├── .gitignore ├── 01_intro ├── Makefile ├── complexity.svg ├── comprehension.svg ├── data_sample.yml ├── gvwilson-gage-2019.png ├── index.md ├── output_sample.out ├── prose.txt ├── python_sample.py └── shell_sample.sh ├── 02_grid ├── grid_01.py ├── grid_02.py ├── grid_03.py ├── grid_04.py └── index.md ├── 03_test ├── grid.py ├── index.md ├── test_01.py ├── test_02.py ├── test_03.py ├── test_04.py ├── test_05.py └── test_06.py ├── 04_parse ├── 003805_indented_table.csv ├── 003805_missing_machine.csv ├── 003805_person_name.csv ├── 003805_quoted_id.csv ├── 003805_readings.csv ├── index.md ├── parse_01.py ├── parse_02.py ├── parse_03.py ├── parse_04.py └── parse_05.py ├── 05_synth ├── index.md ├── params_01.py ├── params_02.py ├── specimens_01.py ├── specimens_02.py ├── test_params_01.py └── test_specimens_01.py ├── 06_scenario ├── assays.py ├── grid.py ├── index.md ├── machines.py ├── params.py ├── persons.py ├── scenario.py ├── specimens.py └── utils.py ├── 97_db └── make_db.py ├── 98_viewer ├── .gitignore ├── README.txt ├── app.py ├── static │ └── snailz.css └── templates │ ├── assays.html │ ├── base.html │ ├── index.html │ ├── machines.html │ ├── persons.html │ └── specimens.html ├── 99_finale ├── Makefile └── index.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE.md ├── Makefile ├── README.md ├── bibliography └── index.md ├── common.mk ├── docs ├── .nojekyll ├── 01_intro │ ├── complexity.svg │ ├── comprehension.svg │ ├── gvwilson-gage-2019.png │ └── index.html ├── 02_grid │ └── index.html ├── 03_test │ └── index.html ├── 04_parse │ └── index.html ├── 05_synth │ └── index.html ├── 06_scenario │ └── index.html ├── 99_finale │ └── index.html ├── bibliography │ └── index.html ├── conduct │ └── index.html ├── contrib │ └── index.html ├── glossary │ └── index.html ├── index.html ├── license │ └── index.html └── static │ ├── favicon.ico │ ├── page.css │ ├── shower.js │ └── slides.css ├── extras └── words.txt ├── glossary └── index.md ├── old ├── 02_parse │ ├── COW.csv │ ├── GBY.csv │ ├── Makefile │ ├── call_tree.svg │ ├── index.md │ ├── naive.py │ ├── naive_GBY.out │ ├── naive_YOU.out │ └── parse.py ├── 03_plugin │ ├── COW.svg │ ├── GBY.svg │ ├── HMB.svg │ ├── Makefile │ ├── YOU.svg │ ├── display.py │ ├── index.md │ ├── plugin_csv.py │ ├── plugin_pandas.py │ ├── plugin_sql.py │ ├── plugin_sqlmodel.py │ ├── plugins.json │ ├── table_structure.svg │ └── util.py ├── 04_cleanup │ ├── Makefile │ ├── grid_array.py │ ├── grid_filled.py │ ├── grid_generic.py │ ├── grid_list.py │ ├── grid_list_randomizer.py │ ├── index.md │ ├── invperc.py │ ├── script.py │ ├── test_grid_filled.py │ ├── test_grid_mock.py │ ├── test_grid_parametrize.py │ ├── test_grid_randomizer.py │ └── test_grid_start.py ├── 05_perf │ ├── Makefile │ ├── full_lazy_list_array.json │ ├── full_list_array.json │ ├── grid_array.py │ ├── grid_generic.py │ ├── grid_lazy.py │ ├── grid_list.py │ ├── index.md │ ├── invperc_single.py │ ├── invperc_sweep.py │ ├── invperc_util.py │ ├── k+lazy+list+array_z+35+55+75+95+115_d+2+10+100_r+50_s+556677.csv │ ├── k+lazy+list+array_z+35+55+75+95+115_d+2+10+100_r+50_s+556677.svg │ ├── k+lazy+list+array_z+35+55_d+2+10_r+2_s+1728394.csv │ ├── k+lazy+list+array_z+35+55_d+2+10_r+2_s+1728394.svg │ ├── k+list+array_z+35+55+75+95+115_d+2+10+100_r+50_s+556677.csv │ ├── k+list+array_z+35+55+75+95+115_d+2+10+100_r+50_s+556677.svg │ ├── k+list+array_z+35+55_d+2+10_r+2_s+1728394.csv │ ├── k+list+array_z+35+55_d+2+10_r+2_s+1728394.svg │ ├── params_single.py │ ├── params_sweep.py │ ├── plot.py │ ├── profile_lazy.json │ ├── profile_lazy.txt │ ├── profile_lazy_head.txt │ ├── profile_list.json │ ├── profile_list.txt │ ├── profile_list_head.txt │ ├── run_profile_lazy.py │ ├── run_profile_list.py │ ├── single_lazy.json │ ├── single_list.json │ ├── small_lazy_list_array.json │ └── small_list_array.json ├── 06_scale │ ├── .gitignore │ ├── Makefile │ ├── flow.py │ ├── grid_generic.py │ ├── grid_lazy.py │ ├── grid_list.py │ ├── index.md │ ├── invperc.py │ ├── measure.py │ ├── params_single.py │ ├── params_sweep.py │ ├── run_short.sh │ ├── run_standalone.sh │ ├── run_sweep.sh │ ├── short.json │ ├── standalone.json │ └── sweep.json ├── 07_prod │ └── index.md ├── 08_mutate │ ├── .gitignore │ ├── Makefile │ ├── all_data_scatter.svg │ ├── all_data_sorted.svg │ ├── analyze.py │ ├── index.md │ ├── sites.csv │ ├── slimmed_data_scatter.svg │ ├── slimmed_data_sorted.svg │ ├── surveys.csv │ ├── synthesize_genomes.py │ └── synthesize_samples.py ├── 09_search │ ├── Makefile │ ├── W962796421.json │ ├── fetch_bib_data.py │ ├── index.md │ ├── make_index.py │ └── tf_idf_search.csv ├── 10_lims │ ├── .gitignore │ ├── Makefile │ ├── assay_params.py │ ├── assays.json │ ├── assays │ │ └── fff9b2d6.csv │ ├── capabilities.json │ ├── create_db.py │ ├── designs │ │ └── fff9b2d6.csv │ ├── index.md │ ├── invalid_user.sh │ ├── lims.py │ ├── lims_perms.tbl │ ├── lint.py │ ├── lint.sh │ ├── listing.sh │ ├── person.json │ ├── test_initial.json │ ├── test_lims.py │ └── upload.sh ├── 11_site │ ├── .gitignore │ ├── index.md │ └── website_screenshot.svg ├── 12_scrape │ ├── Makefile │ ├── find.out │ ├── find.sh │ ├── find_in_page.py │ ├── index.md │ ├── medium.html │ ├── medium.out │ ├── medium.sh │ ├── parse_page.py │ ├── scrape.py │ ├── small.html │ ├── small.out │ └── small.sh ├── 13_serve │ ├── Makefile │ ├── index.md │ ├── model.py │ ├── run_server.out │ ├── run_server.sh │ ├── serve_home_page.svg │ ├── server.py │ ├── static │ │ └── style.css │ └── templates │ │ ├── base.html │ │ ├── details.html │ │ ├── index.html │ │ └── plate.html ├── bin │ ├── assay_data.py │ ├── assay_params.py │ ├── assay_plates.py │ ├── assay_staff.py │ ├── fetch_bib_data.py │ ├── raw_samples.py │ ├── survey_db.py │ ├── tidy_samples.py │ └── util.py ├── examples.mk ├── info │ ├── bibliography.bib │ ├── glossary.yml │ ├── thanks.yml │ └── wordlist.txt ├── package │ ├── .gitignore │ ├── LICENSE.md │ ├── Makefile │ ├── README.md │ ├── build.sh │ ├── docs.sh │ 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