Mercurial > repos > bimib > marea_2
changeset 352:9f5db0e377a6 draft
Uploaded
| author | luca_milaz |
|---|---|
| date | Thu, 29 Aug 2024 20:24:59 +0000 |
| parents | 979337507901 |
| children | 978a883ab2f4 |
| files | marea_2/ras_to_bounds.xml |
| diffstat | 1 files changed, 8 insertions(+), 11 deletions(-) [+] |
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--- 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 @@ -<tool id="RAStoBounds" name="RAStoBounds" version="2.0.0"> +<tool id="RAStoBounds" name="RAS2Bounds" version="2.0.0"> <macros> <import>marea_macros.xml</import> @@ -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 | +============+================+================+