Mercurial > repos > bimib > cobraxy

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
parents 4ed95023af20
children 73f2f7e2be17
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
1 # Tutorials
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
2
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
3 Learn COBRAxy through hands-on tutorials for web-based analysis.
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
4
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
5 ## Available Tutorials
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
6
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
7 | Tutorial | Duration | Description |
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
8 |----------|----------|-------------|
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
9 | [Galaxy Setup](tutorials/galaxy-setup) | 30 min | Set up Galaxy for web-based analysis |
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
10
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
11 ## Web Interface Tutorial
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
12
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
13 ### [Galaxy Setup Tutorial](tutorials/galaxy-setup)
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
14
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
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.
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
16
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
17 ## Prerequisites
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
18
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
19 Before starting the tutorials, make sure you have:
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
20
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
21 - ✅ [COBRAxy installed](installation)
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
22 - ✅ Basic understanding of metabolic modeling (helpful but not required)
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
23 - ✅ Familiarity with command line basics
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
24
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
25 ## Tutorial Data
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
26
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
27 Download example datasets used in tutorials:
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
28
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
29 ```bash
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
30 # Download tutorial data
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
31 wget https://github.com/CompBtBs/COBRAxy/releases/download/v1.0/tutorial_data.zip
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
32 unzip tutorial_data.zip
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
33 ```
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
34
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
35 The tutorial data includes:
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
36 - Sample gene expression datasets
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
37 - Metabolite abundance data
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
38 - Pre-configured Galaxy workflows
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
39 - Expected output files for verification
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
40
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
41 ## Getting Help
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
42
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
43 If you encounter issues during tutorials:
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
44
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
45 1. Check the specific tutorial's troubleshooting section
542
fcdbc81feb45 Uploaded
francesco_lapi
parents: 492
diff changeset
46 2. Refer to the main [Troubleshooting Guide](/troubleshooting.md)
492
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
47
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
48 ## Contributing
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
49
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
50 Found an error or want to improve a tutorial?
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
51
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
52 - [Edit on GitHub](https://github.com/CompBtBs/COBRAxy/tree/main/docs/tutorials)
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
53 - [Report issues](https://github.com/CompBtBs/COBRAxy/issues)
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
54 - Suggest new tutorial topics
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
55
4ed95023af20 Uploaded
francesco_lapi
parents:
diff changeset
56 Ready to start? Pick your first tutorial above! 🚀