# HG changeset patch # User luca_milaz # Date 1724962228 0 # Node ID b375d148a2fb699d6a8320c28274b19c5055fa1c # Parent 8cb467d423db5f9e683a4bdd049f518814cb9f5a Uploaded diff -r 8cb467d423db -r b375d148a2fb marea_2/flux_simulation.xml --- 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`. ]]>