--- a/COBRAxy/docs/README.md	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/docs/README.md	Sun Oct 26 19:27:41 2025 +0000
@@ -1,8 +1,8 @@
 # COBRAxy Documentation
 
-> A Python toolkit for metabolic flux analysis and visualization, with Galaxy integration.
+> A Python-based command-line suite for metabolic flux analysis and visualization, with Galaxy integration.
 
-COBRAxy enables the integration of transcriptomics data with COBRA-based metabolic models, offering a comprehensive framework for studying metabolism in both health and disease. With COBRAxy, users can load and enrich metabolic models by incorporating transcriptomic data and adjusting the model’s medium conditions.
+COBRAxy enables the integration of transcriptomics data with COBRA-based metabolic models, offering a comprehensive framework for studying metabolism in both health and disease. With COBRAxy, users can load and enrich metabolic models by incorporating transcriptomic data and adjusting the model's medium conditions.
 
 ## Overview
 
@@ -30,35 +30,28 @@
 Install COBRAxy and get it running on your system
 
 ### [Tutorials](tutorials/)
-Step-by-step guides for Galaxy and Python usage
+Step-by-step guides for Galaxy usage
 
 ### [Tools Documentation](tools/)
 Complete reference for all COBRAxy tools
 
 ## Data Flow
 
-COBRAxy follows several analysis paths:
+COBRAxy supports three main analysis workflows:
+
+1. **RAS-based Enrichment Analysis**: 
+   Gene Expression → RAS Generation → MAREA → Enriched Pathway Maps
 
-1. **RAS Enrichment Analysis**: RAS computation → MAREA → Enriched Maps
-2. **Flux Enrichment Analysis Simulation**: RAS computation → Model Constraints → Flux Sampling → Flux Maps
-3. **RAS/RPS Enrichment Analysis**: RAS + RPS computation → MAREA → Enriched Maps
+2. **Flux Sampling Analysis**: 
+   Gene Expression → RAS Generation → RAS to Bounds → Flux Simulation → Flux to Map → Flux-enriched Maps
+
+3. **RAS+RPS Combined Enrichment**: 
+   Gene Expression + Metabolite Data → RAS + RPS Generation → MAREA → Multi-omics Enriched Maps
 
 ## Community & Support
 
-- **Documentation**: Complete guides and API reference
-- **Discussions**: Ask questions and share experiences
-- **Issues**: Report bugs and request features
+- **Documentation**: Complete guides and references
+- **Issues**: Report bugs and request features on [GitHub](https://github.com/CompBtBs/COBRAxy/issues)
 - **Contributing**: Help improve COBRAxy
 
-## Quick Links
-
-| Resource | Description |
-|----------|-------------|
-| [Installation Guide](installation.md) | Get COBRAxy running on your system |
-| [Galaxy Tutorial](tutorials/galaxy-setup.md) | Web-based analysis setup |
-| [Python Tutorial](tutorials/python-api.md) | Use COBRAxy programmatically |
-| [Tools Documentation](tools/) | Complete tool reference |
-
----
-
 **Ready to start?** Follow the [Installation Guide](installation.md) to get COBRAxy up and running!
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