Ems vs. OptKnock vs. OptFlux

10 硕 赵美娜

Ems

• Ems 是代谢途径分析的一种方法。• 非基因组尺度代谢模型。

Ems 原理：MPA

根据对于底物和产物的规定，可以减少 Ems 的数量

OptKnock

①genome-scale models of metabolism

②objectives ： the maximization of biomass yield and the minimization of metabolic adjustment (MOMA).

代谢物

通量

FBA

基因敲除模型

二层规划问题

对偶规划问题Single-level MILP

二层规划对偶规划 Single-level MILP

OptFlux

It is the first tool to incorporate strain optimization tasks, i.e.the identification of Metabolic Engineering targetsMetabolic Engineering targets, using Evolutionary AlgorithmsEvolutionary Algorithms / Simulated AnnealinSimulated Annealing metaheuristicsg metaheuristics,or the previously proposed OptKnock algorithmOptKnock algorithm.

• It also allows the use of stoichiometric metabolic models for

• ① phenotype simulation of both wild-typewild-type and mutant organismsmutant organisms

• Flux Balance AnalysisFlux Balance Analysis using the methods of• Minimization of Metabolic Adjustment （（ MoMMoM

AA））• Regulatory on/off Minimization of Metabolic flMinimization of Metabolic fl

ux changesux changes• ② Metabolic Flux AnalysisMetabolic Flux Analysis, computing the ad

missible flux space given a set of measured fluxes

• ③pathway analysis through the calculation of ElElementary Flux Modesementary Flux Modes

• Ems

• Optknock （没有找到软件）• Opflux （根据软件说明不能复原里面的例

子）

Purpose ： XyloseSuccinate借鉴从葡萄糖生产琥珀酸的实验结果，希望与模拟结果进行对比

MG1655/pLOI297

TCS083/pLOI297