snailz 5.4.0

Synthetic data generator for snail mutation survey

Snailz

snailz is a synthetic data generator that models a study of snails in the Pacific Northwest which are growing to unusual size as a result of exposure to pollution. The package generates fully-reproducible datasets of varying sizes and with varying statistical properties, and is intended for classroom use. For example, an instructor can give each learner a unique dataset to analyze, while learners can test their analysis pipelines using datasets they generate themselves.

The Story

Years ago, logging companies dumped toxic waste in a remote region of Vancouver Island. As the containers leaked and the pollution spread, some snails in the region began growing unusually large. Your team is now collecting and analyzing specimens from affected regions to determine if exposure to pollution is responsible.

Usage:

usage: snailz [-h]
              [--defaults]
	      [--outdir OUTDIR]
              [--override OVERRIDE [OVERRIDE ...]]
	      [--params PARAMS]
              [--profile]

options:
  -h, --help            show this help message and exit
  --defaults            show default parameters as JSON
  --outdir OUTDIR       output directory
  --override OVERRIDE [OVERRIDE ...]
                        name=value parameters to override defaults
  --params PARAMS       specify JSON parameter file
  --profile             enable profiling

See the documentation of the Parameters class for a description of data generation parameters.

Schema

An asterisk beside the name of a field indicates that the value may be missing (i.e., the field may be NULL in the final database).

table	field	type	purpose
grid	ident	text	unique identifier for each survey grid
	size	int	height and width of survey grid in cells
	spacing	float	size of survey grid cell (meters)
	lat0	float	southernmost latitude of grid (fractional degrees)
	lon0	float	westernmost longitude of grid (fractional degrees)
grid_cells	grid_id	text	foreign key reference to grid
	lat	float	foreign key reference to grid cell
	lon	float	foreign key reference to grid cell
	value	float	pollution measurement in that grid cell
machine	ident	text	unique identifier for each piece of laboratory equipment
	name	text	name of piece of laboratory equipment
person	ident	text	unique identifier for member of staff
	family	text	family name of staff member
	personal	text	personal name of staff member
	supervisor_id	text*	foreign key reference to person's supervisor
rating	person_id	text	foreign key reference to person
	machine_id	text	foreign key reference to machine
	certified	bool	whether person is certified to use machine
assay	ident	text	unique identifier for soil assay
	lat	float	foreign key reference to grid cell
	lon	float	foreign key reference to grid cell
	person_id	text	foreign key reference to person who did assay
	machine_id	text	foreign key reference to machine used to do assay
	performed*	date	date that assay was done
assay_readings	assay_id	text	foreign key reference to assay
	reading_id	int	serial number within assay
	contents	text	"C" or "T" showing control or treatment
	reading	float	pollution measurement
species	reference	text	reference genome
	susc_locus	int	location of susceptible locus within genome
	susc_base	text	base that causes significant mutation at that locus
species_loci	ident	int	unique locus serial number
	locus	int	locus where mutation might occur
specimen	ident	text	unique identifier for specimen
	lat	float	foreign key reference to grid cell
	lon	float	foreign key reference to grid cell
	genome	text	specimen genome
	mass	float	specimen mass (g)
	diameter	float	specimen diameter (mm)
	collected*	date	when specimen was collected

Colophon

snailz was inspired by the Palmer Penguins dataset and by conversations with Rohan Alexander about his book Telling Stories with Data.

My thanks to everyone who built the tools this project relies on, including:

• faker for synthesizing data.
• mkdocs for documentation.
• ruff for checking the code.
• sqlite and sqlite-utils for persistence.
• taskipy for running tasks.
• uv for managing packages and the virtual environment.

The snail logo was created by sunar.ko.

Acknowledgments

• Greg Wilson is a programmer, author, and educator based in Toronto. He was the co-founder and first Executive Director of Software Carpentry and received ACM SIGSOFT's Influential Educator Award in 2020.