This repository contains code, data, and metabolic models used in the following publication:
S. Blasche et al, "Emergence of stable coexistence in a complex microbial community through metabolic cooperation and spatio-temporal niche partitioning" (pre-print on BioRxiv: https://doi.org/10.1101/541870)
Technical details:
-
The genome-scale metabolic models were built with CarveMe (SBML files provided).
-
Analysis of meta-transcriptomics data was performed with mOTUs2 and DESeq2 (R scripts provided).
-
Flux balance analysis was performed with ReFramed (Jupyter notebooks provided).