Mercurial > repos > bimib > cobraxy

changeset 15:88a649e1b5f4 draft

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Uploaded
author luca_milaz
date Wed, 18 Sep 2024 12:43:05 +0000
parents c10d8b38de84
children 18b10d8c69bd
files COBRAxy/ras_to_bounds.xml
diffstat 1 files changed, 4 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- 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 |