Computational Systems Biotechnology 1

 
Lecturer: Prof. Dr. Wolfgang Wiechert, Dr.-Ing. Stephan Noack
Lecture: 2 hours
Tutorials: 1 hour
Lecture date: See RWTHOnline
Lecture notes: Will be shared on SCIEBO
Lecture semester: Sommersemester
Language: German
Type of exam: Oral

(Molecular) Systems Biology (SB) is a modern discipline in the life science. Seen from an engineering perspective, SB consequently applies process engineering methodology to the description of processes within a living cell. Thus, SB is concerned with structure and function of complex biochemical interaction networks. The most important foundation of SB is the modern arsenal of high-throughput analytical methods (“omics” methods) for the detailed analysis of genetic and metabolic processes in vivo. The hereby generated large and complex data sets are analyzed with the aid of mathematical models yielding an improved systems understanding. The models also enable qualitative predictions to be made which are needed, for example, for the optimization of production organisms or for the targeted design of new informative experiments. For this reason, SB has also an important foundation of modern synthetic biology.

The two independent lectures CSB 1&2 are intended (presently in German language) for an interdisciplinary audience (CSB 1 in SS, CSB 2 in WS). The focus is on computer supported aspects of systems biology since experimental and bioanalytical foundations are already presented in other lectures at RWTH. The level of abstraction is chosen in such a way that students from different academic courses (particularly engineers and biotechnologists) can follow. If necessary, specific teaching modules are introduced for supplying the required mathematical or biological contents. The lectures integrate presentation units with exercises and short projects supported by different software systems (MATLAB, Omix, Madonna, Maple etc.).

CSB 1 focuses on a broad family of methods which are all based on the stoichiometric matrix of a large metabolic network. These methods already find broad industrial application in the analysis of the metabolic capabilities of platform organisms and for bioprocess design. In synthetic biology respectively metabolic engineering they are used for designing new production strains. Mathematical prerequisites are a basic knowledge of linear algebra (matrices, Gaussian algorithm). A corresponding mathematical bridging-course with homework is integrated for the biotechnologist. The engineers, in turn, get a biological bridging-course for understanding the basic biochemical concepts. Essential themes of the lecture are:

  1. Basic terms
    • SB & synthetic biology
    • Omics methods
  1. Biochemical networks
    • Structural modeling
    • Computer representation
    • Network reconstruction
  2. Stoichiometric network analysis
    • Stoichiometry matrix and null space
    • Constraint based methods
    • Elementary mode based methods
    • Network thermodynamics
  3. Metabolic Flux Analysis (MFA)
    • stoichiometric flux analysis
    • 13C MFA