Mercurial > repos > bimib > cobraxy

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

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author francesco_lapi
date Sun, 26 Oct 2025 19:27:41 +0000
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1 # Tutorials
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3 Learn COBRAxy through hands-on tutorials for web-based analysis.
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5 ## Available Tutorials
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7 | Tutorial | Duration | Description |
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8 |----------|----------|-------------|
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9 | [Galaxy Setup](tutorials/galaxy-setup) | 30 min | Set up Galaxy for web-based analysis |
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11 ## Web Interface Tutorial
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13 ### [Galaxy Setup Tutorial](tutorials/galaxy-setup)
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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.
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17 ## Prerequisites
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19 Before starting the tutorials, make sure you have:
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21 - ✅ [COBRAxy installed](installation)
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22 - ✅ Basic understanding of metabolic modeling (helpful but not required)
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23 - ✅ Familiarity with command line basics
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25 ## Tutorial Data
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27 Download example datasets used in tutorials:
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29 ```bash
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30 # Download tutorial data
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31 wget https://github.com/CompBtBs/COBRAxy/releases/download/v1.0/tutorial_data.zip
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32 unzip tutorial_data.zip
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33 ```
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35 The tutorial data includes:
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36 - Sample gene expression datasets
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37 - Metabolite abundance data
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38 - Pre-configured Galaxy workflows
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39 - Expected output files for verification
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41 ## Getting Help
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43 If you encounter issues during tutorials:
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45 1. Check the specific tutorial's troubleshooting section
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46 2. Refer to the main [Troubleshooting Guide](/troubleshooting.md)
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48 ## Contributing
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50 Found an error or want to improve a tutorial?
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52 - [Edit on GitHub](https://github.com/CompBtBs/COBRAxy/tree/main/docs/tutorials)
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53 - [Report issues](https://github.com/CompBtBs/COBRAxy/issues)
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54 - Suggest new tutorial topics
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56 Ready to start? Pick your first tutorial above! 🚀