Mustafa Hani Khammash: Catalogue data in Autumn Semester 2022

Name	Prof. Dr. Mustafa Hani Khammash
Field	Control Theory and Systems Biology
Address	Regelungstheorie u. Systembiologie ETH Zürich, BSS J 13.2 Klingelbergstrasse 48 4056 Basel SWITZERLAND
Telephone	+41 61 387 33 56
E-mail	mustafa.khammash@bsse.ethz.ch
URL	http://www.bsse.ethz.ch/ctsb
Department	Biosystems Science and Engineering
Relationship	Full Professor

Number

Title

ECTS

Hours

Lecturers

227-0920-00L

Seminar in Systems and Control

0 credits

F. Dörfler, R. D'Andrea, E. Frazzoli, M. H. Khammash, J. Lygeros, R. Smith

Abstract

Current topics in Systems and Control presented mostly by external speakers from academia and industry

Learning objective

see above

636-0102-00L

Advanced Bioengineering

Only for Biotechnologie Master, Programme Regulations 2017.

4 credits

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

Abstract

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

Learning objective

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.

Content

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.

Lecture notes

Handouts during class

Literature

Will be announced during the course

Competencies

Subject-specific Competencies	Concepts and Theories	assessed
	Techniques and Technologies	assessed
Personal Competencies	Critical Thinking	assessed

636-0102-10L

Advanced Bioengineering

Only for Biotechnologie Master, Programme Regulations 2021 or doctoral students of D-BSSE

2 credits

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

Abstract

Learning objective

Content

Lecture notes

Handouts during class

Literature

Will be announced during the course

Competencies

Subject-specific Competencies	Concepts and Theories	assessed
	Techniques and Technologies	assessed
Personal Competencies	Critical Thinking	assessed

636-0118-00L

Introduction to Dynamical Systems with Applications to Biology

4 credits

M. H. Khammash, A. Gupta

Abstract

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

Learning objective

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

Content

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

Lecture notes

Will be provided as needed.

Literature

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.

Prerequisites / Notice

Prerequisites: Calculus; a first course in differential equations; basic linear algebra (eigenvalues and eigenvectors). Matlab programming.

636-0301-00L

Current Topics in Biosystems Science and Engineering

For doctoral students only.
Master's students cannot receive credits for the seminar.

2 credits

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, S. Reddy, T. Schroeder, J. Stelling, B. Treutlein

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 https://www.bsse.ethz.ch/news-and-events/seminar-series.html

636-0704-00L

Computational Biology and Bioinformatics Seminar

Number of participants limited to 30
The seminar is addressed primarily at students enrolled in the MSc CBB programme.
Students of other ETH study programmes interested in this course need to ask the lecturer for permission to enrol in the course.

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.

2 credits

N. Beerenwinkel, K. M. Borgwardt, D. Iber, M. H. Khammash, T. Stadler, J. Stelling

Abstract

Computational biology and bioinformatics aim at an understanding of living systems through computation. The seminar combines student presentations and current research project presentations to review the rapidly developing field from a computer science perspective. Areas: DNA sequence analysis, proteomics, optimization and bio-inspired computing, and systems modeling, simulation and analysis.

Learning objective

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.

Content

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.

Literature

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