Params
AssayParams
Bases: BaseModel
Parameters for assay generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
plate_size
|
int
|
plate size |
4
|
mean_control
|
float
|
mean control reading |
0.0
|
mean_normal
|
float
|
mean normal specimen reading |
2.0
|
mean_mutant
|
float
|
mean mutant specimen reading |
5.0
|
reading_noise
|
float
|
standard deviation of plate reading noise |
0.5
|
image_noise
|
int
|
plate image noise (grayscale 0-255) |
32
|
Source code in src/snailz/params.py
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|
SpecimenParams
Bases: BaseModel
Parameters for specimen generation.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
mass_mean
|
float
|
Mean mass |
10.0
|
mass_sd
|
float
|
Relative standard deviation in mass |
1.0
|
genome_length
|
int
|
Length of genomes |
20
|
mut_mass_scale
|
float
|
Scaling for mutant snail mass |
2.0
|
mut_frac
|
float
|
Fraction of significant mutants |
0.2
|
mut_prob
|
float
|
Probability of point mutation |
0.05
|
Source code in src/snailz/params.py
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|
ScenarioParams
Bases: BaseModel
Parameters for entire scenario.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
rng_seed
|
int
|
random number generation seed |
required |
grid_size
|
int
|
sample grid size |
15
|
num_sites
|
int
|
number of sample sites |
3
|
num_specimens
|
int
|
total number of specimens |
10
|
num_machines
|
int
|
number of lab machines |
5
|
num_persons
|
int
|
number of lab staff |
5
|
locale
|
str
|
name generation locale |
'et_EE'
|
assays_per_specimen
|
int
|
assays per specimen |
2
|
specimen_params
|
SpecimenParams
|
specimen generation parameters |
required |
assay_params
|
AssayParams
|
assay generation parameters |
required |
Source code in src/snailz/params.py
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|