Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study.

ABSTRACT: Context-specific genome-scale model (CS-GSM) reconstruction is becoming an efficient strategy for integrating and cross-comparing experimental multi-scale data to explore the relationship between cellular genotypes, facilitating fundamental or applied research discoveries. However, the application of CS modeling for non-conventional microbes is still challenging. Here, we present a graphical user interface that integrates COBRApy, EscherPy, and RIPTiDe, Python-based tools within the BioUML platform, and streamlines the reconstruction and interrogation of the CS genome-scale metabolic frameworks via Jupyter Notebook. The approach was tested using -omics data collected for Methylotuvimicrobium alcaliphilum 20Z^R, a prominent microbial chassis for methane capturing and valori

SUBMITTER: Kulyashov MA 

PROVIDER: S-EPMC11748545 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature