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1 # Import Metabolic Model
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2
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3 Import and extract metabolic model components into tabular format.
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4
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5 ## Overview
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6
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7 Import Metabolic Model extracts metabolic models from SBML/JSON/MAT/YAML formats into tabular summary for analysis.
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8
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9 **Input**: Model file or built-in models
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10 **Output**: Tabular data (CSV/TSV)
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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 → Import Metabolic Model**
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15
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16 1. Select built-in model or upload custom file
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17 2. Set model name and medium configuration
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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 # Import built-in model
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24 importMetabolicModel \
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25 --model ENGRO2 \
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26 --name ENGRO2 \
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27 --medium_selector allOpen \
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28 --out_tabular model_data.csv \
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29 --out_log extraction.log
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30 ```
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31
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32 ## Parameters
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33
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34 ### Model Selection
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35
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36 | Parameter | Flag | Description |
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37 |-----------|------|-------------|
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38 | Built-in Model | `--model` | ENGRO2 or Recon |
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39 | Custom Model | `--input` | Path to SBML/JSON/MAT/YAML file |
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40
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41 **Note**: Use either `--model` OR `--input`.
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42
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43
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44 ### Required
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45
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46 | Parameter | Flag | Description |
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47 |-----------|------|-------------|
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48 | Model Name | `--name` | Model identifier |
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49 | Medium Selector | `--medium_selector` | Medium configuration (use `allOpen`) |
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50 | Output Tabular | `--out_tabular` | Output file (CSV/XLSX) |
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51 | Output Log | `--out_log` | Log file |
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52
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53 ### Optional
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54
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55 | Parameter | Flag | Description | Default |
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56 |-----------|------|-------------|---------|
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57 | Custom Medium | `--custom_medium` | CSV file with medium constraints | - |
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58 | Gene Format | `--gene_format` | Gene ID conversion: Default, ENSG, HGNC_ID, entrez_id | Default |
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59
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60 ## Built-in Models
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61
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62 - **ENGRO2**: ~500 reactions (recommended)
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63 - **Recon**: ~10,000 reactions (genome-wide)
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64
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65 See [Built-in Models](reference/built-in-models) for details.
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66
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67 ## Supported Formats
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68
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69 - **Model formats**: SBML (.xml), JSON (.json), MAT (.mat), YAML (.yml)
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70 - **Compression**: .zip, .gz, .bz2 (e.g., `model.xml.gz`)
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71
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72 Compressed files are automatically detected and extracted.
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73
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74 ## Output Format
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75
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76 **ENGRO2 model:**
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77 ```
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78 ReactionID Formula GPR lower_bound upper_bound ObjectiveCoefficient Pathway_1 Pathway_2 InMedium TranslationIssues
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79 R00001 A + B -> C + D GENE1 or GENE2 -1000.0 1000.0 0.0 Glycolysis Central_Metabolism FALSE
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80 EX_glc_e glc_e <-> - -1000.0 1000.0 0.0 Exchange Transport TRUE
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81 ```
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82
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83 **Other models (Recon):**
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84 ```
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85 ReactionID Formula GPR lower_bound upper_bound ObjectiveCoefficient InMedium TranslationIssues
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86 R00001 A + B -> C + D GENE1 or GENE2 -1000.0 1000.0 0.0 FALSE
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87 EX_glc_e glc_e <-> - -1000.0 1000.0 0.0 TRUE
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88 ```
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89
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90 **File Format Notes:**
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91 - Output can be **tab-separated** (CSV) or Excel (XLSX)
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92 - Contains all model information in tabular format
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93 - Can be edited and re-imported using Export Metabolic Model
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94
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95 ## Understanding Medium Composition
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96
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97 Exchange reactions with `InMedium = TRUE` represent nutrients in the medium:
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98 - **Lower bound**: Uptake rate (negative value, e.g., -10 = uptake 10 mmol/gDW/hr)
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99 - **Upper bound**: Secretion rate (positive value)
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100
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101 Example:
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102 ```
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103 EX_glc_e glc_e <-> - -10.0 1000.0 0.0 TRUE
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104 ```
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105 Glucose uptake: 10 mmol/gDW/hr (lower bound = -10)
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106
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107 More info: [COBRApy Media Documentation](https://cobrapy.readthedocs.io/en/latest/media.html)
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108
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109 ## Examples
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110
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111 ### Extract Built-in Model
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112
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113 ```bash
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114 importMetabolicModel --model ENGRO2 \
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115 --name ENGRO2_extraction \
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116 --medium_selector allOpen \
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117 --out_tabular ENGRO2_data.csv \
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118 --out_log ENGRO2_log.txt
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119 ```
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120
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121 ### Process Custom Model
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122
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123 ```bash
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124 importMetabolicModel --input custom_model.xml \
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125 --name CustomModel \
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126 --medium_selector allOpen \
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127 --out_tabular custom_data.csv \
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128 --out_log custom_log.txt
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129 ```
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130
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131 ## Troubleshooting
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132
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133 | Error | Solution |
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134 |-------|----------|
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135 | "Model file not found" | Check file path |
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136 | "Unsupported format" | Use SBML, JSON, MAT, or YAML |
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137
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138 ## See Also
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139
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140 - [Export Metabolic Model](reference/export-metabolic-model)
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141 - [RAS Generator](tools/ras-generator)
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142 - [RPS Generator](tools/rps-generator)
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