This repository contains data generated in the wet lab needed for characterization and validation of strain specific GEMs
binary_growth_phenotypescontains data, code and analysis of binary growth phenotype experimentsgrowth_kineticscontains data, code and analysis of plate reader experiments for growth curvessupporting_experimentscontains data, code and analysis of other experiments (OD-CFU, manual growth curves)
Corynebacterium striatum, a gram-positive and non-sporulating rod, has recently been discovered for its pathogenic properties. Even though it has been known since the early 20th cen- tury, C.striatum was often disregarded as a pathogen since it is part of the typical human skin microbiota1. Nevertheless, it was found that, especially in immunocompromised patients, C.striatum can be the source for diseases such as Chronic Obstructive Pulmonary Disease, also known as COPD or pneumonia2. Not only is C. striatum active within the respiratory tract, but it was also attributed to long-standing open wound infections3 and prolonged hospitalizations4.
Famke Bäuerle, Gwendolyn O. Döbel, Laura Camus, Simon Heilbronner, and Andreas Dräger. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. Front. Bioinform., oct 2023. doi:10.3389/fbinf.2023.1214074.
We can convert jupyter notebooks to other formats. Use this command to convert to a pdf that can be included in the thesis:
jupyter nbconvert --to pdf plate_reader_curves.ipynb --output-dir '/Users/baeuerle/Organisation/Masterarbeit/thesis/files/jupyter_nb' --template=classic.tplx