392032 Metabolic network analysis (BS) (SoSe 2017)

This short course will provide an overview of metabolic network
analysis, a topic at the intersection of computational biology, systems
biology and mathematical modelling. It will go into detail into the
modeling and analysis of metabolic networks in the constraint-based
formalism, which complement metabolomics data analysis. By the end of
the course the students will have an appreciation for the advantages and
shortcomings of metabolic network models, the tools used for their
analysis, and the open problems currently facing the field. They will
also learn the use of Mongoose, an open-source metabolic network
analysis platform (mongoose.csail.mit.edu).

Tentative Schedule

Day 1: Metabolic network analysis formalisms

topological analysis and deficiency zero theorem
biochemical systems analysis and control theory
constraint-based formalism and flux balance analysis

Day 2: Structural analysis of metabolic network models

blocked reactions classification
enzyme and isozyme subsets
redundant constraint identification

Day 3: Troubleshooting metabolic network models

unblocking blocked reactions
identifying and correcting “free lunches”
network reconciliation and refinement

Day 4: Extensions

inclusion of thermodynamic constraints
metabolic engineering applications
enumeration of elementary modes and minimal cut sets