Mercurial > repos > bimib > cobraxy

changeset 7:515cd9e4f518 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author luca_milaz
date Wed, 18 Sep 2024 12:09:06 +0000
parents deb6d3439342
children 5a69dd906256
files COBRAxy/flux_simulation.xml
diffstat 1 files changed, 13 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/COBRAxy/flux_simulation.xml	Wed Sep 18 12:00:49 2024 +0000
+++ b/COBRAxy/flux_simulation.xml	Wed Sep 18 12:09:06 2024 +0000
@@ -99,26 +99,28 @@
 What it does
 -------------
 
-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.
+This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) or 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). 
+   - 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.
+   - parsimoniuos-FBA (optimized by Biomass)
+   - FVA
+   - Biomass sensitivity analysis (single reaction knock-out). It is the ratio between the optimal of the Biomass reaction computed by FBA 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.
+   - 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.
-    - a log file (.txt).
+   - 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.