GMCSpy: efficient and accurate computation of genetic minimal cut sets in Python.

ABSTRACT:

Motivation

The identification of minimal genetic interventions that modulate metabolic processes constitutes one of the most relevant applications of genome-scale metabolic models (GEMs). The concept of Minimal Cut Sets (MCSs) and its extension at the gene level, genetic Minimal Cut Sets (gMCSs), have attracted increasing interest in the field of Systems Biology to address this task. Different computational tools have been developed to calculate MCSs and gMCSs using both commercial and open-source software.

Results

Here, we present gMCSpy, an efficient Python package to calculate gMCSs in GEMs using both commercial and non-commercial optimization solvers. We show that gMCSpy substantially overperforms our previous computational tool GMCS, which exclusively relied on commerci

SUBMITTER: Rodriguez-Flores CJ 

PROVIDER: S-EPMC11199197 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature