changeset 349:b375d148a2fb draft

Uploaded

--- a/marea_2/flux_simulation.xml	Thu Aug 29 19:49:50 2024 +0000
+++ b/marea_2/flux_simulation.xml	Thu Aug 29 20:10:28 2024 +0000
@@ -99,30 +99,27 @@
 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.
-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.
+This tool generates flux samples from a model in JSON or XML format using the CBS (Corner-based Sampling) and OPTGP (Improved Artificial Centering Hit-and-Run Sampler) algorithms. It can return sampled fluxes by applying summary statistics such as:
+   - Mean
+   - Median
+   - Quantiles (0.25, 0.50, 0.75)
+   
+Additionally, flux analysis can be performed on the metabolic model, including:
+   - Parsimonious-FBA (optimized by Biomass)
+   - FVA (Flux Variability Analysis)
+   - Biomass sensitivity analysis (single reaction knockout), which calculates the ratio between the optimal FBA coefficients of the Biomass reaction after knocking out a reaction and the same coefficients in 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:
--------------
+**Accepted Files:**
+   - A Model: JSON or XML file containing the reactions and rules defined in the model. This can be a single model, multiple models, or a collection of models.
+   - Cell-Specific Bounds: Generated by the **RAS2Bounds** tool.
 
-The tool generates:
-    - Samples: reporting the sampled fluxes for each reaction. Format: csv.
-    - a log file (.txt).
+**Output:**
+--------------
+The tool generates the following:
+   - **Samples:** A CSV file reporting the sampled fluxes for each reaction.
+   - **Log File:** A text file (.txt) containing logs of the operation.
 
-**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.
-
-
+**Tip:** The 'Batches' parameter is useful for managing memory usage by processing samples in smaller batches. For example, if you want to sample 10,000 points, it is recommended to set `n_samples = 1,000` and `n_batches = 10`.
 ]]>
     </help>
     <expand macro="citations" />