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comparison COBRAxy/docs/tutorials/README.md @ 542:fcdbc81feb45 draft

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date Sun, 26 Oct 2025 19:27:41 +0000
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1 # Tutorials 1 # Tutorials
2 2
3 Learn COBRAxy through hands-on tutorials covering the two main usage scenarios. 3 Learn COBRAxy through hands-on tutorials for web-based analysis.
4 4
5 ## Available Tutorials 5 ## Available Tutorials
6 6
7 | Tutorial | Duration | Description | 7 | Tutorial | Duration | Description |
8 |----------|----------|-------------| 8 |----------|----------|-------------|
9 | [Galaxy Setup](galaxy-setup.md) | 30 min | Set up Galaxy for web-based analysis | 9 | [Galaxy Setup](tutorials/galaxy-setup) | 30 min | Set up Galaxy for web-based analysis |
10 | [Python API Usage](python-api.md) | 45 min | Programmatic analysis with Python |
11 10
12 ## Choose Your Path 11 ## Web Interface Tutorial
13 12
14 ### Web Interface → [Galaxy Setup Tutorial](galaxy-setup.md) 13 ### [Galaxy Setup Tutorial](tutorials/galaxy-setup)
15 14
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. 15 Set up a local Galaxy instance with COBRAxy tools for point-and-click analysis. Perfect for users who prefer graphical interfaces and reproducible workflows.
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 16
22 ## Prerequisites 17 ## Prerequisites
23 18
24 Before starting the tutorials, make sure you have: 19 Before starting the tutorials, make sure you have:
25 20
26 - ✅ [COBRAxy installed](../installation.md) 21 - ✅ [COBRAxy installed](installation)
27 - ✅ Basic understanding of metabolic modeling (helpful but not required) 22 - ✅ Basic understanding of metabolic modeling (helpful but not required)
28 - ✅ Familiarity with command line or Python (depending on tutorial) 23 - ✅ Familiarity with command line basics
29 24
30 ## Tutorial Data 25 ## Tutorial Data
31 26
32 Download example datasets used in tutorials: 27 Download example datasets used in tutorials:
33 28
41 - Sample gene expression datasets 36 - Sample gene expression datasets
42 - Metabolite abundance data 37 - Metabolite abundance data
43 - Pre-configured Galaxy workflows 38 - Pre-configured Galaxy workflows
44 - Expected output files for verification 39 - Expected output files for verification
45 40
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 41 ## Getting Help
57 42
58 If you encounter issues during tutorials: 43 If you encounter issues during tutorials:
59 44
60 1. Check the specific tutorial's troubleshooting section 45 1. Check the specific tutorial's troubleshooting section
61 2. Refer to the main [Troubleshooting Guide](../troubleshooting.md) 46 2. Refer to the main [Troubleshooting Guide](/troubleshooting.md)
62 3. Ask questions in [GitHub Discussions](https://github.com/CompBtBs/COBRAxy/discussions)
63 47
64 ## Contributing 48 ## Contributing
65 49
66 Found an error or want to improve a tutorial? 50 Found an error or want to improve a tutorial?
67 51