Benchmarking-Initiative
Add Mishra_MetabEng2023
A kinetic metabolic model of lipid metabolism in Saccharomyces cerevisiae that integrates fatty acid biosynthesis, glycerophospholipid metabolism, sphingolipid metabolism, storage lipids, lumped sterol synthesis, and the synthesis and transport of relevant target-chemicals, such as fatty acids and fatty alcohols. The model was trained on lipidomic data of a reference S. cerevisiae strain, single knockout mutants, and lipid overproduction strains reported in literature. https://doi.org/10.1016/j.ymben.2022.11.003
Model is available in PEtab format: https://github.com/Zhao-Group/Mishra-Saccharomyces-lipid-kinetic-model
Will be closed by #254 The implementation was taken directly from the PEtab files provided by the authors. So far the optimization has been difficult because it is a big model. Using 300 starts with fides did not produce the results shown in the paper. Higher number of starts or different optimizer need to be applied. Code for reproducing the measurement vs. simulation plot from the publication is provided in the README.md. In the paper the objective function was minimized to 10433 +/- 1000 in 2150 +/- 10 steps (Suppl. Fig. 4, extracted with webplotdigitizer)
