# HG changeset patch # User luca_milaz # Date 1724963099 0 # Node ID 9f5db0e377a67a3a56b9758f423773e372429ab6 # Parent 979337507901bcf7cd978342dbe89c9760cf2920 Uploaded diff -r 979337507901 -r 9f5db0e377a6 marea_2/ras_to_bounds.xml --- a/marea_2/ras_to_bounds.xml Thu Aug 29 20:15:41 2024 +0000 +++ b/marea_2/ras_to_bounds.xml Thu Aug 29 20:24:59 2024 +0000 @@ -1,4 +1,4 @@ - + marea_macros.xml @@ -74,21 +74,18 @@ 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 reaction bounds for a given metabolic model (in JSON or XML format), both with and without the integration of Reaction Activity Scores (RAS) into the metabolic model. +Additionally, it allows the use of custom or pre-defined growth media to constrain exchange reactions (see format example here below). +If a RAS matrix, generated by the **Expression2RAS** tool, is used, then a separate 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. +**Accepted Files:** + - **Model:** A JSON or XML file containing the reactions and rules defined in the model. + - **RAS Matrix:** A tab-separated file with RAS data as generated by the **Expression2RAS** tool. + - **Medium:** A tab-separated file specifying the lower and upper bounds of medium reactions. Example medium file ------------- -Custom medium: - +------------+----------------+----------------+ | Reaction ID| lower_bound | upper_bound | +============+================+================+