--- a/COBRAxy/docs/tutorials/README.md	Sat Oct 25 15:20:55 2025 +0000
+++ b/COBRAxy/docs/tutorials/README.md	Sun Oct 26 19:27:41 2025 +0000
@@ -1,31 +1,26 @@
 # Tutorials
 
-Learn COBRAxy through hands-on tutorials covering the two main usage scenarios.
+Learn COBRAxy through hands-on tutorials for web-based analysis.
 
 ## Available Tutorials
 
 | Tutorial | Duration | Description |
 |----------|----------|-------------|
-| [Galaxy Setup](galaxy-setup.md) | 30 min | Set up Galaxy for web-based analysis |
-| [Python API Usage](python-api.md) | 45 min | Programmatic analysis with Python |
+| [Galaxy Setup](tutorials/galaxy-setup) | 30 min | Set up Galaxy for web-based analysis |
 
-## Choose Your Path
+## Web Interface Tutorial
 
-### Web Interface → [Galaxy Setup Tutorial](galaxy-setup.md)
-
-Set up a local Galaxy instance with COBRAxy tools for point-and-click analysis. Perfect for users who prefer graphical interfaces and don't want to write code.
+### [Galaxy Setup Tutorial](tutorials/galaxy-setup)
 
-### Python Programming → [Python API Tutorial](python-api.md)
-
-Learn to call COBRAxy tools programmatically in your analysis pipelines. Ideal for integrating COBRAxy into custom workflows and automation.
+Set up a local Galaxy instance with COBRAxy tools for point-and-click analysis. Perfect for users who prefer graphical interfaces and reproducible workflows.
 
 ## Prerequisites
 
 Before starting the tutorials, make sure you have:
 
-- ✅ [COBRAxy installed](../installation.md)
+- ✅ [COBRAxy installed](installation)
 - ✅ Basic understanding of metabolic modeling (helpful but not required)
-- ✅ Familiarity with command line or Python (depending on tutorial)
+- ✅ Familiarity with command line basics
 
 ## Tutorial Data
 
@@ -43,23 +38,12 @@
 - Pre-configured Galaxy workflows
 - Expected output files for verification
 
-## Learning Path
-
-We recommend following tutorials in this order:
-
-1. **[Data Formats](data-formats.md)** - Understand input requirements
-2. **[Basic Workflow](workflow.md)** - Learn the analysis pipeline
-3. Choose your interface:
-   - **[Galaxy Setup](galaxy-setup.md)** for web-based analysis
-   - **[Python API](python-api.md)** for programmatic analysis
-
 ## Getting Help
 
 If you encounter issues during tutorials:
 
 1. Check the specific tutorial's troubleshooting section
-2. Refer to the main [Troubleshooting Guide](../troubleshooting.md)
-3. Ask questions in [GitHub Discussions](https://github.com/CompBtBs/COBRAxy/discussions)
+2. Refer to the main [Troubleshooting Guide](/troubleshooting.md)
 
 ## Contributing