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comparison COBRAxy/ras_to_bounds.xml @ 128:a78d83753cce draft

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Uploaded
author luca_milaz
date Mon, 14 Oct 2024 08:50:52 +0000
parents 6cb85065b38b
children b2fe67bba4f5
comparison
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127:d40d5d5435df 128:a78d83753cce
82 ------------- 82 -------------
83 83
84 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. 84 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.
85 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. 85 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.
86 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. 86 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.
87 By default, all reactions in model.medium that are not present in the medium file have lower bound set to 0.0 and not set to the default model value.
87 88
88 Accepted files: 89 Accepted files:
89 - A model: JSON or XML file reporting reactions and rules contained in the model. 90 - A model: JSON or XML file reporting reactions and rules contained in the model.
90 - RAS matrix: tab-separated RAS file as returned by RAS generator. Multiple RAS files can be uploaded too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells. 91 - RAS matrix: tab-separated RAS file as returned by RAS generator. Multiple RAS files can be uploaded too (e.g. one RAS matrix for normal cells and one for cancer cells). Note that if multiple RAs matrices are uploaded, the bounds are normalzed across all cells.
91 - Medium: tab-separated file containing lower and upper-bounds of medium reactions. 92 - Medium: tab-separated file containing lower and upper-bounds of medium reactions.