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comparison COBRAxy/docs/tutorials/README.md @ 547:73f2f7e2be17 draft

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author francesco_lapi
date Tue, 28 Oct 2025 10:44:07 +0000
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2 2
3 Learn COBRAxy through hands-on tutorials for web-based analysis. 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 | Description |
8 |----------|----------|-------------| 8 |----------|-------------|
9 | [Galaxy Setup](tutorials/galaxy-setup) | 30 min | Set up Galaxy for web-based analysis | 9 | [Galaxy Setup](tutorials/galaxy-setup) | Set up Galaxy for web-based analysis |
10 10 | | |
11 ## Web Interface Tutorial 11 | | |
12
13 ### [Galaxy Setup Tutorial](tutorials/galaxy-setup)
14
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.
16
17 ## Prerequisites
18
19 Before starting the tutorials, make sure you have:
20
21 - ✅ [COBRAxy installed](installation)
22 - ✅ Basic understanding of metabolic modeling (helpful but not required)
23 - ✅ Familiarity with command line basics
24 12
25 ## Tutorial Data 13 ## Tutorial Data
26 14
27 Download example datasets used in tutorials: 15 Download example datasets used in tutorials:
28 16
29 ```bash 17 ```bash
30 # Download tutorial data 18 # Download tutorial data
31 wget https://github.com/CompBtBs/COBRAxy/releases/download/v1.0/tutorial_data.zip 19 wget https://github.com/CompBtBs/COBRAxy/blob/main/data_tutorial/data_tutorial.zip
32 unzip tutorial_data.zip 20 unzip tutorial_data.zip
33 ``` 21 ```
34 22
35 The tutorial data includes: 23 The tutorial data includes Sample gene expression datasets (Cancer.txt and Normal.txt)
36 - Sample gene expression datasets
37 - Metabolite abundance data
38 - Pre-configured Galaxy workflows
39 - Expected output files for verification
40 24
41 ## Getting Help 25 ## Getting Help
42 26
43 If you encounter issues during tutorials: 27 If you encounter issues during tutorials:
44 28
45 1. Check the specific tutorial's troubleshooting section 29 1. Check the specific tutorial's troubleshooting section
46 2. Refer to the main [Troubleshooting Guide](/troubleshooting.md) 30 2. Refer to the main [Troubleshooting Guide](troubleshooting)
47 31
48 ## Contributing 32 ## Contributing
49 33
50 Found an error or want to improve a tutorial? 34 Found an error or want to improve a tutorial?
51 35