rd ed), Cold Spring Haror Laboratory Press Uri Alon, An Introduction to Systems Biology, Chapman & Hall | |||||
| Prerequisites / Notice | 1) Though we do not place a formal requirement for previous participation in particular courses, we expect all participants to be familiar with a certain level of biology and of mathematics. Specifically, there will be material for self study available on http://www.bsse.ethz.ch/bpl/education/index as of mid January, and everybody is expected to be fully familiar with this material BEFORE THE CLASS BEGINS to be able to follow the different lectures. Please contact sven.panke@bsse.ethz.ch for access to material 2) The course is also thought as a preparation for the participation in the international iGEM synthetic biology summer competition (www.syntheticbiology.ethz.ch, http://www.igem.org). This competition is also the contents of the course Synthetic Biology II. http://www.bsse.ethz.ch/bpl/education/index | |||||
| 636-0116-00L | Nanomachines of the Cell (Part II): Engineering and Application Attention: This course was offered in previous semesters with the number: 636-0008-00L "Nanomachines of the Cell II". Students that already passed course 636-0008-00 cannot receive credits for course 636-0116-00. Prerequisites: Students should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering. | W | 4 credits | 3G | D. J. Müller | |
| Abstract | This second part of the lecture series "Nanomachines of the Cell" extends what has been learned in the first module. "Engineering and application" will be thus a consolidation of the concepts of functional biomolecular units of the cell as nanoscopic machines. The specific aim is to be able to use these cellular machines in more complex biotechnological processes as nanoscale functional elements. | |||||
| Learning objective | Gain of an interdisciplinary research and development competence which qualifies for scientific work (master`s or doctoral thesis) as well as for work in the research and development department of a biotechnological company. The module is of general use in nano- and biotechnological courses of study focusing modern biomolecular technologies. | |||||
| Content | Assembly of fibrillar structures. Filamentous structures inside and outside the cell. Principles of polymerisation dynamics: Nucleation, polarity, equilibrium and non-equilibrium driven polymerization, treadmilling, energy consumption, asymmetric building blocks, ... Self-assembly processes in polymer chemistry and physics. Self-assembly processes into two- and three-dimensions. Filaments of the cell: F-actin, intermediate filaments, microtubuli, and collagen. Filaments of the cell fulfil several functions: Structural integrity and functionalization of the environment. How does the cell control these functions? Example: The collagen family. Molecular and supramolecular structure of collagens. On the importance of motifs on the molecular packing mechanism of collagen. Occurrence of collagens and functional roles. Diseases related to collagen malfunction. Properties of collagen: Flexibility, elasticity, strength, persistence length, conformations, binding sites, signal transduction, ... Proteins that functionalize collagens. Can we use these proteins as a biomolecular toolbox to build up three-dimensional functional scaffolds? Directing and controlling the self-assembly of collagen type I. Learning which factors determine the supramolecular structure of self-assembled collagen. Using this knowledge to guide the self-assembly of collagen into nanoscopic scaffolds. Creating intelligent collagen scaffolds to guide cellular functions. Ways to functionalize collagen matrices for their use in biotechnology and tissue engineering. The great challenges: How can we create three-dimensional collagen scaffolds? DNA origami. Using DNA to build artificial three-dimensional structures at nanometer precision. From smilies to mechanical building blocks to three-dimensional containers almost every three-dimensional structure can be build. Self-assembly process of DNA. 'Programming the DNA': How to engineer the DNA sequence to promote it's self-assembly into a three-dimensional structure. How to engineer the DNA sequence to promote the self-assembly of the DNA into a precise three-dimensional nanoscopic arrangement. Engineering lessons: How to functionalize three-dimensional DNA containers so that they have a different fluorescent protein on each corner? How to functionalize a functionalize three-dimensional DNA container so that it frees its cargo on response to an external stimuli? How to functionalize a three-dimensional DNA container so that a cell can opens it and extract the cargo? Where may DNA origami be in 10 years? Comparative approaches using peptides to design origami. Microtubuli. Occurrence, structure, function, and properties. Cell mechanics, motility and dynamic. Mitosis. Cargo transport by motor proteins. Assembly mechanisms, tubulin subunits, nucleation, polarity, kinetics, concentration dependent growth, GTP dependency, dynamic instability, capping, ..). Designing three-dimensional structures using microtubuli. Creating a racing track: Motility assays. Designing and microstructuring of supports as circuits for molecular shuttles. Biofunctionalization of the circuits. Transporting molecular cargo along circuits. Engineering molecular devices to switch the transport 'on' and 'off'. Motor proteins. Introduction: Translational motors, rotary motors, chemical driven motors, light-driven motors, unidirectional and bidirectional motors, reversibility, molecular ratchets, future visions. Example of rotary motors: F-ATP synthase and flagella motor. F-ATP synthase was introduced in (Nanomachines of the cell Part I). Common and different engineering principles of the F-ATP synthase and the flagella motor. Structure, function, energy source, and rotational modes. Controlled assembly of a complex machinery such as the flagella motor. Are there ways to exchange the building blocks of the motor and to 'tune' it? Motor proteins of the cytoskeleton. iViruses. Prediction, design und engineering of cellular machines. | |||||
| Lecture notes | Hand out will be given to students at lecture. | |||||
| Literature | lberts et al: Molecular Biology of the cell Biochemistry (5th edition), Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; ISBN 0-7167-4684-0, Freeman Principles of Biochemistry, Nelson & Cox; ISBN: 1-57259-153-6, Worth Publishers, New York Cell Biology, Pollard & Earnshaw; ISBN:0-7216-3997-6, Saunder, Pennsylvania Intermolecular & Surface Forces, Israelachvili; ISBN: 0-12-375181-0, Academic Press, London Proteins: Biochemistry and Biotechnolgy, Walsh; ISBN: 0-471-899070, Wiley & Sons, New York Textbook of Biochemistry with Clinical Correlations, Devlin; ISBN: 0-471-411361, Wiley & Sons, New York Molecular Virology, Modrow et al.; ISBN: 3-8274-1086-X, Spektrum Verlag, Heidelberg | |||||
| Prerequisites / Notice | Students should have an interdisciplinary background (bachelor) in molecular biotechnology, biochemistry, cell biology, physics, bioinformatics or molecular bioengineering. The module is composed of 3 SWS (3 hours/week): 2-hour lecture, 1-hour seminar. For the seminar, students prepare oral presentations on specific in-depth subjects with/under the guidance of the teacher. | |||||
| Research Projects and Internship Students need to acquire a total of 20 ECTS in this category. Either choose Research Project I (8 ECTS) and Research Project II (12 ECTS) Or choose Research Project I (8 ECTS) and Industry Internship (12 ECTS) | ||||||
| Research Projects | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0802-00L | Research Project I Only for Biotechnology MSc, Programme Regulations 2017. | O | 8 credits | 23A | Professors | |
| Abstract | In a research project students extend their knowledge in a particular field, get acquainted with the scientific way of working, and learn to work on an actual research topic. Research projects are carried out in a core or optional subject area as chosen by the student. | |||||
| Learning objective | Students get acquainted with scientific working methods and deepen their knowledge in a particular research area | |||||
| 636-0803-00L | Research Project II Enrollment only for students that don`t do an industry internship but two research projects. Only for Biotechnology MSc, Programme Regulations 2017. | W | 12 credits | 34A | Professors | |
| Abstract | In a research project students extend their knowledge in a particular field, get acquainted with the scientific way of working, and learn to work on an actual research topic. Research projects are carried out in a core or optional subject area as chosen by the student. | |||||
| Learning objective | Students get acquainted with scientific working methods and deepen their knowledge in a particular research area | |||||
| Internship | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0804-00L | Industry Internship Only for Biotechnology MSc, Programme Regulations 2017. | W | 12 credits | 34A | Professors | |
| Abstract | Industry internship of at least 12 weeks, completed with a written report. | |||||
| Learning objective | Students gain experience in an industrial environment and an overview of different research areas by applying concepts taught in the courses. | |||||
| Prerequisites / Notice | The students look for a placement themselves. | |||||
| Master Studies (Programme Regulations 2009) | ||||||
| Research Project | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0801-00L | Research Project | O | 20 credits | 46A | Lecturers | |
| Abstract | In a research project students extend their knowledge in a particular field, get acquainted with the scientific way of working, and learn to work on an actual research topic. Research projects are carried out in a core or optional subject area as chosen by the student. | |||||
| Learning objective | Students get acquainted with scientific working methods and deepen their knowledge in a particular research area | |||||
| Electives The MSc Electives will be held in Zürich or Basel | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0510-00L | Proteomics and Drug Discovery Research Does not take place this semester. | W | 2 credits | 2V | external organisers | |
| Abstract | ||||||
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| 636-0512-00L | Intensive Courses in the Plant Sciences | W | 2 credits | 1V | external organisers | |
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| 636-0518-00L | Molecular Medicine II | W+ | 2 credits | 2V | external organisers | |
| Abstract | ||||||
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| 636-0514-00L | Dynamics and Maintenance of the Genome: DNA Replication, Repair, Recombination | W+ | 2 credits | 2V | external organisers | |
| Abstract | ||||||
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| 636-0516-00L | Transcription, Regulation and Gene Expression in Eukaryotes | W+ | 2 credits | 2V | external organisers | |
| Abstract | ||||||
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| 636-0522-00L | Evaluation of Compound Properties | W+ | 1 credit | 1S | external organisers | |
| Abstract | ||||||
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| 636-0524-00L | Pharmacogenomics and Toxicogenomics: Basics and Application in Drug Development | W+ | 1 credit | 1V | external organisers | |
| Abstract | ||||||
| Learning objective | ||||||
| 636-0532-00L | Machine Learning for Vision Applications | W+ | 6 credits | 4G | external organisers | |
| Abstract | ||||||
| Learning objective | ||||||
| 636-0536-00L | G4: Chromatin and Epigenetics Does not take place this semester. | W+ | 2 credits | 2V | external organisers | |
| Abstract | ||||||
| Learning objective | ||||||
| 636-0006-00L | Computational Systems Biology: Deterministic Approaches | W | 4 credits | 3G | J. Stelling, D. Iber | |
| Abstract | The course introduces computat. methods for systems biology under ‘real-world’ conditions of limiting biological knowledge, uncertain model scopes and predictions, and spatial effects. Focus is on systems identification for mechanistic, deterministic models and the corresponding numerical approaches. Topics include uncertainty evaluation, experim. design, and numerical methods for spatial models | |||||
| Learning objective | The aim of the course is to provide students with mathematical and computational methods for the analysis of biological systems in a ‘real world’ setting. This implies (i) incomplete knowledge of components, interactions, and their quantitative features in cellular networks, (ii) resulting uncertainties in model predictions and iterations between models and experiments, and (iii) spatial effects. All these factors make direct representations of biological mechanisms in mechanistic, deterministic mathematical models challenging. Based on general concepts of systems identification and on corresponding numerical methods, the course aims at providing an in-depth understanding of computational approaches that enable the analysis of mechanisms of biological network operation in detail, using iterations between experimental and theoretical systems analysis. | |||||
| Content | Lecture topics: (1) Mechanistic mathematical models and systems identification challenges; (2-4) Structural models and data integration; (5-8) Identification and experimental design for ODE models; (9-10) Uncertainty quantification; (11-13) Numerical methods for partial differential equation (PDE) models to describe spatial effects. | |||||
| Lecture notes | Course material will be made available at: http://www.csb.ethz.ch | |||||
| Literature | Background literature will be available on-line at the start of the course. | |||||
| Prerequisites / Notice | For this advanced course, participants are expected to have a solid background in the mathematical modelling of biological systems, as conveyed by the combination of the following two courses in the MSc Computational Biology and Bioinformatics: ‘Computational systems biology’ and ‘Spatio-temporal modeling in biology’. | |||||
| 636-0016-00L | Computational Systems Biology: Stochastic Approaches | W | 4 credits | 3G | M. H. Khammash, A. Gupta | |
| Abstract | This course is concerned with the development of computational methods for modeling, simulation, and analysis of stochasticity in living cells. Using these tools, the course explores the richness of stochastic phenomena, how it arises from the interactions of dynamics and noise, and its biological implications. | |||||
| Learning objective | To understand the origins and implications of stochastic noise in living cells, and to learn the computational tools for the modeling, simulation, analysis, and identification of stochastic biochemical reaction networks. | |||||
| Content | The cellular environment is abuzz with noise. A key source of this noise is the randomness that characterizes the motion of cellular constituents at the molecular level. Cellular noise not only results in random fluctuations (over time) within individual cells, but it is also a main source of phenotypic variability among clonal cell populations. Review of basic probability and stochastic processes; Introduction to stochastic gene expression; deterministic vs. stochastic models; the stochastic chemical kinetics framework; a rigorous derivation of the chemical master equation; moment computations; linear vs. nonlinear propensities; linear noise approximations; Monte Carlo simulations; Gillespie's Stochastic Simulation Algorithm (SSA) and variants; direct methods for the solution of the Chemical Master Equation; moment closure methods; intrinsic and extrinsic noise in gene expression; parameter identification from noise; propagation of noise in cell networks; noise suppression in cells; the role of feedback; exploiting noise; bimodality and stochastic switches. | |||||
| Literature | Literature will be distributed during the course as needed. | |||||
| Prerequisites / Notice | Students are expected to have completed the course `Mathematical modeling for systems biology (BSc Biotechnology) or `Computational systems biology (MSc Computational biology and bioinformatics). Concurrent enrollment in `Computational Systems Biology: Deterministic Approaches is recommended. | |||||
| 636-0019-00L | Data Mining II Prerequisites: Basic understanding of mathematics, as taught in basic mathematics courses at the Bachelor`s level. Ideally, students will have attended Data Mining I before taking this class. | W | 6 credits | 3G + 2A | K. M. Borgwardt | |
| Abstract | Data Mining, the search for statistical dependencies in large databases, is of utmost important in modern society, in particular in biological and medical research. Building on the basic algorithms and concepts of data mining presented in the course "Data Mining I", this course presents advanced algorithms and concepts from data mining and the state-of-the-art in applications of data mining. | |||||
| Learning objective | The goal of this course is that the participants gain an advanced understanding of data mining problems and algorithms to solve these problems, in particular in biological and medical applications, and to enable them to conduct their own research projects in the domain of data mining. | |||||
| Content | The goal of the field of data mining is to find patterns and statistical dependencies in large databases, to gain an understanding of the underlying system from which the data were obtained. In computational biology, data mining contributes to the analysis of vast experimental data generated by high-throughput technologies, and thereby enables the generation of new hypotheses. In this course, we will present advanced topics in data mining and its applications in computational biology. Tentative list of topics: 1. Dimensionality Reduction 2. Association Rule Mining 3. Text Mining 4. Graph Mining | |||||
| Lecture notes | Course material will be provided in form of slides. | |||||
| Literature | Will be provided during the course. | |||||
| GESS Science in Perspective | ||||||
| » see Science in Perspective: Language Courses ETH/UZH | ||||||
| » see Science in Perspective: Type A: Enhancement of Reflection Capability | ||||||
| Master's Thesis | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0900-00L | Master's Thesis Only students who fulfill the following criteria are allowed to begin with their master thesis: a. successful completion of the bachelor programme; b. fulfilling of any additional requirements necessary to gain admission to the master programme. | O | 40 credits | 91D | Lecturers | |
| Abstract | In the Master thesis students prove their ability to independent, structured and scientific working. The Master thesis is carried out under the supervision of a professor in a research group of the D-BSSE, usually at the D-BSSE. Students are free to choose the area. | |||||
| Learning objective | In the Master Thesis students prove their ability to independent, structured and scientific working. | |||||
| Additional Requirements The courses below are only available for MSc students with additional admission requirements. | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-1001-AAL | Bio I: General Biology Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 5 credits | 7R | D. J. Müller | |
| Abstract | ||||||
| Learning objective | ||||||
| Literature | Campbell “Biology“, chapters: 1 – 28, 40, 42, 43, 45 | |||||
| 636-1002-AAL | Bio II: Biochemistry Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 5 credits | 7R | S. Panke | |
| Abstract | ||||||
| Learning objective | ||||||
| Literature | Stryer “Biochemistry”, chapters: 1-18, 24, 27-32 | |||||
| 636-1004-AAL | Bio IV: Genetics Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 5 credits | 7R | R. Platt | |
| Abstract | ||||||
| Learning objective | ||||||
| Literature | Lewin, Genes XI, chapters: 3,15, 16, 19-23, 26-30 | |||||
| 636-1003-AAL | Bio III: Cellular Biology Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 5 credits | 7R | D. J. Müller | |
| Abstract | ||||||
| Learning objective | ||||||
| Literature | Alberts “Molecular biology of the cell”, chapters: 7-13, 15-17 | |||||
| 636-1005-AAL | Bio V: Bioinformatics Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 5 credits | 7R | R. Paro | |
| Abstract | ||||||
| Learning objective | ||||||
| Literature | Pevsner, Bioinformatics and Functional Genomics, chapters: 1 – 7 | |||||
| 636-1006-AAL | Bio Lab I: General Biology Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 1 credit | 3R | P. S. Dittrich | |
| Abstract | ||||||
| Learning objective | ||||||
| Content | General lab instructions (safety in the lab, buffers, media, pipetting, monoseptic working, proteins and protein degradation, PAGE, enzyme assays | |||||
| 636-1007-AAL | Bio Lab II: Microbiology Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 1 credit | 3R | S. Reddy | |
| Abstract | ||||||
| Learning objective | ||||||
| Content | E. coli cultures, growth curves in different formats (shake flasks, µTPs) and readouts, making competent cells, transformation and electroporation, plasmid isolation, ELISA | |||||
| 636-1008-AAL | Bio Lab III: Molecular Biology I Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 1 credit | 3R | R. Platt | |
| Abstract | ||||||
| Learning objective | ||||||
| Content | PCR, restriction digest, ligation, transformation, gel analysis, Sanger sequencing, Gibson assembly | |||||
| 636-1010-AAL | Bio Lab V: Molecular Biology III Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 1 credit | 3R | R. Paro | |
| Abstract | ||||||
| Learning objective | ||||||
| Content | “-omics” analyses in eukaryotic cells (sample preparation for and analysis of omics data) | |||||
| 636-1009-AAL | Bio Lab IV: Molecular Biology II Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | E- | 1 credit | 3R | S. Panke | |
| Abstract | ||||||
| Learning objective | ||||||
| Content | Gene expression in prokaryotes: Construction of reporter constructs, induction and readout under different conditions, influence of degradation tags, genome editing in bacteria | |||||
| Seminars, Colloquia and Additional Courses The credit points of the here listed subjects won't be taken in account for the MSc programm. | ||||||
| Number | Title | Type | ECTS | Hours | Lecturers | |
| 636-0301-00L | Current Topics in Biosystems Science and Engineering | E- Dr | 2 credits | 1S | T. Stadler, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Panke, R. Paro, R. Platt, S. Reddy, T. Schroeder, J. Stelling | |
| Abstract | This seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology. | |||||
| Learning objective | To provide an overview of current systems biology research. | |||||
| Content | The final list of topics will be available at http://www.bsse.ethz.ch/education/. | |||||