# COMETS Metabolic Model Files

1. Stoichiometric Matrix

A matrix element of the stoichiometric matrix S_{i,j} denotes the number of molecules of metabolite i that participate in reaction j. All entries of this filed are integer numbers. Only the non-zero matrix elements should be listed. The rest are given zero value by default.

SMATRIX num_rows num_cols row_1 col_1 stoichiometry row_2 col_2 stoichiometry row_3 col_3 stoichiometry . . . //

2. Flux Bounds

All flux bounds are set to the default_lower_bound and default_upper_bound values unless they are listed below. The reaction indices start with 1.

BOUNDS default_lower_bound default_upper_bound rxn_1 lb ub rxn_2 lb ub rxn_3 lb ub . . . //

3. Objective Reaction

The index of the objective reaction.

OBJECTIVE objective_reaction_index //

4. Metabolite Names

The metabolite names in the order consistent with the stoichiometric matrix.

METABOLITE_NAMES name_1 name_2 name_3 . . . //

5. Reaction Names

The reaction names in the order consistent with the stoichiometric matrix.

REACTION_NAMES name_1 name_2 name_3 . . . //

6. Exchange Reaction Indices

Exchange reaction indices as listed under reaction_names, starting with 1.

EXCHANGE_REACTIONS reaction_idx_1 reaction_idx_2 reaction_idx_3 . . . //

7. Diffusion Constants

**Deprecated: This won’t cause any errors if you leave it in, but it’s not used by COMETS**

References the indices in the **exchange reaction** block. That is, if there are 10 reaction indices, then there should be up to 10 lines in the block.

DIFFUSION_CONSTANTS default_value exch_1 value exch_2 value exch_3 value . . . //

8. Alpha Values

**Deprecated: This won’t cause any errors if you leave it in, but it’s not used by COMETS**

References the indices in the **exchange reaction** block. That is, if there are 10 reaction indices, then there should be up to 10 lines in the block.

ALPHA_VALUES default_alpha exch_1 alpha_1 exch_2 alpha_2 exch_3 alpha_3 . . . //

9. W Values

**Deprecated: This won’t cause any errors if you leave it in, but it’s not used by COMETS**

References the indices in the **exchange reaction** block. That is, if there are 10 reaction indices, then there should be up to 10 lines in the block.

W_VALUES default_W exch_1 W_1 exch_2 W_2 exch_3 W_3 . . . //

10. Km Values

References the indices in the **exchange reaction** block. That is, if there are 10 reaction indices, then there should be up to 10 lines in the block.

KM_VALUES default_Km exch_1 Km_1 exch_2 Km_2 exch_3 Km_3 . . . //

11. Vmax Values

References the indices in the **exchange reaction** block. That is, if there are 10 reaction indices, then there should be up to 10 lines in the block.

VMAX_VALUES default_Vmax exch_1 Vmax_1 exch_2 Vmax_2 exch_3 Vmax_3 . . . //

12. Hill Coefficients

References the indices in the **exchange reaction** block. That is, if there are 10 reaction indices, then there should be up to 10 lines in the block.

HILL_COEFFICIENTS default_Hill exch_1 Hill_1 exch_2 Hill_2 exch_3 Hill_3 . . . //

13. Objective Style

Sets the objective style. The objective_style_string can be one of the values:

MAXIMIZE_OBJECTIVE_FLUX MINIMIZE_OBJECTIVE_FLUX MAXIMIZE_TOTAL_FLUX MINIMIZE_TOTAL_FLUX MAX_OBJECTIVE_MAX_TOTAL MAX_OBJECTIVE_MIN_TOTAL MIN_OBJECTIVE_MAX_TOTAL MIN_OBJECTIVE_MIN_TOTAL

The default is MAXIMIZE_OBJECTIVE_FLUX. If combined with GUROBI optimizer only

MAXIMIZE_OBJECTIVE_FLUX and MAX_OBJECTIVE_MIN_TOTAL are functional.

OBJECTIVE_STYLE objective_style_string //

14. Optimizer

Only version 2.0.0 and up. Sets the optimizer. The optimizer_string can be one of the values:

GUROBI GLPK

The default is GUROBI.

OPTIMIZER optimizer_string