Mercurial > repos > bimib > marea_2_0

changeset 179:eebdc9119bd8 draft

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Uploaded
author luca_milaz
date Thu, 04 Jul 2024 12:22:41 +0000
parents 42f77c379f45
children e9d885907c33
files marea_2_0/flux_sampling.xml
diffstat 1 files changed, 13 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/marea_2_0/flux_sampling.xml	Wed Jul 03 19:16:34 2024 +0000
+++ b/marea_2_0/flux_sampling.xml	Thu Jul 04 12:22:41 2024 +0000
@@ -43,16 +43,18 @@
                 	<option value="OPTGP">OPTGP</option>
         	</param>
         	<when value="OPTGP">
-        		<param name="thinning" argument="--thinning" type="integer" label="Thinning:"  value="100"/>
+        		<param name="thinning" argument="--thinning" type="integer" label="Thinning:"  value="100" help="Number of iterations to wait before taking a sample."/>
         	</when>
 
 		</conditional>
 
-        <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="1"/>
 
         <param name="n_samples" argument="--n_samples" type="integer" label="Samples:" value="1000"/>
 
-        <param name="seed" argument="--seed" type="integer" label="Seed:" value="0"/>
+        <param name="n_batches" argument="--n_batches" type="integer" label="Batches:" value="1" help="The output file will contain n_batches*n_samples samples. 
+        This is useful for computational perfomances."/>
+
+        <param name="seed" argument="--seed" type="integer" label="Seed:" value="0" helph="Random seed."/>
         
         <param name="output_format" argument="--output_format" type="select" label="Output files format:">
             <option value="p" selected="true">pickle extension (binary, non-editable, pre-parsed)</option>
@@ -74,19 +76,22 @@
 What it does
 -------------
 
-This tool generates feasible 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) and OPTGP (mproved Artificial Centering Hit-and-Run sampler) sampling algorithms.
 
 Accepted files:
-    - A model: JSON or XML file reporting reactions and rules contained in the model.   
-
+    - 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. 
 
 Output:
 -------------
 
 The tool generates:
-    - Samples: reporting the sampled fluxes for each reaction in the custom model given. Format: csv or pickle.
+    - Samples: reporting the sampled fluxes for each reaction. Format: csv or pickle.
     - 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.
+
+
+]]>
     </help>
     <expand macro="citations" />
 </tool>
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