Mercurial > repos > tduigou > doe_synbio_sampler

comparison sampler.xml @ 2:cd6d2c983e69 draft

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planemo upload for repository ['https://github.com/brsynth/icfree-ml', 'https://github.com/pablocarb/doebase'] commit b29963ef22900ba666d9be11f1dc09e4e3febf8b
author tduigou
date Sat, 01 Jul 2023 01:31:52 +0000
parents 164616ec7f18
children 0111a6eb7b98
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1:81b079d1642c 2:cd6d2c983e69
85 * Proceed with full random sampling. 85 * Proceed with full random sampling.
86 * Generate all the combinations. 86 * Generate all the combinations.
87 87
88 Input 88 Input
89 ----- 89 -----
90 * **CFPS Parameters File**: The first column is the parameter (or factor) names. The second column is the maxValue of the parameter that will be used in the sampling. The third column is the concnetration of the stock. The fourth column is the deadVolume of the parameter. This is used to calculate the volume of the parameter that will not be pipetted by the robot (because of viscosity). The fifth column is the specific ratios we want to have for this parameter. If nothing defined, then take ratios given in program options. If one single number is given, then take this number as a const value. 90
91 Below is an example of an input file:
92
93 | Parameter | maxValue | Ratios |
94 |-----------|----------|---------------------|
95 | CP | 125 | 0.0 0.1 0.3 0.5 1.0 |
96 | CPK | 125 | 1 |
97 | tRNA | 125 | |
98 | AA | 125 | |
99 | ribosomes | 125 | |
100 | mRNA | 125 | |
101 | Mg | 125 | |
102 | K | 125 | |
103
104 The first column is the parameter (or factor) names.
105
106 The second column is the maxValue of the parameter that will be used in the sampling.
107
108 The third column is the specific ratios we want to have for this parameter. If nothing defined, then take ratios given in program options.
109 If one single number is given, then take this number as a const value.
110 If no value is given, then take the default ratios (`nb_samples` linear ratios from 0 to 1).
91 111
92 Advanced options: 112 Advanced options:
93 ----------------- 113 -----------------
94 * **Number of sampling steps**: Number of values for all factors when performing the sampling (default: 5) 114 * **Number of sampling steps**: Number of values for all factors when performing the sampling (default: 5)
95 * **Sampling ratios**: Ratios for all factors when performing the sampling 115 * **Sampling ratios**: Ratios for all factors when performing the sampling