# HG changeset patch
# User luca_milaz
# Date 1726662654 0
# Node ID 3788bd8c278b561ae1f299abc3e42081415c9110
# Parent  7c01dab3e961cb5be19f47308023e9a46d54688a
Uploaded

diff -r 7c01dab3e961 -r 3788bd8c278b COBRAxy/flux_simulation.xml
--- a/COBRAxy/flux_simulation.xml	Wed Sep 18 12:16:40 2024 +0000
+++ b/COBRAxy/flux_simulation.xml	Wed Sep 18 12:30:54 2024 +0000
@@ -99,7 +99,7 @@
 What it does
 -------------
 
-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.
+This tool generates flux samples starting from a model in JSON or XML format by using CBS (Corner-based sampling) or OPTGP (Improved Artificial Centering Hit-and-Run sampler) sampling algorithms.
 
 It can return sampled fluxes by appliying summary statistics: 
    - mean
@@ -123,9 +123,45 @@
    - 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.
-
+**TIP**: The Thinning parameter of the OPTGP algorithm is useful to converge to a stationary distribution (see cited articles by Galuzzi, Milazzo and Damiani).
 
 ]]>
     </help>
-    <expand macro="citations" />
+
+    <xml name="citations">
+        <citations> 
+            <citation type="bibtex">
+                @article{galuzzi2024adjusting,
+                title={Adjusting for false discoveries in constraint-based differential metabolic flux analysis},
+                author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
+                journal={Journal of Biomedical Informatics},
+                volume={150},
+                pages={104597},
+                year={2024},
+                publisher={Elsevier}
+                }
+            </citation>
+            <citation type="bibtex">
+                @inproceedings{galuzzi2022best,
+                title={Best practices in flux sampling of constrained-based models},
+                author={Galuzzi, Bruno G and Milazzo, Luca and Damiani, Chiara},
+                booktitle={International Conference on Machine Learning, Optimization, and Data Science},
+                pages={234--248},
+                year={2022},
+                organization={Springer}
+                }
+            </citation>
+            <citation type="bibtex">
+                @article{ebrahim2013cobrapy,
+                    title={COBRApy: constraints-based reconstruction and analysis for python},
+                    author={Ebrahim, Ali and Lerman, Joshua A and Palsson, Bernhard O and Hyduke, Daniel R},
+                    journal={BMC systems biology},
+                    volume={7},
+                    pages={1--6},
+                    year={2013},
+                    publisher={Springer}
+                    }
+            </citation>
+        </citations>
+   </xml>
 </tool>
\ No newline at end of file