Table 1 Main steps of the preprocessing procedure
From: F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks
Step | Rule |
|---|---|
1. | Identify dead-end metabolites and the corresponding blocked reactions. |
2. | Apply Reduction Rule 1 to remove the rows (resp. columns) corresponding to dead-end metabolites (resp. blocked reactions) from the stoichiometric matrix. |
3. | Apply the TFC rule to determine reactions which are proportional to each other and update their reversibility type. |
4. | Apply Reduction Rule 2 to keep only one column for each set of reactions which are proportional to each other. |
5. | Repeat Steps 1-4 until neither a dead-end metabolite nor a pair of fully coupled reactions can be identified. |
6. | Update the reversibility type of each reaction and remove the columns corresponding to blocked reactions from the stoichiometric matrix. |
7. | Use a basis of the kernel of the stoichiometric matrix to identify fully coupled reactions. This step is optional as the kernel computation may lead to numerical problems. |
8. | Classify reactions according to their reversibility type. |