Mercurial > repos > bimib > cobraxy
changeset 128:a78d83753cce draft
Uploaded
| author | luca_milaz |
|---|---|
| date | Mon, 14 Oct 2024 08:50:52 +0000 |
| parents | d40d5d5435df |
| children | dfb6a1dc6dbc |
| files | COBRAxy/ras_to_bounds.xml |
| diffstat | 1 files changed, 1 insertions(+), 0 deletions(-) [+] |
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--- a/COBRAxy/ras_to_bounds.xml Mon Oct 14 08:48:54 2024 +0000 +++ b/COBRAxy/ras_to_bounds.xml Mon Oct 14 08:50:52 2024 +0000 @@ -84,6 +84,7 @@ 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. +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. Accepted files: - A model: JSON or XML file reporting reactions and rules contained in the model.