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comparison COBRAxy/flux_simulation.xml @ 9:7c01dab3e961 draft

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author luca_milaz
date Wed, 18 Sep 2024 12:16:40 +0000
parents 5a69dd906256
children 3788bd8c278b
comparison
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8:5a69dd906256 9:7c01dab3e961
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
103 It can return sampled fluxes by appliying summary statistics: 104 It can return sampled fluxes by appliying summary statistics:
104 - mean 105 - mean
105 - median 106 - median
106 - quantiles (0.25, 0.50, 0.75). 107 - quantiles (0.25, 0.50, 0.75).
107 Moreover, flux analysis can be perfomed over the metabolic model: 108
109 Flux analysis can be perfomed over the metabolic model:
108 - parsimoniuos-FBA (optimized by Biomass) 110 - parsimoniuos-FBA (optimized by Biomass)
109 - FVA 111 - FVA
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. 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.
111 113
112 Accepted files: 114 Accepted files:
113 - 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. 115 - A model: JSON or XML file reporting reactions and rules contained in the model. It can be ENGRO2 or a custom model.
114 - Cell-specific bounds: generated by RAS to Bounds tool. 116 - Context-specific bounds: generated by RAS to Bounds tool. This can be a collection of bounds too (one bounds file per context).
115 117
116 Output: 118 Output:
117 ------------- 119 -------------
118 120
119 The tool generates: 121 The tool generates:
120 - Samples: reporting the sampled fluxes for each reaction. Format: csv. 122 - Samples: reporting the sampled fluxes for each reaction (reaction names on the rows and sample names on the columns). Format: csv.
121 - a log file (.txt). 123 - a log file (.txt).
122 124
123 **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. 125 **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.
124 126
125 127