Mercurial > repos > bimib > marea_2

changeset 339:a00dba74f39b draft

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Uploaded
author luca_milaz
date Mon, 26 Aug 2024 08:10:57 +0000
parents 0605f8830a13
children 3f1cfd63fb81
files marea_2/flux_simulation.xml
diffstat 1 files changed, 10 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/marea_2/flux_simulation.xml	Mon Aug 26 08:10:34 2024 +0000
+++ b/marea_2/flux_simulation.xml	Mon Aug 26 08:10:57 2024 +0000
@@ -100,15 +100,24 @@
 -------------
 
 This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms.
+It can return sampled fluxes by appliying summary statistics: 
+    - mean
+    - median
+    - quantiles (0.25, 0.50, 0.75). 
+Moreover, flux analysis can be perfomed over the metabolic model:
+    - parsimoniuos-FBA (optimized by Biomass)
+    - FVA
+    - Biomass sensitivity analysis (single reaction knock-out). It the ratio between the optimal FBA coefficients of the Biomass reaction after knocking-out a reaction and the same over the complete model.
 
 Accepted files:
     - A model: JSON or XML file reporting reactions and rules contained in the model. It can be a single model, multiple models or a collection of models. 
+    - Cell-specific bounds: generated by RAS to Bounds tool.
 
 Output:
 -------------
 
 The tool generates:
-    - Samples: reporting the sampled fluxes for each reaction. Format: csv or pickle.
+    - Samples: reporting the sampled fluxes for each reaction. Format: csv.
     - a log file (.txt).
 
 **TIP**: The Batches parameter is useful to mantain in memory just a batch of samples at time. For example, if you wish to sample 10.000 points, than it is suggested to select n_samples = 1.000 and n_batches=10.