Suchergebnis: Katalogdaten im Herbstsemester 2017

Computational Biology and Bioinformatics Master Information
More informations at: Link
Master-Studium (Studienreglement 2017)
Vertiefungsfächer
A total of 30 ECTS needs to be acquired in the Advanced Courses category. Thereof 18 ECTS in the Theory and 12 ECTS in the Biology category.
Theorie
At least 18 ECTS need to be acquired in this category.
NummerTitelTypECTSUmfangDozierende
401-0663-00LNumerical Methods for CSE Information W7 KP4V + 2UR. Alaifari
KurzbeschreibungThe course gives an introduction into fundamental techniques and algorithms of numerical mathematics which play a central role in numerical simulations in science and technology. The course focuses on fundamental ideas and algorithmic aspects of numerical methods. The exercises involve actual implementation of numerical methods in C++.
Lernziel* Knowledge of the fundamental algorithms in numerical mathematics
* Knowledge of the essential terms in numerical mathematics and the
techniques used for the analysis of numerical algorithms
* Ability to choose the appropriate numerical method for concrete problems
* Ability to interpret numerical results
* Ability to implement numerical algorithms afficiently
Inhalt1. Direct Methods for linear systems of equations
2. Least Squares Techniques
3. Data Interpolation and Fitting
4. Filtering Algorithms
8. Approximation of Functions
9. Numerical Quadrature
10. Iterative Methods for non-linear systems of equations
11. Single Step Methods for ODEs
12. Stiff Integrators
SkriptLecture materials (PDF documents and codes) will be made available to the participants through the course web page:
Link
LiteraturU. ASCHER AND C. GREIF, A First Course in Numerical Methods, SIAM, Philadelphia, 2011.

A. QUARTERONI, R. SACCO, AND F. SALERI, Numerical mathematics, vol. 37 of Texts in Applied Mathematics, Springer, New York, 2000.

W. Dahmen, A. Reusken "Numerik für Ingenieure und Naturwissenschaftler", Springer 2006.

M. Hanke-Bourgeois "Grundlagen der Numerischen Mathematik und des wissenschaftlichen Rechnens", BG Teubner, 2002

P. Deuflhard and A. Hohmann, "Numerische Mathematik I", DeGruyter, 2002
Voraussetzungen / BesonderesThe course will be accompanied by programming exercises in C++ relying on the template library EIGEN. Familiarity with C++, object oriented and generic programming is an advantage. Participants of the course are expected to learn C++ by themselves.
263-5210-00LProbabilistic Artificial Intelligence Information W4 KP2V + 1UA. Krause
KurzbeschreibungThis course introduces core modeling techniques and algorithms from statistics, optimization, planning, and control and study applications in areas such as sensor networks, robotics, and the Internet.
LernzielHow can we build systems that perform well in uncertain environments and unforeseen situations? How can we develop systems that exhibit "intelligent" behavior, without prescribing explicit rules? How can we build systems that learn from experience in order to improve their performance? We will study core modeling techniques and algorithms from statistics, optimization, planning, and control and study applications in areas such as sensor networks, robotics, and the Internet. The course is designed for upper-level undergraduate and graduate students.
InhaltTopics covered:
- Search (BFS, DFS, A*), constraint satisfaction and optimization
- Tutorial in logic (propositional, first-order)
- Probability
- Bayesian Networks (models, exact and approximative inference, learning) - Temporal models (Hidden Markov Models, Dynamic Bayesian Networks)
- Probabilistic palnning (MDPs, POMPDPs)
- Reinforcement learning
- Combining logic and probability
Voraussetzungen / BesonderesSolid basic knowledge in statistics, algorithms and programming
401-0647-00LIntroduction to Mathematical Optimization Information W5 KP2V + 1UD. Adjiashvili
KurzbeschreibungIntroduction to basic techniques and problems in mathematical optimization, and their applications to a variety of problems in engineering.
LernzielThe goal of the course is to obtain a good understanding of some of the most fundamental mathematical optimization techniques used to solve linear programs and basic combinatorial optimization problems. The students will also practice applying the learned models to problems in engineering.
InhaltTopics covered in this course include:
- Linear programming (simplex method, duality theory, shadow prices, ...).
- Basic combinatorial optimization problems (spanning trees, shortest paths, network flows, ...).
- Modelling with mathematical optimization: applications of mathematical programming in engineering.
LiteraturInformation about relevant literature will be given in the lecture.
Voraussetzungen / BesonderesThis course is meant for students who did not already attend the course "Mathematical Optimization", which is a more advance lecture covering similar topics. Compared to "Mathematical Optimization", this course has a stronger focus on modeling and applications.
227-0225-00LLinear System TheoryW6 KP5GM. Kamgarpour
KurzbeschreibungThe class is intended to provide a comprehensive overview of the theory of linear dynamical systems, stability analysis, and their use in control and estimation. The focus is on the mathematics behind the physical properties of these systems.
LernzielStudents should be able to apply the fundamental results in linear system theory to analyze and control linear dynamical systems.
Inhalt- Linear spaces, normed linear spaces and Hilbert spaces.
- Ordinary differential equations, existence and uniqueness of solutions.
- Continuous and discrete-time, time-varying linear systems. Time domain solutions. Time invariant systems treated as a special case.
- Controllability and observability, duality. Time invariant systems treated as a special case.
- Stability and stabilization, observers, state and output feedback, separation principle.
SkriptAvailable online on course website.
Voraussetzungen / Besonderes1) Sufficient mathematical maturity with special focus on linear algebra, analysis, and basic logic.
2) Control Systems I (227-0103-00) or equivalent.
151-0575-01LSignals and Systems Information W4 KP2V + 2UR. D'Andrea
KurzbeschreibungSignals arise in most engineering applications. They contain information about the behavior of physical systems. Systems respond to signals and produce other signals. In this course, we explore how signals can be represented and manipulated, and their effects on systems. We further explore how we can discover basic system properties by exciting a system with various types of signals.
LernzielMaster the basics of signals and systems. Apply this knowledge to problems in the homework assignments and programming exercise.
InhaltDiscrete-time signals and systems. Fourier- and z-Transforms. Frequency domain characterization of signals and systems. System identification. Time series analysis. Filter design.
SkriptLecture notes available on course website.
Voraussetzungen / BesonderesControl Systems I is helpful but not required.
529-0004-00LComputer Simulation in Chemistry, Biology and Physics Information W7 KP4GP. H. Hünenberger
KurzbeschreibungMolecular models, Force fields, Boundary conditions, Electrostatic interactions, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation.
LernzielIntroduction to computer simulation of (bio)molecular systems, development of skills to carry out and interpret computer simulations of biomolecular systems.
InhaltMolecular models, Force fields, Spatial boundary conditions, Calculation of Coulomb forces, Molecular dynamics, Analysis of trajectories, Quantum-mechanical simulation, Structure refinement, Application to real systems. Exercises: Analysis of papers on computer simulation, Molecular simulation in practice, Validation of molecular dynamics simulation.
SkriptAvailable (copies of powerpoint slides distributed before each lecture)
LiteraturSee: Link
Voraussetzungen / BesonderesSince the exercises on the computer do convey and test essentially different skills as those being conveyed during the lectures and tested at the oral exam, the results of the exercises are taken into account when evaluating the results of the exam.

For more information about the lecture: Link
252-0237-00LConcepts of Object-Oriented Programming Information W6 KP3V + 2UP. Müller
KurzbeschreibungCourse that focuses on an in-depth understanding of object-oriented programming and compares designs of object-oriented programming languages. Topics include different flavors of type systems, inheritance models, encapsulation in the presence of aliasing, object and class initialization, program correctness, reflection
LernzielAfter this course, students will:
Have a deep understanding of advanced concepts of object-oriented programming and their support through various language features. Be able to understand language concepts on a semantic level and be able to compare and evaluate language designs.
Be able to learn new languages more rapidly.
Be aware of many subtle problems of object-oriented programming and know how to avoid them.
InhaltThe main goal of this course is to convey a deep understanding of the key concepts of sequential object-oriented programming and their support in different programming languages. This is achieved by studying how important challenges are addressed through language features and programming idioms. In particular, the course discusses alternative language designs by contrasting solutions in languages such as C++, C#, Eiffel, Java, Python, and Scala. The course also introduces novel ideas from research languages that may influence the design of future mainstream languages.

The topics discussed in the course include among others:
The pros and cons of different flavors of type systems (for instance, static vs. dynamic typing, nominal vs. structural, syntactic vs. behavioral typing)
The key problems of single and multiple inheritance and how different languages address them
Generic type systems, in particular, Java generics, C# generics, and C++ templates
The situations in which object-oriented programming does not provide encapsulation, and how to avoid them
The pitfalls of object initialization, exemplified by a research type system that prevents null pointer dereferencing
How to maintain the consistency of data structures
LiteraturWill be announced in the lecture.
Voraussetzungen / BesonderesPrerequisites:
Mastering at least one object-oriented programming language (this course will NOT provide an introduction to object-oriented programming); programming experience
262-6140-00LRandom Processes: Theory and Applications from Physics to FinanceW4 KP3Gexterne Veranstalter
Kurzbeschreibung
Lernziel
262-6150-00LProgramming for Life SciencesW4 KP2Pexterne Veranstalter
Kurzbeschreibung
Lernziel
262-6160-00LTheoretical BiophysicsW4 KP2Gexterne Veranstalter
Kurzbeschreibung
Lernziel
636-0015-00LAn Introduction to Probability Theory and Stochastic Processes with Applications to BiologyW4 KP3GA. Gupta
KurzbeschreibungBiology is becoming increasingly quantitative and mathematical modeling is now an integral part of biological research. In many biological processes, ranging from gene-expression to evolution, randomness plays an important role that can only be understood using stochastic models. This course will provide the students with a theoretical foundation for developing such stochastic models and analyzing
LernzielThe aim of this course is to introduce certain topics in Probability Theory and Stochastic Processes that have been specifically selected with an eye on biological applications. This course will teach students the tools and techniques for modeling and analyzing random phenomena. Throughout the course, several biological applications will be discussed and students will be encouraged to do additional reading based on their research interests.
InhaltThe first half of the course will cover the basics of Probability Theory while the second half will delve into the theory of Stochastic Processes. Below is the list of topics that will be covered in the course.

1. The mathematical representation of random phenomena: The probability space, properties of the probability measure, Independence of events, Conditional probability and Bayes formula, applications to parameter inference.

2. Random Variables and their distributions: Discrete and continuous random variables, Expectation and Variance, Important Examples of Random Variables, Independent random variables and their sums, Conditional Distribution and Conditional Expectation, Markov and Chebyshev inequalities. Law of total variation, estimation of intrinsic and extrinsic noise in biological systems.

3. Convergence of Random Variables: Modes of convergence, Laws of large numbers, the central limit theorem, the law of the iterated logarithm, Applications to the analysis of cell population data.

4. Generating functions and their applications: Definition and important examples, Random Walks, Branching processes, Coalescent processes, Modeling epidemic processes and stem-cell differentiation.

5. Markov chains: Transition functions and related computations, Classification of states and classification of chains. Concepts of recurrence, transience, irreducibility and periodicity, Stationary distributions, Continuous time Markov Chain model of a biochemical reaction network.

6. Stochastic Processes: Existence and Construction, Stationary Processes, Renewal Processes, The Wiener Process, The Ergodic Theorem, Leveraging experimental techniques in Biology.

7. Introduction to the theory of Martingales: Basic definitions, Martingale differences and Hoeffding's inequality, Martingale Convergence Theorem, Crossings and convergence, Stopping times and the optional sampling theorem, Doob's maximal inequalities, Applications to the analysis of stochastic biochemical reaction networks.
LiteraturWhile no specific textbook will be followed, much of the material and homework problems will be taken from the following books:
An Introduction to Stochastic Processes with Applications to Biology, Linda Allen, Second Edition, Chapman and Hall, 2010.
Probability And Random Processes, Grimmett and Stirzaker, Third Edition, Oxford University Press, 2001.
Voraussetzungen / BesonderesThe course will involve a healthy balance between mathematical rigor (theorem proving) and biological applications. Students are expected to have a good grasp of Linear Algebra and Multivariable Calculus. Basic knowledge of set theory will also be needed. Students should
be prepared for abstract reasoning.
263-3010-00LBig Data Information Belegung eingeschränkt - Details anzeigen W8 KP3V + 2U + 2AG. Fourny
KurzbeschreibungThe key challenge of the information society is to turn data into information, information into knowledge, knowledge into value. This has become increasingly complex. Data comes in larger volumes, diverse shapes, from different sources. Data is more heterogeneous and less structured than forty years ago. Nevertheless, it still needs to be processed fast, with support for complex operations.
LernzielThis combination of requirements, together with the technologies that have emerged in order to address them, is typically referred to as "Big Data." This revolution has led to a completely new way to do business, e.g., develop new products and business models, but also to do science -- which is sometimes referred to as data-driven science or the "fourth paradigm".

Unfortunately, the quantity of data produced and available -- now in the Zettabyte range (that's 21 zeros) per year -- keeps growing faster than our ability to process it. Hence, new architectures and approaches for processing it were and are still needed. Harnessing them must involve a deep understanding of data not only in the large, but also in the small.

The field of databases evolves at a fast pace. In order to be prepared, to the extent possible, to the (r)evolutions that will take place in the next few decades, the emphasis of the lecture will be on the paradigms and core design ideas, while today's technologies will serve as supporting illustrations thereof.

After visiting this lecture, you should have gained an overview and understanding of the Big Data landscape, which is the basis on which one can make informed decisions, i.e., pick and orchestrate the relevant technologies together for addressing each business use case efficiently and consistently.
InhaltThis course gives an overview of database technologies and of the most important database design principles that lay the foundations of the Big Data universe. The material is organized along three axes: data in the large, data in the small, data in the very small. A broad range of aspects is covered with a focus on how they fit all together in the big picture of the Big Data ecosystem.

- physical storage: distributed file systems (HDFS), object storage(S3), key-value stores

- logical storage: document stores (MongoDB), column stores (HBase), graph databases (neo4j), data warehouses (ROLAP)

- data formats and syntaxes (XML, JSON, RDF, Turtle, CSV, XBRL, YAML, protocol buffers, Avro)

- data shapes and models (tables, trees, graphs, cubes)

- type systems and schemas: atomic types, structured types (arrays, maps), set-based type systems (?, *, +)

- an overview of functional, declarative programming languages across data shapes (SQL, XQuery, JSONiq, Cypher, MDX)

- the most important query paradigms (selection, projection, joining, grouping, ordering, windowing)

- paradigms for parallel processing, two-stage (MapReduce) and DAG-based (Spark)

- resource management (YARN)

- what a data center is made of and why it matters (racks, nodes, ...)

- underlying architectures (internal machinery of HDFS, HBase, Spark, neo4j)

- optimization techniques (functional and declarative paradigms, query plans, rewrites, indexing)

- applications.

Large scale analytics and machine learning are outside of the scope of this course.

Guest lectures planned so far:
- Bart Samwel (Google) on F1, Spanner
LiteraturPapers from scientific conferences and journals. References will be given as part of the course material during the semester.
Voraussetzungen / BesonderesThis course, in the autumn semester, is only intended for:
- Computer Science students
- Data Science students
- CBB students with a Computer Science background

Another version of this course will be offered in Spring for students of other departments. However, if you would like to already start learning about databases now, a course worth taking as a preparation/good prequel to the Spring edition of Big Data is the "Information Systems for Engineers" course, offered this Fall for other departments as well, and introducing relational databases and SQL.
Biologie
At least 12 ECTS need to be acquired in this category.
NummerTitelTypECTSUmfangDozierende
529-0733-00LEnzymesW7 KP3GD. Hilvert
KurzbeschreibungVermittlung eines Überblicks über die Chemie von Enzymen, enzymkatalysierten Reaktionen, metabolischen Prozessen.
LernzielVermittlung eines Überblicks über die Chemie von Enzymen, enzymkatalysierten Reaktionen, metabolischen Prozessen.
InhaltPrinzipien der enzymatischen Katalyse, Enzymkinetiken, Mechanismen enzymkatalysierter Reaktionen (Gruppentransferreaktion, Kohlenstoff-Kohlenstoff-Bindungsknüpfungen, Eliminierungen, Isomerisierungen und Umlagerungen), Kofaktorenchemie, Enzyme in der organischen Synthese und in der Naturstoffbiosynthese, katalytische Antikörper.
SkriptA script will not be handed out.
LiteraturGeneral:
T. Bugg, An Introduction to Enzyme and Coenzyme Chemistry, Blackwell Science Ltd., Oxford, 1997.

In addition, citations from the original literature relevant to the individual lectures will be assigned weekly.
551-0309-00LConcepts in Modern GeneticsW6 KP4VY. Barral, D. Bopp, A. Hajnal, M. Stoffel, O. Voinnet
KurzbeschreibungConcepts of modern genetics and genomics, including principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference.
LernzielThis course focuses on the concepts of classical and modern genetics and genomics.
InhaltThe topics include principles of classical genetics; yeast genetics; gene mapping; forward and reverse genetics; structure and function of eukaryotic chromosomes; molecular mechanisms and regulation of transcription, replication, DNA-repair and recombination; analysis of developmental processes; epigenetics and RNA interference.
SkriptScripts and additional material will be provided during the semester.
551-0313-00LMicrobiology (Part I) Information W3 KP2VW.‑D. Hardt, L. Eberl, H.‑M. Fischer, J. Piel, M. Pilhofer
KurzbeschreibungAdvanced lecture class providing a broad overview on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
LernzielThis concept class will be based on common concepts and introduce to the enormous diversity among bacteria and archaea. It will cover the current research on bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
InhaltAdvanced class covering the state of the research in bacterial cell structure, genetics, metabolism, symbiosis and pathogenesis.
SkriptUpdated handouts will be provided during the class.
LiteraturCurrent literature references will be provided during the lectures.
Voraussetzungen / BesonderesEnglish
The lecture "Grundlagen der Biologie II: Mikrobiologie" is the basis for this advanced lecture.
551-0317-00LImmunology I Information W3 KP2VA. Oxenius, M. Kopf
KurzbeschreibungEinführung in strukturelle und funktionelle Eigenschaften des Immunsystems.
Grundlegendes Verständnis der Mechanismen und der Regulation einer Immunantwort.
LernzielEinführung in strukturelle und funktionelle Eigenschaften des Immunsystems.
Grundlegendes Verständnis der Mechanismen und der Regulation einer Immunantwort.
Inhalt- Einleitung und historischer Hintergrund
- Angeborene und adaptive Immunantwort, Zellen und Organe des Immunsystems
- B Zellen und Antikörper
- Generation von Diversität
- Antigen-Präsentation und Histoinkompatibilitätsantigene (MHC)
- Thymus und T Zellselektion
- Autoimmunität
- Zytotoxische T Zellen und NK Zellen
- Th1 und Th2 Zellen, regulatorische T Zellen
- Allergien
- Hypersensitivititäten
- Impfungen und immun-therapeutische Interventionen
SkriptDie Studenten haben elekronischen Zugriff auf die Vorlesungsunterlagen. Der Link ist unter "Lernmaterialien" zu finden.
Literatur- Kuby, Immunology, 7th edition, Freemen + Co., New York, 2009
Voraussetzungen / BesonderesImmunology I (WS) und Immunology II (SS) werden in einer Sessionsprüfung im Anschluss an Immunology II als eine Lerneinheit geprüft.
636-0105-00LIntroduction to Biological Computers
Attention: This course was offered in previous semesters with the number: 636-0011-00L "Introduction to Biological Computers". Students that already passed course 636-0011-00L cannot receive credits for course 636-0105-00L.
W4 KP3GY. Benenson
KurzbeschreibungBiological computers are man-made biological networks that interrogate and control cells and organisms in which they operate. Their key features, inspired by computer science, are programmability, modularity, and versatility. The course will show how to rationally design, implement and test biological computers using molecular engineering, DNA nanothechnology and synthetic biology.
LernzielThe course has the following objectives:

* Familiarize students with parallels between theories in computer science and engineering and information-processing in live cells and organisms

* Introduce basic theories of computation

* Introduce approaches to creating novel biological computing systems in non-living environment and in living cells including bacteria, yeast and mammalian/human cells.

The covered approaches will include
- Nucleic acids engineering
- DNA and RNA nanotechnology
- Synthetic biology and gene circuit engineering
- High-throughput genome engineering and gene circuit assembly

* Equip the students with computer-aided design (CAD) tools for biocomputing circuit engineering. A number of tutorials will introduce MATLAB SimBiology toolbox for circuit design and simulations

* Foster creativity, research and communication skills through semester-long "Design challenge" assignment in the broad field of biological computing and biological circuit engineering.
InhaltNote: the exact subjects can change, the details below should only serve for general orientation

Lecture 1. Introduction: what is molecular computation (part I)?

* What is computing in general?
* What is computing in the biological context (examples from development, chemotaxis and gene regulation)
* The difference between natural computing and engineered biocomputing systems

Lecture 2: What is molecular computation (part II) + State machines

1st hour

* Detailed definition of an engineered biocomputing system
* Basics of characterization
* Design challenge presentation

2nd hour

* Theories of computation: state machines (finite automata and Turing machines)

Lecture 3: Additional models of computation

* Logic circuits
* Analog circuits
* RAM machines

Basic approaches to computer science notions relevant to molecular computation. (i) State machines; (ii) Boolean networks; (iii) analog computing; (iv) distributed computing. Design Challenge presentation.

Lecture 4. Classical DNA computing

* Adleman experiment
* Maximal clique problem
* SAT problem

Lecture 5: Molecular State machines through self-assembly

* Tiling implementation of state machine
* DNA-based tiling system
* DNA/RNA origami as a spin-off of self-assembling state machines

Lecture 6: Molecular State machines that use DNA-encoded tapes

* Early theoretical work
* Tape extension system
* DNA and enzyme-based finite automata for diagnostic applications

Lecture 7: Introduction to cell-based logic and analog circuits

* Computing with (bio)chemical reaction networks
* Tuning computation with ultrasensitivity and cooperativity
* Specific examples

Lecture 8: Transcriptional circuits I

* Introducing transcription-based circuits
* General features and considerations
* Guidelines for large circuit construction

Lecture 9: Transcriptional circuits II

* Large-scale distributed logic circuits in bacteria
* Toward large-scale circuits in mammalian cells

Lecture 10: RNA circuits I

* General principles of RNA-centered circuit design
* Riboswitches and sRNA regulation in bacteria
* Riboswitches in yeast and mammalian cells
* General approach to RNAi-based computing

Lecture 11: RNA circuits II

* RNAi logic circuits
* RNAi-based cell type classifiers
* Hybrid transcriptional/posttranscriptional approaches

Lecture 12: In vitro DNA-based logic circuits

* DNAzyme circuits playing tic-tac-toe against human opponents
* DNA brain


Lecture 13: Advanced topics

* Engineered cellular memory
* Counting and sequential logic
* The role of evolution
* Fail-safe design principles

Lecture 14: Design challenge presentation
SkriptLecture notes will be available online
LiteraturAs a way of general introduction, the following two review papers could be useful:

Benenson, Y. RNA-based computation in live cells. Current Opinion in Biotechnology 2009, 20:471:478

Benenson, Y. Biocomputers: from test tubes to live cells. Molecular Biosystems 2009, 5:675:685

Benenson, Y. Biomolecular computing systems: principles, progress and potential (Review). Nature Reviews Genetics 13, 445-468 (2012).
Voraussetzungen / BesonderesBasic knowledge of molecular biology is assumed.
636-0511-00LDevelopmental Neuroscience (HS)W2 KP2Vexterne Veranstalter
Kurzbeschreibung
Lernziel
636-0515-00LMolecular Medicine IW2 KP2Vexterne Veranstalter
Kurzbeschreibung
Lernziel
262-6170-00LMolecular Mechanisms of DevelopmentW2 KP2Vexterne Veranstalter
Kurzbeschreibung
Lernziel
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