636-0007-00L  Computational Systems Biology

Semester Autumn Semester 2017
Lecturers J. Stelling
Periodicity yearly course
Language of instruction English



Catalogue data

Abstract Study of fundamental concepts, models and computational methods for the analysis of complex biological networks. Topics: Systems approaches in biology, biology and reaction network fundamentals, modeling and simulation approaches (topological, probabilistic, stoichiometric, qualitative, linear / nonlinear ODEs, stochastic), and systems analysis (complexity reduction, stability, identification).
Objective The aim of this course is to provide an introductory overview of mathematical and computational methods for the modeling, simulation and analysis of biological networks.
Content Biology has witnessed an unprecedented increase in experimental data and, correspondingly, an increased need for computational methods to analyze this data. The explosion of sequenced genomes, and subsequently, of bioinformatics methods for the storage, analysis and comparison of genetic sequences provides a prominent example. Recently, however, an additional area of research, captured by the label "Systems Biology", focuses on how networks, which are more than the mere sum of their parts' properties, establish biological functions. This is essentially a task of reverse engineering. The aim of this course is to provide an introductory overview of corresponding computational methods for the modeling, simulation and analysis of biological networks. We will start with an introduction into the basic units, functions and design principles that are relevant for biology at the level of individual cells. Making extensive use of example systems, the course will then focus on methods and algorithms that allow for the investigation of biological networks with increasing detail. These include (i) graph theoretical approaches for revealing large-scale network organization, (ii) probabilistic (Bayesian) network representations, (iii) structural network analysis based on reaction stoichiometries, (iv) qualitative methods for dynamic modeling and simulation (Boolean and piece-wise linear approaches), (v) mechanistic modeling using ordinary differential equations (ODEs) and finally (vi) stochastic simulation methods.
Lecture notes Link
Literature U. Alon, An introduction to systems biology. Chapman & Hall / CRC, 2006.

Z. Szallasi et al. (eds.), System modeling in cellular biology. MIT Press, 2006.

Performance assessment

Performance assessment information (valid until the course unit is held again)
Performance assessment as a semester course
ECTS credits 6 credits
Examiners J. Stelling
Type session examination
Language of examination English
Course attendance confirmation required No
Repetition The performance assessment is offered every session. Repetition possible without re-enrolling for the course unit.
Mode of examination written 120 minutes
Written aids keine
This information can be updated until the beginning of the semester; information on the examination timetable is binding.

Learning materials

 
Main link Lecture Material
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Courses

Number Title Hours Lecturers
636-0007-00 V Computational Systems Biology 3 hrs
Wed 14-17 HG D 3.2 »
J. Stelling
636-0007-00 U Computational Systems Biology 2 hrs
Fri 10-12 CAB G 11 »
J. Stelling

Restrictions

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