Mercurial > repos > bimib > marea_2
changeset 339:a00dba74f39b draft
Uploaded
| author | luca_milaz |
|---|---|
| date | Mon, 26 Aug 2024 08:10:57 +0000 |
| parents | 0605f8830a13 |
| children | 3f1cfd63fb81 |
| files | marea_2/flux_simulation.xml |
| diffstat | 1 files changed, 10 insertions(+), 1 deletions(-) [+] |
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--- a/marea_2/flux_simulation.xml Mon Aug 26 08:10:34 2024 +0000 +++ b/marea_2/flux_simulation.xml Mon Aug 26 08:10:57 2024 +0000 @@ -100,15 +100,24 @@ ------------- 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. 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: ------------- The tool generates: - - Samples: reporting the sampled fluxes for each reaction. Format: csv or pickle. + - 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.