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1 # Built-in Models
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2
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3 COBRAxy includes two pre-installed metabolic models for human metabolism analysis.
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4
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5 ## ENGRO2 (Recommended)
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6
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7 **Best for**: General metabolic analysis
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8
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9 - ~2,000 reactions, ~1,500 metabolites, ~500 genes
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10 - Balanced coverage
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11 - Core metabolic pathways well-represented
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12 - **Use for**: Tissue profiling, disease comparisons, time-series analysis
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13
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14 ## Recon (Comprehensive)
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15
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16 **Best for**: Genome-wide studies
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17
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18 - ~10,000 reactions, ~5,000 metabolites, ~2,000 genes
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19 - Most complete human metabolic network
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20 - Includes rare and specialized pathways
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21 - **Use for**: Comprehensive studies, rare diseases
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22
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23 ## Usage
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24
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25 ```bash
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26 # Specify model name in any COBRAxy tool
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27 tool_name --model ENGRO2 [options]
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28 ```
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29
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30 ## Technical Notes
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31
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32 **Gene IDs**: All models support HGNC ID (e.g., `HGNC:5`), HGNC Symbol (e.g., `ALDOA`), Ensembl, and Entrez formats.
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33
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34 **GPR Rules**: Gene-Protein-Reaction associations use Boolean logic (`and`, `or`).
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35
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36 **Custom Models**: Use [Import Metabolic Model](../tools/import-metabolic-model) to extract and [Export Metabolic Model](../tools/export-metabolic-model) to create custom models.
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37
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38 ## See Also
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39
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40 - [RAS Generator](../tools/ras-generator) - Uses model GPR rules
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41 - [RAS to Bounds](../tools/ras-to-bounds) - Applies flux constraints to models
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42 - [Flux Simulation](../tools/flux-simulation) - Samples model flux distributions
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43 - [Import Metabolic Model](../tools/import-metabolic-model) - Extract model data
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44 - [Export Metabolic Model](../tools/export-metabolic-model) - Create custom models
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