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