Name | Frau Prof. Dr. Dagmar Iber |

Lehrgebiet | Rechnergestützte Biologie |

Adresse | Professur f. Computational Biology ETH Zürich, BSS G 11.1 Klingelbergstrasse 48 4056 Basel SWITZERLAND |

Telefon | +41 61 387 32 10 |

dagmar.iber@bsse.ethz.ch | |

URL | http://www.bsse.ethz.ch/cobi |

Departement | Biosysteme |

Beziehung | Ausserordentliche Professorin |

Nummer | Titel | ECTS | Umfang | Dozierende | |
---|---|---|---|---|---|

636-0301-00L | Current Topics in Biosystems Science and Engineering | 2 KP | 1S | R. Platt, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, D. J. Müller, S. Panke, P. Pantazis, R. Paro, S. Reddy, T. Schroeder, T. Stadler, J. Stelling | |

Kurzbeschreibung | This seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology. | ||||

Lernziel | To provide an overview of current systems biology research. | ||||

Inhalt | The final list of topics will be available at http://www.bsse.ethz.ch/education/. | ||||

636-0704-00L | Computational Biology and Bioinformatics SeminarThe Seminar will be offered in autumn semester in Basel and in spring semester in Zürich. | 2 KP | 2S | N. Beerenwinkel, M. Claassen, D. Iber, T. Stadler, J. Stelling | |

Kurzbeschreibung | Computational Biology und Bioinformatik analysieren lebende Systeme mit Methoden der Informatik. Das Seminar kombiniert Präsentationen von Studierenden und Forschenden, um das sich schnell entwickelnde Gebiet aus der Informatikperspektive zu skizzieren. Themenbereiche sind Sequenzanalyse, Proteomics, Optimierung und Bio-inspired computing, Systemmodellierung, -simulation und -analyse. | ||||

Lernziel | Studying and presenting fundamental papers of Computational Biology and Bioinformatics. Learning how to make a scientific presentation and how classical methods are used or further developed in current research. | ||||

Inhalt | Computational biology and bioinformatics aim at advancing the understanding of living systems through computation. The complexity of these systems, however, provides challenges for software and algorithms, and often requires entirely novel approaches in computer science. The aim of the seminar is to give an overview of this rapidly developing field from a computer science perspective. In particular, it will focus on the areas of (i) DNA sequence analysis, sequence comparison and reconstruction of phylogenetic trees, (ii) protein identification from experimental data, (iii) optimization and bio-inspired computing, and (iv) systems analysis of complex biological networks. The seminar combines the discussion of selected research papers with a major impact in their domain by the students with the presentation of current active research projects / open challenges in computational biology and bioinformatics by the lecturers. Each week, the seminar will focus on a different topic related to ongoing research projects at ETHZ, University of Basel and University of Zurich, thus giving the students the opportunity of obtaining knowledge about the basic research approaches and problems as well as of gaining insight into (and getting excited about) the latest developments in the field. | ||||

Literatur | Original papers to be presented by the students will be provided in the first week of the seminar. | ||||

636-0706-00L | Spatio-Temporal Modelling in Biology | 4 KP | 3G | D. Iber | |

Kurzbeschreibung | This course focuses on modeling spatio-temporal problems in biology, in particular on the cell and tissue level. The main focus is on mechanisms and concepts, but mathematical and numerical techniques are introduced as required. Biological examples discussed in the course provide an introduction to key concepts in developmental biology. | ||||

Lernziel | Students will learn state-of-the-art approaches to modelling spatial effects in dynamical biological systems. The course provides an introduction to dynamical system, and covers the mathematical analysis of pattern formation in growing, developing systems, as well as the description of mechanical effects at the cell and tissue level. The course also provides an introduction to image-based modelling, i.e. the use of microscopy data for model development and testing. The course covers classic as well as current approaches and exposes students to open problems in the field. In this way, the course seeks to prepare students to conduct research in the field. The course prepares students for research in developmental biology, as well as for applications in tissue engineering, and for biomedical research. | ||||

Inhalt | LECTURES 1. Introduction to Modelling in Biology (Sep 22) Sep 29th: NO LECTURE & NO TUTORIAL 2. Dynamical Systems (Oct 6) 3. Morphogen Gradients (Oct 13) 4. Mathematical Description of Growing Biological Systems (Oct 20) 5. Travelling Waves & Wave Pinning (Oct 27th) 6 Turing Patterns (Nov 3) Nov 10th: NO LECTURE & NO TUTORIAL (ETH FACULTY RETREAT) 7. Chemotaxis & Branching Processes (Nov 17th) 8. Image-Based Modelling (Nov 24th ) 9. Tissue Mechanics (Dec 1st) 10. Growth Control (Dec 8th) 11. Cell-cell Signalling (Dec 15th - Dr Boareto) 12. Summary (Dec 22nd) TUTORIALS Sep 29: Mathematical Methods required for the course Oct 6: Case Study: I: Dorso-ventral axis formation Oct 13: Dynamical Systems Oct 20: Morphogen Gradients Oct 27: Growing Domains Nov 3: Travelling Waves Nov 17: Turing Patterns Nov 24: Chemotaxis & Branching Processes Dec 1: Case Study II: Organogenesis & Image-based Modelling Dec 8: Tissue Mechanics Dec 15: Cell-cell Signalling Dec 22: Summary, Open Questions & Mock Exam | ||||

Skript | All lecture material will be made available online https://www.bsse.ethz.ch/cobi/education/636-0706-00L_Spatial_Modelling_in_Biology.html | ||||

Literatur | The lecture course is not based on any textbook. The following textbooks are related to some of its content. The textbooks may be of interest for further reading, but are not necessary to follow the course: Murray, Mathematical Biology, Springer Forgacs and Newman, Biological Physics of the Developing Embryo, CUP Keener and Sneyd, Mathematical Physiology, Springer Fall et al, Computational Cell Biology, Springer Szallasi et al, System Modeling in Cellular Biology, MIT Press Wolkenhauer, Systems Biology Kreyszig, Engineering Mathematics, Wiley | ||||

Voraussetzungen / Besonderes | The course is self-contained. The course assumes no background in biology but a good foundation regarding mathematical and computational techniques. | ||||

851-0147-02L | Images of BiologyParticularly suitable for students of D-BIOL, D-BSSE | 3 KP | 2V | M. Hampe, D. Iber | |

Kurzbeschreibung | Students should be made acquainted with the different understandings of biology, especially with the relevance of mathematical methods for latest biological research by looking at exemplary cases of research, which will be presented by different lectureres. | ||||

Lernziel | Development of a broad understanding of the methods of biology by using philosophical and historical perspectives onto the subject. |