Mercurial > repos > bimib > cobraxy

changeset 485:12894ade26ef draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author luca_milaz
date Tue, 23 Sep 2025 07:19:49 +0000
parents 1c6fcf97cabe
children 14232f4c4440
files COBRAxy/flux_simulation_beta.xml
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/COBRAxy/flux_simulation_beta.xml	Tue Sep 23 07:19:29 2025 +0000
+++ b/COBRAxy/flux_simulation_beta.xml	Tue Sep 23 07:19:49 2025 +0000
@@ -169,7 +169,7 @@
    - median
    - quantiles (0.25, 0.50, 0.75)
 
-Flux analysis can be performed over the metabolic model:
+Flux analysis can be performed over the metabolic model by using the objective function already set in the model. The following analyses are supported:
    - parsimonious-FBA (optimized by Biomass)
    - FVA (with configurable optimality percentage)
    - Biomass sensitivity analysis (single reaction knock-out)
@@ -182,7 +182,9 @@
    - a log file (.txt).
 
 **TIP**: The Batches parameter helps maintain memory efficiency. For 10,000 samples, use n_samples=1,000 and n_batches=10.
+
 **TIP**: The Thinning parameter for OPTGP helps converge to stationary distribution.
+
 **TIP**: FVA optimality percentage allows you to explore suboptimal flux ranges. 100% restricts to optimal solutions, while lower values (e.g., 90%) allow broader flux ranges.
 ]]>
     </help>