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Ems vs. OptKnock vs. OptFlux

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. 所有途径. 增加限制 减少 Ems. 过表达 增加所需要途径的通量. OptKnock. ①genome-scale models of metabolism.

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Ems vs. OptKnock vs. OptFlux

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  1. Ems vs. OptKnock vs. OptFlux 10硕 赵美娜

  2. Ems • Ems是代谢途径分析的一种方法。 • 非基因组尺度代谢模型。

  3. Ems原理：MPA 根据对于底物和产物的规定，可以减少Ems的数量

  4. 所有途径 增加限制 减少Ems 过表达 增加所需要途径的通量

  5. OptKnock ①genome-scale models of metabolism ②objectives：the maximization of biomass yield and the minimization of metabolic adjustment (MOMA).

  6. FBA 代谢物 通量 基因敲除模型

  7. Single-level MILP 对偶规划问题 二层规划问题 二层规划对偶规划Single-level MILP

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

  9. It also allows the use of stoichiometric metabolic models for • ① phenotype simulation of both wild-type and mutant organisms • Flux Balance Analysis using the methods of • Minimization of Metabolic Adjustment （MoMA） • Regulatory on/off Minimization of Metabolic flux changes • ② Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes • ③pathway analysis through the calculation of Elementary Flux Modes

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

  11. Purpose：XyloseSuccinate 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

  12. MG1655/pLOI297 TCS083/pLOI297

  13. 欢迎大家批评指正

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