# HG changeset patch # User luca_milaz # Date 1726663385 0 # Node ID 88a649e1b5f41966e4865a0c133e761bcad2972d # Parent c10d8b38de8473e5ce6218fead80f7ac3259f55e Uploaded diff -r c10d8b38de84 -r 88a649e1b5f4 COBRAxy/ras_to_bounds.xml --- a/COBRAxy/ras_to_bounds.xml Wed Sep 18 12:37:06 2024 +0000 +++ b/COBRAxy/ras_to_bounds.xml Wed Sep 18 12:43:05 2024 +0000 @@ -75,19 +75,16 @@ What it does ------------- -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. -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. -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. +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. +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. +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. Accepted files: - A model: JSON or XML file reporting reactions and rules contained in the model. - RAS matrix: tab-separated RAS file as returned by RAS generator. - Medium: tab-separated file containing lower and upper-bounds of medium reactions. -Example medium file -------------- - -Custom medium: +Example of custum growth medium file: +------------+----------------+----------------+ | Reaction ID| lower_bound | upper_bound |