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Information on preparatory courses

On Sunday February 28, two parallel preparatory courses will be held from morning until evening. These courses are intended to teach the basics to students who are not firm in the respective topics.

Registering for one of these courses will require an extra night’s accommodation and meals, which we will book for you and it will require us to charge an extra registration fee (€ 150). The registration for the precourse can be found in the travel form under the User Profile (login required). The number of places for these courses are limited and will be assigned on a first come, first served basis.

PC-01 Mathematical models of biochemical pathways and networks

Wolfram Liebermeister & Elad Noor

In this precourse, participants with a biological background will be introduced to quantitative, dynamical modelling of biochemical networks.  Mathematical models based on linear programming problems or differential equations are frequently used approaches that facilitate
systematic network analyses. These models allow to test hypotheses about biological processes, e.g., in metabolic or signalling pathways, and to predict cellular properties that are not accessible by experiments. The precourse is designed for those less familiar with the mathematical aspects of modelling and systems biology. It provides a basic introduction to some of the main mathematical concepts and computational techniques used to represent biochemical systems.We will start with describing simple examples of molecular interactions
based on mass action kinetics. Then, more complex enzyme kinetics will be explained, and we get acquainted with kinetic and stoichiometric models of metabolism. Finally, some basics of other modelling approaches, including Boolean and stochastic simulations, will be discussed. The introduced concepts will allow the participants to formulate dynamic models of exemplary metabolic or signalling pathways. A background in mathematics or computational biology is not required for this precourse; a basic knowledge of cell biology is of advantage.

PC-02 The Rocky Road From Wet (Data) to Dry (Models) in Systems Biology

Karl Kuchler

Systems biology (SysBio) aims to gain a systems-level understanding of organismic, cellular or even subcellular pathway behaviour to identify novel as well as emerging principles of a living system. One of the key features of SysBio is the integration of a multitude of as much as possible quantitative biological data (deep-sequencing, SNP and mutations, genetic interactions, microarrays, proteomics, metabolomics, etc.) with various applicable mathematical modelling approaches. While modelling and the use of proper algorithms depends on the question and hypothesis to be addressed, the generation of quantitative biological data often poses unsurmountable technical problems or is even impossible with the current methodologies. This is especially true for measuring the dynamics and time-scale of biological processes from transcription, translation to post-translational modification as well as the kinetics of intracellular biomolecule trafficking, and the dynamics an anon-linearity of most if not all cellular processes. Likewise, pathway architectures and features often result from complex genetic interactions, which respond to various types of input, making parameter estimation for modeling a challenging task. In this pre-course teaching on molecular genetics / biology for theoreticians and modellers, I will try to discuss how and which experimental (genetic / biological) data can be obtained from living cells in a (near)-quantitative manner. We will discuss technical issues and pitfalls applying to the some of the state-of-the-art technologies used to study the dynamics of biological processes through systems biology approaches.