|Herr Prof. Dr. Mustafa Hani Khammash
|Regelungstheorie und Systembiologie
Regelungstheorie u. Systembiologie
ETH Zürich, BSS J 13.2
|+41 61 387 33 56
|Seminar in Systems and Control
|F. Dörfler, R. D'Andrea, E. Frazzoli, M. H. Khammash, J. Lygeros, R. Smith
|Current topics in Systems and Control presented mostly by external speakers from academia and industry
|S. Panke, Y. Benenson, P. S. Dittrich, M. Fussenegger, A. Hierlemann, M. H. Khammash, A. Moor, D. J. Müller, M. Nash, R. Platt, J. Stelling, B. Treutlein
|This course provides an overview of modern concepts of bioengineering across different levels of complexity, from single molecules to systems, microscaled reactors to production environments, and across different fields of applications
|Students will be able to recognize major developments in bioengineering across different organisms and levels of complexity and be able to relate it to major technological and conceptual advances in the underlying sciences.
|Molecular and cellular engineering; Synthetic biology: Engineering strategies in biology; from single molecules to systems; downscaling bioengineering; Bioengineering in chemistry, pharmaceutical sciences, and diagnostics, personalized medicine.
|Handouts during class
|Will be announced during the course
|Introduction to Dynamical Systems with Applications to Biology
|M. H. Khammash, A. Gupta
|Many physical systems are dynamic and are characterized by internal variables that change with time. Describing the quantitative and qualitative features of this change is the topic of dynamical systems theory. Dynamical systems arise naturally in virtually all scientific disciplines including physics, biology, chemistry and engineering. This course is a broad introduction to the topic dynamical s
|The goal of this course is to introduce the student to dynamical systems and to develop a solid understanding of their fundamental properties. The theory will be developed systematically, focusing on analytical methods for low dimensional systems, geometric intuition, and application examples from biology. Computer simulations using matlab will be used to demonstrate various concepts
|A dynamical view of the world; the importance of nonlinearity; solutions of differential equations; solving equations on the computer; the phase plane; fixed points and stability; linear stability analysis; classifications of linear systems; Liapunov functions and nonlinear stability; cycles and oscillations; bifurcations and bifurcation diagrams. Many biological examples will be used through the course to demonstrate the concepts
|Will be provided as needed.
|Strogatz, S. H. (2018). Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering. CRC Press.
Segel, L. A., & Edelstein-Keshet, L. (2013). A Primer in Mathematical Models in Biology (Vol. 129). SIAM.
|Voraussetzungen / Besonderes
|Prerequisites: Calculus; a first course in differential equations; basic linear algebra (eigenvalues and eigenvectors). Matlab programming.
|Current Topics in Biosystems Science and Engineering
For doctoral students only.
Master's students cannot receive credits for the seminar.
|R. Platt, N. Beerenwinkel, Y. Benenson, K. M. Borgwardt, P. S. Dittrich, M. Fussenegger, A. Hierlemann, D. Iber, M. H. Khammash, A. Moor, D. J. Müller, S. Panke, S. Reddy, T. Schroeder, T. Stadler, J. Stelling, B. Treutlein
|This seminar will feature invited lectures about recent advances and developments in systems biology, including topics from biology, bioengineering, and computational biology.
|To provide an overview of current systems biology research.
|The final list of topics will be available at https://www.bsse.ethz.ch/news-and-events/seminar-series.html
|Computational Biology and Bioinformatics Seminar
The Seminar will be offered in autumn semester in Basel (involving professors and lecturers from the University of Basel) and in spring semester in Zurich (involving professors and lecturers from the University of Zurich). Professors and lecturers from ETH Zurich are involved in both semesters.
|N. Beerenwinkel, K. M. Borgwardt, D. Iber, M. H. Khammash, T. Stadler, J. Stelling
|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.
|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.
|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.
|Original papers to be presented by the students will be provided in the first week of the seminar.