Important Note: Our corresponding paper has just been published, and the code in this repository is currently being updated to reflect the final version presented in the paper. The update is expected to be completed by Sept 4, 2023. We appreciate your patience and interest in our work. Thank you!
重要提示: 我们对应的论文刚刚发表，本仓库中的代码正在更新中，以反映在论文中呈现的最终版本。预计2023-9-4前就会更新完成。感谢您的耐心和对我们工作的关注，谢谢！
Enzyme mass minimization decomposition (EMMD) is a method for decomposing flux distributions to identify active elementary flux modes by incorporating thermodynamic and enzymatic constraints into stoichiometric metabolic network models. This repository contains MATLAB code for EMMD, implemented in Matlab 2018b.
For some of the MATLAB functions, the following MATLAB toolboxes must be installed
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Clone the following GitHub repositories
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matlab-utils- Utility functions -
metabolic-network-toolbox- Metabolic Network Toolbox -
sbtab-matlab- SBtab toolbox
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SBML toolbox (optional - needed only if SBML files are used)
Make sure all the directories and subdirectories are included in your Matlab path
- Data preprocessing
- Parameter Balance - By running the parameter balance tool Parameter Balancing, the obtained enzyme kinetic parameters are generated with a complete and consistent parameter set
- Model - Read the parameter-balanced data, calculate the EFM of the model and convert the calculated EFM to the MDF input format
- The Max-min Driving Force (MDF) - Calculate the absolute concentration of metabolites and the Gibbs free energy of reaction for each EFM using the MDF method
- Calculate Enzyme Mass - According to the thermodynamic and enzymatic data calculated in a, b, c, calculate the enzyme mass of each EFM
- EMMD - Decomposition of flux distribution calculated by FBA into EFM combinations
If you have any questions or suggestions with the code, please let us know. Contact Yiran Huang at hyr@gxu.edu.cn