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1 # RAS to Bounds
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2
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3 Apply Reaction Activity Scores (RAS) as constraints to metabolic model bounds.
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4
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5 ## Overview
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6
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7 RAS to Bounds integrates RAS values into metabolic model flux bounds, creating sample-specific constrained models.
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8
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9 ## Galaxy Interface
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10
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11 In Galaxy: **COBRAxy → RAS to Bounds**
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12
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13 1. Select model and upload RAS scores file
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14 2. Configure medium and constraint options
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15 3. Click **Execute**
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16
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17 ## Usage
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18
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19 ```bash
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20 ras_to_bounds -ms ENGRO2 \
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21 -ir ras_scores.tsv \
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22 -rs true \
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23 -mes allOpen \
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24 -idop constrained_bounds/
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25 ```
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26
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27 ## Parameters
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28
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29 | Parameter | Flag | Description | Default |
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30 |-----------|------|-------------|---------|
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31 | Model Selector | `-ms` | ENGRO2, Recon, or Custom | ENGRO2 |
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32 | RAS Input | `-ir` | RAS scores TSV file | - |
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33 | RAS Selector | `-rs` | Enable RAS constraints | false |
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34 | Medium Selector | `-mes` | Medium configuration | allOpen |
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35 | Save Models | `--save_models` | Save complete models with bounds | false |
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36 | Output Path | `-idop` | Output directory | ras_to_bounds/ |
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37 | Custom Model | `-mo` | Path to custom SBML model | - |
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38 | Custom Medium | `-meo` | Custom medium file | - |
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39
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40 ## Input Format
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41
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42 RAS scores file (TSV):
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43
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44 ```
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45 Reaction Sample1 Sample2 Sample3
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46 R00001 1.25 0.85 1.42
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47 R00002 0.65 1.35 0.72
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48 ```
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49
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50 **File Format Notes:**
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51 - Use **tab-separated** values (TSV)
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52 - First row must contain column headers (Reaction, Sample names)
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53 - Reaction IDs must match model reaction IDs
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54 - Numeric values for RAS scores
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55
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56 ## Output Format
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57
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58 Bounds files for each sample:
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59
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60 ```
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61 reaction lower_bound upper_bound
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62 R00001 -125.0 125.0
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63 R00002 -65.0 65.0
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64 ```
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65
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66 ## Output Collections
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67
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68 The tool generates three types of output:
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69
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70 1. **Bounds files** (`ras_to_bounds/`): Individual bound files per sample (TSV format)
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71 2. **Cell classes** (`cell_class`): Sample-to-class mapping file
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72 3. **Complete models** (optional, `saved_models/`): Full tabular models with bounds applied
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73
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74 To save complete models with integrated bounds, set `--save_models true`. This creates ready-to-use model files that can be directly used with Flux Simulation or other downstream tools.
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75
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76 ## Examples
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77
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78 ### Basic Usage
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79
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80 ```bash
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81 ras_to_bounds -ms ENGRO2 \
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82 -ir ras_scores.tsv \
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83 -rs true \
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84 -idop output/
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85 ```
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86
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87 ### With Custom Model
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88
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89 ```bash
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90 ras_to_bounds -ms Custom \
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91 -mo custom_model.xml \
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92 -ir ras_scores.tsv \
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93 -rs true \
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94 -idop output/
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95 ```
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96
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97 ## Troubleshooting
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98
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99 | Error | Solution |
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100 |-------|----------|
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101 | "Model not found" | Check model file path |
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102 | "RAS file invalid" | Verify TSV format |
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103 | "Infeasible solution" | Relax RAS scaling or constraints |
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104
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105 ## See Also
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106
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107 - [RAS Generator](tools/ras-generator)
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108 - [Flux Simulation](tools/flux-simulation)
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109 - [Built-in Models](reference/built-in-models)
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