Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_simulation.xml @ 8:5a69dd906256 draft

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author luca_milaz
date Wed, 18 Sep 2024 12:10:55 +0000
parents 515cd9e4f518
children 7c01dab3e961
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7:515cd9e4f518 8:5a69dd906256
98 <![CDATA[ 98 <![CDATA[
99 What it does 99 What it does
100 ------------- 100 -------------
101 101
102 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. 102 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.
103
104 It can return sampled fluxes by appliying summary statistics: 103 It can return sampled fluxes by appliying summary statistics:
105 - mean 104 - mean
106 - median 105 - median
107 - quantiles (0.25, 0.50, 0.75). 106 - quantiles (0.25, 0.50, 0.75).
108
109 Moreover, flux analysis can be perfomed over the metabolic model: 107 Moreover, flux analysis can be perfomed over the metabolic model:
110 - parsimoniuos-FBA (optimized by Biomass) 108 - parsimoniuos-FBA (optimized by Biomass)
111 - FVA 109 - FVA
112 - Biomass sensitivity analysis (single reaction knock-out). It is the ratio between the optimal of the Biomass reaction computed by FBA after knocking-out a reaction and the same over the complete model. 110 - Biomass sensitivity analysis (single reaction knock-out). It is the ratio between the optimal of the Biomass reaction computed by FBA after knocking-out a reaction and the same over the complete model.
113 111