SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework.

摘要: A recurrent problem in genome-scale metabolic models (GEMs) is to correctly represent lipids as biomass requirements, due the numerous of possible combinations individual lipid species and corresponding lack fully detailed data. In this study we present SLIMEr, a formalism for representing requirements GEMs using commonly available experimental SLIMEr enhances GEM with mathematical constructs where Split Lipids Into Measurable Entities (SLIME reactions), addition constraints on both classes acyl chain distribution. By implementing consensus Saccharomyces cerevisiae, can accurate amounts species, analyze flexibility resulting distribution, compute energy costs moving from one state another. The approach shows potential better understanding metabolism yeast under different conditions. freely at https://github.com/SysBioChalmers/SLIMEr .