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18.05.2021

Automating the refinement of C. striatum

Famke Bäuerle implemented a template for reconstruction and used it for C. striatum as her research project.

The project template for genome-scale reconstructions prepared by Ms. Bäuerle.

Over the last years, more and more multi-drug resistant strains of Corynebacterium striatum have been found in clinical settings. Due to antibiotic resistance and other mechanisms, these bacteria can lead to diseases like pneumonia and chronic obstructive pulmonary disease. Thus, any hints on how these bacteria work can help prevent diseases, especially in immunocompromised patients. Based on a previous draft model created by Tanja Urz, Famke Bäuerle worked on the further refined genome-scale metabolic model of C. striatum. With growth simulations on different media, Ms. Bäuerle investigated the behavior of C. striatum in different settings.

The refinement of genome-scale metabolic models requires a lot of manual curation work. Some of those tasks can, however, be abbreviated by complementary scripts or even be automated. In the second part of this research project, Famke Bäuerle worked on automating the refinement. A collection of python scripts was developed, which can be used and extended by all group members. These scripts cover fundamental analysis, such as numbers that always go into publications and growth simulations of media definitions collected by the group members. All scripts were collected in a Python module called refinegems and saved to a GitHub repository.

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