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1 Complete reference for all COBRAxy tools with parameters, examples, and usage guidelines.
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2
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3 ## Available Tools
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4
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5 | Tool | Purpose | Input | Output |
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6 |------|---------|--------|--------|
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542
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7 | [Import Metabolic Model](tools/import-metabolic-model) | Import and extract model components | SBML/JSON/MAT/YAML model | Tabular model data |
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8 | [Export Metabolic Model](tools/export-metabolic-model) | Export tabular data to model format | Tabular model data | SBML/JSON/MAT/YAML model |
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9 | [RAS Generator](tools/ras-generator) | Compute reaction activity scores | Gene expression + GPR rules | RAS values |
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10 | [RPS Generator](tools/rps-generator) | Compute reaction propensity scores | Metabolite abundance | RPS values |
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11 | [MAREA](tools/marea) | Statistical pathway enrichment | RAS/RPS data | Enriched maps + statistics |
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12 | [RAS to Bounds](tools/ras-to-bounds) | Apply RAS constraints to model | RAS + SBML model | Constrained bounds |
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13 | [Flux Simulation](tools/flux-simulation) | Sample metabolic fluxes | Constrained model | Flux distributions |
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14 | [Flux to Map](tools/flux-to-map) | Visualize flux data on maps | Flux samples + statistical comparison | Color-coded pathway maps |
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15 | [MAREA Cluster](tools/marea-cluster) | Cluster analysis | Expression/RAS/RPS/flux data | Sample clusters + validation plots |
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16
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17
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18 ## Analysis Workflows
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19
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20 **Enrichment Analysis**: Gene Expression → RAS Generator → MAREA → Pathway Maps
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21
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22 **Flux Simulation**: Gene Expression → RAS Generator → RAS to Bounds → Flux Simulation → Flux to Map
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23
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24 ## Usage Patterns
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25
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538
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26 ### Galaxy Integration
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27 All tools include Galaxy XML wrappers for web-based usage through the Galaxy interface.
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28
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492
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29 ### Command Line Usage
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30 ```bash
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31 # Basic pattern for all tools
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32 tool_name -td $(pwd) [tool-specific options]
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33
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34 # Example: Generate RAS scores
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35 ras_generator -td $(pwd) -in expression.tsv -ra ras_output.tsv -rs ENGRO2
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36 ```
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37
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38 ## Parameter Reference
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39
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40 ### File Format Requirements
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41
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42 **Gene Expression Files**
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43 - Format: TSV (tab-separated values)
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44 - Structure: Genes (rows) × Samples (columns)
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45 - First column: Gene IDs (HGNC, Ensembl, etc.)
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46 - Subsequent columns: Expression values
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47
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48 **Metabolite Files**
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49 - Format: TSV (tab-separated values)
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50 - Structure: Metabolites (rows) × Samples (columns)
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51 - First column: Metabolite names
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52 - Subsequent columns: Abundance values
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53
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54 **Model Files**
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55 - Format: SBML (.xml) or tabular rules (.tsv)
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56 - Content: Metabolic network with GPR rules
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57
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58 ### Built-in Models
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59
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60 | Model | Organism | Reactions | Genes | Best For |
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61 |-------|----------|-----------|-------|----------|
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62 | **ENGRO2** | Human | ~500 | ~500 | Focused analysis, faster computation |
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63 | **RECON3D** | Human | ~10,000 | ~2,000 | Comprehensive metabolism |
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64
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65 ## Tool Selection Guide
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66
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67 ### Choose Your Analysis Path
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68
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69 **For Pathway Enrichment**
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70 1. [RAS Generator](tools/ras-generator) → Generate activity scores
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71 2. [RPS Generator](tools/rps-generator) → Generate propensity scores (optional)
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72 3. [MAREA](tools/marea) → Statistical analysis and visualization
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73
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74 **For Flux Analysis**
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75 1. [RAS Generator](tools/ras-generator) → Generate activity scores
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76 2. [RAS to Bounds](tools/ras-to-bounds) → Apply constraints
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77 3. [Flux Simulation](tools/flux-simulation) → Sample fluxes
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78 4. [Flux to Map](tools/flux-to-map) → Create visualizations
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79
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80 **For Model Exploration**
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81 1. [Import Metabolic Model](tools/import-metabolic-model) → Extract model info
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82 2. Analyze model structure and gene coverage
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83
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84 **For Model Creation**
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85 1. Create/edit tabular model data
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86 2. [Export Metabolic Model](tools/export-metabolic-model) → Create SBML/JSON/MAT/YAML model
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87
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88 **For Sample Classification**
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89 1. Generate RAS/RPS scores
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90 2. [MAREA Cluster](tools/marea-cluster) → Cluster samples
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91
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92
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93
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94 ## Troubleshooting
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95
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96 ### Common Issues Across Tools
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97
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98 **Model Issues**
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99 - Verify model file format and gene ID consistency
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100 - Check gene ID mapping between data and model
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101 - Use built-in models to avoid compatibility issues
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102
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103 ### Getting Help
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104
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105 For tool-specific issues:
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106 1. Check individual tool documentation
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107 2. Review parameter requirements and formats
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108 3. Test with smaller datasets first
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109 4. Consult [troubleshooting guide](/troubleshooting.md)
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110
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111 ## Contributing
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112
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113 Help improve tool documentation:
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114 - Report unclear instructions
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115 - Suggest additional examples
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116 - Contribute usage patterns
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117 - Fix documentation errors
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118
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119 Each tool page includes detailed parameter descriptions, examples, and troubleshooting tips. Select a tool from the sidebar to get started! |
