Mercurial > repos > bimib > cobraxy
comparison COBRAxy/ras_to_bounds.xml @ 15:88a649e1b5f4 draft
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| author | luca_milaz |
|---|---|
| date | Wed, 18 Sep 2024 12:43:05 +0000 |
| parents | 41f35c2f0c7b |
| children | 7e1d2b5df5cb |
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| 14:c10d8b38de84 | 15:88a649e1b5f4 |
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| 73 <![CDATA[ | 73 <![CDATA[ |
| 74 | 74 |
| 75 What it does | 75 What it does |
| 76 ------------- | 76 ------------- |
| 77 | 77 |
| 78 This tool generates the reactions bounds for a given metabolic model (JSON or XML format) with and without the injection of the Reaction Activity Scores (RAS) within the metabolic model. | 78 This tool generates the reactions bounds for a given metabolic model (JSON or XML format) both with and without the use of the Reaction Activity Scores (RAS) matrix generated by RAS generator. |
| 79 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For custom medium, It is suggested to use the template file returned by the Custom Data Generator tool. | 79 Moreover, it enables to use custom/pre-defined growth mediums to constrain exchange reactions. For a custom medium, It is suggested to use the template file returned by the Custom Data Generator tool. |
| 80 If the RAS matrix, generated by the RAS generator tool, is used, then a file of bounds is generated for each cell. Otherwise, a single bounds file is returned. | 80 If the RAS matrix, generated by the RAS generator tool, is used, then a bounds file is generated for each cell. Otherwise, a single bounds file is returned. |
| 81 | 81 |
| 82 Accepted files: | 82 Accepted files: |
| 83 - A model: JSON or XML file reporting reactions and rules contained in the model. | 83 - A model: JSON or XML file reporting reactions and rules contained in the model. |
| 84 - RAS matrix: tab-separated RAS file as returned by RAS generator. | 84 - RAS matrix: tab-separated RAS file as returned by RAS generator. |
| 85 - Medium: tab-separated file containing lower and upper-bounds of medium reactions. | 85 - Medium: tab-separated file containing lower and upper-bounds of medium reactions. |
| 86 | 86 |
| 87 Example medium file | 87 Example of custum growth medium file: |
| 88 ------------- | |
| 89 | |
| 90 Custom medium: | |
| 91 | 88 |
| 92 +------------+----------------+----------------+ | 89 +------------+----------------+----------------+ |
| 93 | Reaction ID| lower_bound | upper_bound | | 90 | Reaction ID| lower_bound | upper_bound | |
| 94 +============+================+================+ | 91 +============+================+================+ |
| 95 | r1 | 0.123167 | 0.371355 | | 92 | r1 | 0.123167 | 0.371355 | |