Thesis Construction and simulation of metabolic network models

Biogas is produced by a complex microbial community consisting of bacteria and archaea. Species-specific metabolic network models allow for simulation of the biogas production on (meta)genome-scale. Each network model encodes the metabolic potential of a community member. Flux balance analysis can then be used to predict the activity of each member under different process conditions. For modelling the whole biogas process, the individual models are combined to a community-wide model.

The aim of the proposed thesis project is to generate metabolic networks. Therefore, genomes, reconstructed from metagenomes, have to be annotated. For the network reconstruction the software Pathway Tools based on the MetaCyc database which includes a reconstruction algorithm is to be used. Generated network models shall be simulated and results compared with literature knowledge.

Your tasks:

• Metabolic network reconstruction
• Simulation of metabolic network models using flux balance analysis
• Coupling of individual models to community-wide models
• Literature research and automated comparison of model results with literature knowledge

Your profile:

• Studies of bioinformatics, biochemistry or related sciences
• Knowledge of metabolic pathways
• Basic knowledge of a common programming, scripting language like Java, C, Python, Bash, Matlab is desired
• Knowledge about genome data and their annotation are an advantage
• Highly motivated
• Ability to work independently

We offer:

• Great insights into the work in a leading research institute
• Individual supervision with the possibility to contribute your own ideas

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