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

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 commercial software. Moreover, we compared gMCSpy with recently published competing algorithms in the literature, finding significant improvements in both accuracy and computation time. All these advances make gMCSpy an attractive tool for researchers in the field of Systems Biology for different applications in health and biotechnology. AVAILABILITY AND IMPLEMENTATION: The Python package gMCSpy and the data underlying this manuscript can be accessed at: https://github.com/PlanesLab/gMCSpy.

The role of stimulus combinations in the repeated assessment of resurgence.

The current study examined the role of stimulus combinations on the repeated assessment of resurgence. Using a within-session resurgence procedure, rats were exposed to different conditions, each with distinct stimulus combinations (AAA, ABA, ABB, ABC and AAB). Two arrangements of stimulus changes were compared: Experiment 1 involved changes in stimulus combinations every five sessions, while Experiment 2 implemented changes every session. Resurgence was observed in both experiments; however, Experiment 2 demonstrated more consistent and repeated resurgence when stimulus combinations changed every session. Notably, the ABA, ABB and ABC conditions showed the highest percentage of sessions in which resurgence was observed. Lastly, the current study extends the application of the within-session resurgence procedure to rats and auditory stimuli, providing a reliable method for assessing resurgence in single subjects under different variable conditions.