Name | Prof. Dr. Dagmar Iber |
Field | Computational Biology |
Address | Professur f. Computational Biology ETH Zürich, BSS G 11.1 Klingelbergstrasse 48 4056 Basel SWITZERLAND |
Telephone | +41 61 387 32 10 |
dagmar.iber@bsse.ethz.ch | |
URL | http://www.bsse.ethz.ch/cobi |
Department | Biosystems Science and Engineering |
Relationship | Associate Professor |
Number | Title | ECTS | Hours | Lecturers | |
---|---|---|---|---|---|
636-0021-00L | Mathematical Modelling in Systems Biology | 5 credits | 3G | D. Iber | |
Abstract | Basic concepts and mathematical tools to explore biochemical reaction kinetics and biological network dynamics. | ||||
Objective | The aim of the course is to provide an introductory overview of mathematical and computational methods to analyse biological network dynamics. | ||||
Content | 1. Introduction to Mathematical Modeling 2. Introduction to Biochemical Reaction Modeling 3. Model Analysis: Phase Plane 4. Model Analysis: Linear Stability Analysis 5. Model Analysis: Bifurcation Analysis 6. Regulatory Feedback: Switches 7. Regulatory Feedback: Adaptation 8. Regulatory Feedback: Oscillations and Delay Equations 9. Receptor Signaling and Signaling Cascades 10. Network Properties: Sensitivity and Robustness 11. Introduction to Parameter Estimation | ||||
Lecture notes | https://www.bsse.ethz.ch/cobi/education/626-0005-00l-mathematical-modelling-in-systems-biology.html | ||||
Literature | - Wolkenhauer, Systems Biology, http: // www.sbi.uni-rockstock.de/files/p_sb.pdf - Keener and Sneyd, Mathematical Physiology, Springer - Klipp et al, Systems Biology in Practice, Wiley - Kreyszig, Engineering Mathematics, Wiley | ||||
Prerequisites / Notice | Introductory courses in Mathematics (Linear Algebra, Differential Equations, Numerics) and basic concepts of programming. | ||||
636-0301-00L | Current Topics in Biosystems Science and Engineering | 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, P. Pantazis, 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. | ||||
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/. | ||||
636-0706-00L | Spatio-Temporal Modelling in Biology | 5 credits | 3G | D. Iber | |
Abstract | This course focuses on modeling spatio-temporal problems in biology, in particular on the cell and tissue level. A wide range of mathematical techniques will be presented as part of the course, including concepts from non-linear dynamics (ODE and PDE models), stochastic techniques (SDE, Master equations, Monte Carlo simulations), and thermodynamic descriptions. | ||||
Objective | The aim of the course is to introduce students to state-of-the-art mathematical modelling of spatio-temporal problems in biology. Students will learn how to chose from a wide range of modelling techniques and how to apply these to further our understanding of biological mechanisms. The course aims at equipping students with the tools and concepts to conduct successful research in this area; both classical as well as recent research work will be discussed. | ||||
Content | 1. Introduction to Modelling in Biology 2. Morphogen Gradients 3. Turing Pattern 4. Travelling Waves & Wave Pinning 5. Application Example 1: Dorso-ventral axis formation 6. Chemotaxis, Cell Adhesion & Migration 7. Introduction to Numerical Methods 8. Simulations on Growing Domains 9. Image-Based Modelling 10. Branching Processes 11. Cell-based Simulation Frameworks 12. Application Example 2: Limb Development 13. Summary | ||||
Lecture notes | All lecture material will be made available online https://www.bsse.ethz.ch/cobi/education/636-0706-00L_Spatial_Modelling_in_Biology.html | ||||
Literature | 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 | ||||
Prerequisites / Notice | The course builds on introductory courses in Computational Biology. The course assumes no background in biology but a good foundation regarding mathematical and computational techniques. |