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comparison COBRAxy/docs/tutorials/README.md @ 492:4ed95023af20 draft

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date Tue, 30 Sep 2025 14:02:17 +0000
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1 # Tutorials
2
3 Learn COBRAxy through hands-on tutorials covering the two main usage scenarios.
4
5 ## Available Tutorials
6
7 | Tutorial | Duration | Description |
8 |----------|----------|-------------|
9 | [Galaxy Setup](galaxy-setup.md) | 30 min | Set up Galaxy for web-based analysis |
10 | [Python API Usage](python-api.md) | 45 min | Programmatic analysis with Python |
11
12 ## Choose Your Path
13
14 ### Web Interface → [Galaxy Setup Tutorial](galaxy-setup.md)
15
16 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.
17
18 ### Python Programming → [Python API Tutorial](python-api.md)
19
20 Learn to call COBRAxy tools programmatically in your analysis pipelines. Ideal for integrating COBRAxy into custom workflows and automation.
21
22 ## Prerequisites
23
24 Before starting the tutorials, make sure you have:
25
26 - ✅ [COBRAxy installed](../installation.md)
27 - ✅ Basic understanding of metabolic modeling (helpful but not required)
28 - ✅ Familiarity with command line or Python (depending on tutorial)
29
30 ## Tutorial Data
31
32 Download example datasets used in tutorials:
33
34 ```bash
35 # Download tutorial data
36 wget https://github.com/CompBtBs/COBRAxy/releases/download/v1.0/tutorial_data.zip
37 unzip tutorial_data.zip
38 ```
39
40 The tutorial data includes:
41 - Sample gene expression datasets
42 - Metabolite abundance data
43 - Pre-configured Galaxy workflows
44 - Expected output files for verification
45
46 ## Learning Path
47
48 We recommend following tutorials in this order:
49
50 1. **[Data Formats](data-formats.md)** - Understand input requirements
51 2. **[Basic Workflow](workflow.md)** - Learn the analysis pipeline
52 3. Choose your interface:
53 - **[Galaxy Setup](galaxy-setup.md)** for web-based analysis
54 - **[Python API](python-api.md)** for programmatic analysis
55
56 ## Getting Help
57
58 If you encounter issues during tutorials:
59
60 1. Check the specific tutorial's troubleshooting section
61 2. Refer to the main [Troubleshooting Guide](../troubleshooting.md)
62 3. Ask questions in [GitHub Discussions](https://github.com/CompBtBs/COBRAxy/discussions)
63
64 ## Contributing
65
66 Found an error or want to improve a tutorial?
67
68 - [Edit on GitHub](https://github.com/CompBtBs/COBRAxy/tree/main/docs/tutorials)
69 - [Report issues](https://github.com/CompBtBs/COBRAxy/issues)
70 - Suggest new tutorial topics
71
72 Ready to start? Pick your first tutorial above! 🚀