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comparison COBRAxy/docs/reference/built-in-models.md @ 547:73f2f7e2be17 draft

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