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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COBRAxy/docs/reference/built-in-models.md	Tue Oct 28 10:44:07 2025 +0000
@@ -0,0 +1,44 @@
+# Built-in Models
+
+COBRAxy includes two pre-installed metabolic models for human metabolism analysis.
+
+## ENGRO2 (Recommended)
+
+**Best for**: General metabolic analysis
+
+- ~2,000 reactions, ~1,500 metabolites, ~500 genes
+- Balanced coverage
+- Core metabolic pathways well-represented
+- **Use for**: Tissue profiling, disease comparisons, time-series analysis
+
+## Recon (Comprehensive)
+
+**Best for**: Genome-wide studies
+
+- ~10,000 reactions, ~5,000 metabolites, ~2,000 genes
+- Most complete human metabolic network
+- Includes rare and specialized pathways
+- **Use for**: Comprehensive studies, rare diseases
+
+## Usage
+
+```bash
+# Specify model name in any COBRAxy tool
+tool_name --model ENGRO2 [options]
+```
+
+## Technical Notes
+
+**Gene IDs**: All models support HGNC ID (e.g., `HGNC:5`), HGNC Symbol (e.g., `ALDOA`), Ensembl, and Entrez formats.
+
+**GPR Rules**: Gene-Protein-Reaction associations use Boolean logic (`and`, `or`).
+
+**Custom Models**: Use [Import Metabolic Model](../tools/import-metabolic-model) to extract and [Export Metabolic Model](../tools/export-metabolic-model) to create custom models.
+
+## See Also
+
+- [RAS Generator](../tools/ras-generator) - Uses model GPR rules
+- [RAS to Bounds](../tools/ras-to-bounds) - Applies flux constraints to models
+- [Flux Simulation](../tools/flux-simulation) - Samples model flux distributions
+- [Import Metabolic Model](../tools/import-metabolic-model) - Extract model data
+- [Export Metabolic Model](../tools/export-metabolic-model) - Create custom models