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1 # Export Metabolic Model
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2
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3 Convert tabular data into COBRA metabolic model.
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4
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5 ## Overview
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6
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7 Export Metabolic Model converts structured tabular data (CSV/TSV) into functional COBRA models in SBML, JSON, MATLAB, or YAML formats.
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8
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9 **Input**: Tabular model data (CSV/TSV)
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10 **Output**: SBML/JSON/MAT/YAML model files
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11
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12 ## Galaxy Interface
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13
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14 In Galaxy: **COBRAxy → Export Metabolic Model**
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15
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16 1. Upload tabular model data file
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17 2. Select output format (SBML/JSON/MAT/YAML)
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18 3. Click **Run tool**
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19
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20 ## Command-line console
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21
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22 ```bash
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23 exportMetabolicModel \
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24 --input model_data.csv \
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25 --format sbml \
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26 --output custom_model.xml \
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27 --out_log conversion.log
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28 ```
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29
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30 ## Parameters
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31
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32 | Parameter | Flag | Description |
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33 |-----------|------|-------------|
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34 | Input File | `--input` | Tabular file (CSV/TSV) with model data |
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35 | Output Format | `--format` | Model format: sbml, json, mat, yaml |
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36 | Output File | `--output` | Output model file path |
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37 | Output Log | `--out_log` | Log file |
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38
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39 ## Input Format
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40
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41 Required columns:
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42
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43 ```csv
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44 ReactionID,Formula,GPR,lower_bound,upper_bound,ObjectiveCoefficient,InMedium,TranslationIssues
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45 R00001,A + B -> C + D,GENE1 or GENE2,-1000.0,1000.0,0.0,FALSE,
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46 EX_glc_e,glc_e <->,-,-1000.0,1000.0,0.0,TRUE,
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47 ```
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48
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49 **File Format Notes:**
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50 - Use **comma-separated** (CSV) or **tab-separated** (TSV)
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51 - First row must contain column headers
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52 - Required columns: ReactionID, Formula, lower_bound, upper_bound
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53 - Optional columns: GPR, ObjectiveCoefficient, InMedium, Pathway_1, Pathway_2
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54
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55 ## Reaction Formula Syntax
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56
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57 ```
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58 # Irreversible
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59 A + B -> C + D
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60
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61 # Reversible
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62 A + B <-> C + D
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63
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64 # With stoichiometry
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65 2 A + 3 B -> 1 C + 4 D
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66 ```
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67
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68 ## GPR Rule Syntax
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69
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70 ```
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71 # Single gene
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72 GENE1
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73
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74 # Alternative genes (OR)
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75 GENE1 or GENE2
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76
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77 # Required complex (AND)
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78 GENE1 and GENE2
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79
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80 # Nested logic
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81 (GENE1 and GENE2) or GENE3
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82 ```
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83
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84 ## Output Formats
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85
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86 - **SBML**: XML standard, maximum compatibility
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87 - **JSON**: COBRApy native format
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88 - **MATLAB**: COBRA Toolbox compatibility
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89 - **YAML**: Human-readable format
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90
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91 ## Examples
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92
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93 ### Basic Export
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94
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95 ```bash
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96 exportMetabolicModel --input model.csv \
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97 --format sbml \
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98 --output model.xml \
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99 --out_log conversion.log
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100 ```
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101
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102 ## Troubleshooting
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103
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104 | Error | Solution |
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105 |-------|----------|
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106 | "Formula parsing failed" | Check reaction formula syntax |
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107 | "Model infeasible" | Review bounds and exchange reactions |
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108
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109 ## See Also
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110
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111 - [Import Metabolic Model](reference/import-metabolic-model)
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112 - [RAS to Bounds](tools/ras-to-bounds)
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113 - [Flux Simulation](tools/flux-simulation)
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