CHESSLabConstants API Reference

CHESSLabConstants is overwhelmingly data – registered reagents, organisms, location kinds, instruments, and standard stock recipes, defined via CHESSCore's registration macros (see Registering Lab Constants). The tables below are built directly from registry_summary, so they stay in sync with what's actually registered.

Hand-written functions

CHESSLabConstants.register_reagent! — Function

register_reagent!(type::DataType,lab_id::AbstractString,name::AbstractString,pubchemid::Union{Integer,Missing}=missing;opaque::Bool=false)

Author-time tool: look up lab_id's formula, molecular weight, and density in the local cache (chemical_cache_path); on a cache miss, fetch them from PubChem via get_molecular_formula and get_mw_density (requires pubchemid) and cache the result. Returns a ready-to-paste @reagent line – it does not eval anything or write to solids.jl/liquids.jl itself. Paste the returned line into the appropriate file (alphabetized) and commit.

type must be CHESSCore.Solid or CHESSCore.Liquid. The line gives the reagent's elemental formula, from PubChem, in place of a molecular weight, so the weight is derived from atomic masses. PubChem describes the compound of the PubChem ID, so check that it is the form that is actually weighed out: a hydrate needs the hydrate's PubChem ID, and a salt that dissolves into ions needs a Dissolution in place of the formula (see @reagent). When PubChem's formula cannot be used, because it is charged or cannot be read as an elemental formula, the tool warns and the line falls back to the stored molecular weight.

Omit pubchemid for a compound with no PubChem entry, such as a rich-media broth. The line then has missing chemistry, or opaque if opaque=true for an undefined mixture whose atoms are intentionally not described.

Example:

julia> register_reagent!(CHESSCore.Solid,"boric_acid","Boric Acid",7628)
"@reagent boric_acid \"Boric Acid\" Solid \"BH3O3\" 1.435u\"g/mL\" 7628"

source

CHESSLabConstants.register_organism! — Function

register_organism!(lab_id::AbstractString,genus::AbstractString,species::AbstractString,strain::AbstractString="";
                    atcc_id::Union{AbstractString,Missing}=missing,notes::AbstractString="")

Author-time tool, mirroring register_reagent!: records lab_id's genus/species/strain (plus atcc_id/notes for the record – CHESSCore.Organism itself only models genus/species/ strain, so those two are cached but not part of the returned line) in the local cache (chemical_cache_path), then returns a ready-to-paste @organism line. Paste it into organisms.jl to register it, or keep it in a private, gitignored file purely for your own records if it shouldn't be public – a private file like this is not included by the package itself, so anything kept there is never actually registered.

Example:

julia> register_organism!("SMU_UA159","Streptococcus","mutans","UA159";atcc_id="700610",notes="wild type")
"@organism SMU_UA159 \"Streptococcus\" \"mutans\" \"UA159\""

source

CHESSLabConstants.register_species! — Function

register_species!(lab_id::AbstractString,name::AbstractString,charge::Integer,pubchemid::Integer)

Author-time tool, mirroring register_reagent! for CHESSCore.Species (ions and neutral species) instead of CHESSCore.Reagents: looks up lab_id's formula and molecular weight in the local cache (chemical_cache_path); on a cache miss, fetches them from PubChem via get_molecular_formula and get_mw_density (density is fetched but discarded – Species has no density field) and caches the result. Returns a ready-to-paste @species line giving the elemental formula, from which the molecular weight is derived. PubChem writes an ion's charge as a suffix of its formula ("Na+", "O4S-2"); the tool removes it after checking that it agrees with charge. When the formula cannot be used, because its charge disagrees or it cannot be read as an elemental formula, the tool warns and the line falls back to the stored molecular weight. The line carries no PubChem ID, so the ID is authoring convenience only, not permanent provenance. Paste the returned line into the appropriate file in chemicals/ and commit.

Example:

julia> register_species!("Na⁺","Na+",1,923)
"@species Na⁺ \"Na+\" 1 \"Na\""

source

CHESSLabConstants.get_mw_density — Function

get_mw_density(cid::Integer)

Query the PubChem database for the chemical properties of the compound with PubChem ID cid,

get_mw_density returns the molecular weight (g/mol) and density (g/mL) as a Tuple.

source

CHESSLabConstants.get_molecular_formula — Function

get_molecular_formula(cid::Integer)

Query PubChem for the molecular formula of the compound with PubChem ID cid, as PubChem writes it: Hill order, with the charge of an ion as a suffix ("Na+", "O4S-2"). Returns missing if PubChem has no formula for the compound, and throws an ArgumentError if the compound is not found.

source

CHESSLabConstants.chemical_cache_path — Constant

const chemical_cache_path

Path to the SQLite cache of PubChem-derived properties, keyed by LabID: Reagents (Name/Type/MolecularWeight/Density/CID/Formula, backing register_reagent!) and Species (Name/Charge/MolecularWeight/CID/Formula, backing register_species!, which produces CHESSCore.Species definitions). Used only by those two author-time tools – package load never touches this file or the network.

source

Reagents

Name	Type	Molecular Weight	Density	PubChem ID
`HCl`	Solid	36.46 g mol⁻¹	1.05 g mL⁻¹	313
`NaOH`	Solid	40.0 g mol⁻¹	1.5 g mL⁻¹	14798
`acetamide`	Solid	59.07 g mol⁻¹	1.16 g mL⁻¹	178
`acetic_acid`	Liquid	60.05 g mol⁻¹	1.05 g mL⁻¹	176
`acid_red_1`	Solid	509.41 g mol⁻¹	–	19522
`adenine`	Solid	135.13 g mol⁻¹	–	190
`adenosine`	Solid	267.24 g mol⁻¹	–	60961
`adonitol`	Solid	152.15 g mol⁻¹	–	6912
`agar`	Solid	336.34 g mol⁻¹	–	71571511
`agmatine`	Solid	130.2 g mol⁻¹	–	199
`alanine`	Solid	89.09 g mol⁻¹	–	602
`alpha_amylase`	Solid	–	–	–
`alpha_cyclodextrin`	Solid	972.85 g mol⁻¹	–	444913
`alpha_ketoglutaric_acid`	Solid	146.1 g mol⁻¹	–	51
`amitrole`	Solid	84.08 g mol⁻¹	1.14 g mL⁻¹	1639
`ammonium_chloride`	Solid	53.49 g mol⁻¹	1.53 g mL⁻¹	25517
`ammonium_nitrate`	Solid	80.04 g mol⁻¹	1.72 g mL⁻¹	22985
`ammonium_sulfate`	Solid	132.13 g mol⁻¹	1.78 g mL⁻¹	6097028
`amoxicillin`	Solid	365.4 g mol⁻¹	–	33613
`ampicillin`	Solid	349.4 g mol⁻¹	–	6249
`arabinan`	Solid	–	–	–
`arabinose`	Solid	150.13 g mol⁻¹	–	66308
`arbutin`	Solid	272.25 g mol⁻¹	–	440936
`arginine`	Solid	174.2 g mol⁻¹	–	6322
`ascorbate`	Solid	176.12 g mol⁻¹	–	54670067
`asparagine`	Solid	132.12 g mol⁻¹	1.54 g mL⁻¹	6267
`aspartic_acid`	Solid	133.1 g mol⁻¹	1.66 g mL⁻¹	5960
`b_nadph`	Solid	743.41 g mol⁻¹	–	5885
`beef_extract`	Solid	–	–	–
`beef_heart`	Solid	–	–	–
`benzamadine`	Solid	120.16 g mol⁻¹	–	2332
`beta_methyl_d_glucoside`	Solid	203.19 g mol⁻¹	–	445238
`bhi`	Solid	–	–	–
`biotin`	Solid	244.31 g mol⁻¹	–	171548
`bleomycin`	Solid	1415.6 g mol⁻¹	–	5360373
`boric_acid`	Solid	61.83 g mol⁻¹	1.44 g mL⁻¹	7628
`butyric_acid`	Liquid	88.11 g mol⁻¹	0.96 g mL⁻¹	264
`calcium_chloride`	Solid	147.01 g mol⁻¹	1.85 g mL⁻¹	6093260
`calcium_l_threonate`	Solid	310.27 g mol⁻¹	–	13388558
`carbenicillin`	Solid	378.4 g mol⁻¹	–	20824
`carnitine`	Solid	161.2 g mol⁻¹	–	288
`ceftriaxone`	Solid	554.57 g mol⁻¹	–	5479530
`cellobiose`	Solid	342.3 g mol⁻¹	–	294
`cellulose_triacetate`	Solid	–	–	–
`chloramphenicol`	Solid	323.13 g mol⁻¹	–	5959
`chlortetracycline`	Solid	515.34 g mol⁻¹	–	54682468
`choline_chloride`	Solid	139.62 g mol⁻¹	–	6209
`ciprofloxacin`	Solid	331.35 g mol⁻¹	–	2764
`citric_acid`	Solid	192.12 g mol⁻¹	1.54 g mL⁻¹	311
`citruline`	Solid	175.19 g mol⁻¹	–	9750
`cobalt_chloride`	Solid	237.92 g mol⁻¹	1.92 g mL⁻¹	24643
`cobalt_nitrate`	Solid	291.03 g mol⁻¹	1.88 g mL⁻¹	24821
`colistin`	Solid	1155.46 g mol⁻¹	–	5311054
`copper_chloride`	Solid	170.48 g mol⁻¹	2.54 g mL⁻¹	61482
`copper_sulfate`	Solid	249.68 g mol⁻¹	2.29 g mL⁻¹	24463
`cyclohexamide`	Solid	281.35 g mol⁻¹	–	6197
`cycloserine`	Solid	102.09 g mol⁻¹	–	6234
`cysteine`	Solid	175.63 g mol⁻¹	–	23462
`cystine`	Solid	240.29 g mol⁻¹	–	67678
`cytosine`	Solid	111.1 g mol⁻¹	–	597
`d_alanine`	Solid	89.09 g mol⁻¹	–	71080
`d_arabitol`	Solid	152.15 g mol⁻¹	–	94154
`d_galactarate`	Solid	210.14 g mol⁻¹	–	3037582
`d_galactonate`	Solid	448.39 g mol⁻¹	–	129700926
`d_galacturonate`	Solid	212.15 g mol⁻¹	–	44654794
`d_glucarate`	Solid	320.26 g mol⁻¹	–	11954337
`d_gluconate`	Solid	234.25 g mol⁻¹	–	16760467
`d_glucosamine`	Solid	215.63 g mol⁻¹	–	91431
`d_glucuronate`	Solid	194.14 g mol⁻¹	–	94715
`d_malic_acid`	Solid	134.09 g mol⁻¹	–	92824
`d_psicose`	Solid	180.16 g mol⁻¹	–	441036
`d_ribose`	Solid	150.13 g mol⁻¹	–	10975657
`d_serine`	Solid	105.09 g mol⁻¹	–	71077
`d_tagatose`	Solid	180.16 g mol⁻¹	–	439312
`dextrin`	Solid	504.44 g mol⁻¹	–	62698
`diacetyl`	Liquid	86.09 g mol⁻¹	0.99 g mL⁻¹	650
`dihydroxyacetone`	Solid	90.08 g mol⁻¹	–	670
`dmso`	Liquid	78.13 g mol⁻¹	1.1 g mL⁻¹	679
`doxycycline`	Solid	480.9 g mol⁻¹	–	54685920
`dulcitol`	Solid	182.17 g mol⁻¹	–	11850
`ectoine`	Solid	142.16 g mol⁻¹	–	126041
`edta`	Solid	292.24 g mol⁻¹	0.86 g mL⁻¹	6049
`erythromycin`	Solid	733.94 g mol⁻¹	–	12560
`ethanol`	Liquid	46.07 g mol⁻¹	0.79 g mL⁻¹	702
`ethanolamine`	Liquid	61.08 g mol⁻¹	1.02 g mL⁻¹	700
`folic_acid`	Solid	441.4 g mol⁻¹	–	135398658
`formamide`	Solid	45.04 g mol⁻¹	1.13 g mL⁻¹	713
`formic_acid`	Solid	46.03 g mol⁻¹	1.22 g mL⁻¹	284
`fructose`	Solid	180.16 g mol⁻¹	–	5984
`fusaric_acid`	Solid	179.22 g mol⁻¹	–	3442
`fusayama_meyer_saliva`	Liquid	–	–	–
`fusidic_acid`	Solid	516.72 g mol⁻¹	–	3000226
`galactose`	Solid	180.16 g mol⁻¹	–	6036
`gentamicin`	Solid	477.6 g mol⁻¹	–	3467
`gifu_anaerobic_broth`	Solid	–	–	–
`glcnac`	Solid	221.21 g mol⁻¹	–	439174
`glucose`	Solid	180.16 g mol⁻¹	1.2 g mL⁻¹	5793
`glutamic_acid`	Solid	147.13 g mol⁻¹	1.54 g mL⁻¹	33032
`glutamine`	Solid	146.15 g mol⁻¹	1.36 g mL⁻¹	5961
`glutathione`	Solid	307.32 g mol⁻¹	–	124886
`glycerol`	Liquid	92.09 g mol⁻¹	1.26 g mL⁻¹	753
`glycine`	Solid	75.07 g mol⁻¹	1.16 g mL⁻¹	750
`guanidine`	Solid	59.07 g mol⁻¹	–	3520
`guanine`	Solid	187.59 g mol⁻¹	–	135436483
`guanosine`	Solid	283.24 g mol⁻¹	–	135398635
`histidine`	Solid	155.16 g mol⁻¹	–	6274
`hs_com`	Solid	164.17 g mol⁻¹	–	23662354
`hydrogen_peroxide`	Liquid	34.01 g mol⁻¹	1.11 g mL⁻¹	784
`hydrolyzed_mucin`	Solid	–	–	–
`hypoxanthine`	Solid	136.11 g mol⁻¹	–	135398638
`inosine`	Solid	268.23 g mol⁻¹	–	135398641
`iron_chloride`	Solid	162.2 g mol⁻¹	2.8 g mL⁻¹	24380
`iron_nitrate`	Solid	403.99 g mol⁻¹	1.68 g mL⁻¹	16211566
`iron_sulfate`	Solid	278.01 g mol⁻¹	1.9 g mL⁻¹	62662
`isoleucine`	Solid	131.18 g mol⁻¹	–	6306
`kanamycin`	Solid	484.5 g mol⁻¹	–	6032
`l_alanine`	Solid	89.09 g mol⁻¹	1.43 g mL⁻¹	5950
`l_arabinose`	Solid	150.13 g mol⁻¹	–	439195
`l_fucose`	Solid	164.16 g mol⁻¹	–	17106
`l_lyxose`	Solid	150.13 g mol⁻¹	–	644176
`l_malic_acid`	Solid	134.09 g mol⁻¹	–	222656
`l_sorbose`	Solid	180.16 g mol⁻¹	–	439192
`lactic_acid`	Liquid	102.36 g mol⁻¹	1.2 g mL⁻¹	612
`lactose`	Solid	342.3 g mol⁻¹	–	6134
`lactulose`	Solid	342.3 g mol⁻¹	–	11333
`lb`	Solid	–	–	–
`leucine`	Solid	131.18 g mol⁻¹	1.29 g mL⁻¹	6106
`lincomycin`	Solid	406.54 g mol⁻¹	–	3000540
`lipoic_acid`	Solid	206.32 g mol⁻¹	–	6112
`lysine`	Solid	182.65 g mol⁻¹	–	69568
`magnesium_sulfate`	Solid	246.47 g mol⁻¹	1.68 g mL⁻¹	24843
`malic_acid`	Solid	134.09 g mol⁻¹	1.6 g mL⁻¹	525
`maltodextrin`	Solid	–	–	–
`maltose`	Solid	342.3 g mol⁻¹	–	439186
`manganese_chloride`	Solid	197.9 g mol⁻¹	2.01 g mL⁻¹	643989
`manganese_sulfate`	Solid	169.01 g mol⁻¹	2.95 g mL⁻¹	177577
`mannitol`	Solid	182.17 g mol⁻¹	1.49 g mL⁻¹	6251
`mannose`	Solid	180.16 g mol⁻¹	–	18950
`marine_broth`	Solid	–	–	–
`melibiose`	Solid	342.3 g mol⁻¹	–	11458
`methionine`	Solid	149.21 g mol⁻¹	1.18 g mL⁻¹	6137
`middlebrook_7h9_broth`	Solid	–	–	–
`miltefosine`	Solid	407.58 g mol⁻¹	–	3599
`minocycline`	Solid	493.94 g mol⁻¹	–	54685925
`mops`	Solid	209.26 g mol⁻¹	–	70807
`mrs_broth`	Solid	–	–	–
`mucin_type_ii`	Solid	–	–	–
`myo_inositol`	Solid	180.16 g mol⁻¹	–	892
`n_acetylgalactosamine`	Solid	221.21 g mol⁻¹	–	35717
`n_acetylneuraminate`	Solid	309.27 g mol⁻¹	–	439197
`neomycin`	Solid	146.19 g mol⁻¹	0.98 g mL⁻¹	8738
`niacinamide`	Solid	122.13 g mol⁻¹	1.4 g mL⁻¹	936
`nickel_chloride`	Solid	129.59 g mol⁻¹	3.55 g mL⁻¹	24385
`nutrient_broth`	Solid	–	–	–
`ofloxacin`	Solid	361.37 g mol⁻¹	–	4583
`ornithine`	Solid	132.16 g mol⁻¹	–	6262
`oxacillin`	Solid	401.44 g mol⁻¹	–	6196
`oxalic_acid`	Solid	90.03 g mol⁻¹	1.9 g mL⁻¹	971
`paba`	Solid	137.14 g mol⁻¹	1.37 g mL⁻¹	978
`palatinose`	Solid	342.3 g mol⁻¹	–	83686
`pantothenate`	Solid	476.54 g mol⁻¹	–	443753
`paromomycin`	Solid	615.63 g mol⁻¹	–	165580
`penicillin_g`	Solid	334.39 g mol⁻¹	–	5904
`peptone`	Solid	–	–	–
`phenylalanine`	Solid	165.19 g mol⁻¹	–	6140
`polymyxin_b`	Solid	1301.57 g mol⁻¹	–	5702105
`potassium_aluminum_sulfate`	Solid	474.37 g mol⁻¹	1.72 g mL⁻¹	62667
`potassium_chloride`	Solid	74.55 g mol⁻¹	1.98 g mL⁻¹	4873
`potassium_phosphate_di`	Solid	174.17 g mol⁻¹	–	24450
`potassium_phosphate_mono`	Solid	136.08 g mol⁻¹	2.34 g mL⁻¹	516951
`proline`	Solid	115.13 g mol⁻¹	1.06 g mL⁻¹	145742
`promethazine`	Solid	284.42 g mol⁻¹	–	4927
`propionic_acid`	Solid	74.08 g mol⁻¹	1.0 g mL⁻¹	1032
`putrescine`	Solid	88.15 g mol⁻¹	0.88 g mL⁻¹	1045
`pyridoxal`	Solid	203.62 g mol⁻¹	–	6171
`pyridoxamine`	Solid	241.11 g mol⁻¹	–	10664
`raffinose`	Solid	504.44 g mol⁻¹	–	439242
`resazurin`	Solid	229.19 g mol⁻¹	–	11077
`riboflavin`	Solid	376.37 g mol⁻¹	–	493570
`ribothymidine`	Solid	258.23 g mol⁻¹	–	445408
`rifampicin`	Solid	822.95 g mol⁻¹	–	135398735
`salicin`	Solid	286.28 g mol⁻¹	–	439503
`serine`	Solid	105.09 g mol⁻¹	1.6 g mL⁻¹	5951
`sheep_blood`	Liquid	–	–	–
`shikimic_acid`	Solid	174.15 g mol⁻¹	–	8742
`silver_nitrate`	Solid	169.87 g mol⁻¹	4.35 g mL⁻¹	24470
`sodium_acetate_anhydrous`	Solid	82.03 g mol⁻¹	1.53 g mL⁻¹	517045
`sodium_acetate_trihydrate`	Solid	136.08 g mol⁻¹	1.53 g mL⁻¹	23665404
`sodium_bicarbonate`	Solid	84.01 g mol⁻¹	2.16 g mL⁻¹	516892
`sodium_butyrate`	Solid	110.09 g mol⁻¹	–	5222465
`sodium_carbonate`	Solid	105.99 g mol⁻¹	2.54 g mL⁻¹	10340
`sodium_chloride`	Solid	58.44 g mol⁻¹	–	5234
`sodium_citrate_dihydrate`	Solid	294.1 g mol⁻¹	–	71474
`sodium_dichromate`	Solid	297.99 g mol⁻¹	2.35 g mL⁻¹	108005
`sodium_molybdate`	Solid	241.96 g mol⁻¹	3.5 g mL⁻¹	16211258
`sodium_phosphate_di`	Solid	268.06 g mol⁻¹	–	6096963
`sodium_phosphate_di_anhydrous`	Solid	141.96 g mol⁻¹	–	24203
`sodium_phosphate_mono`	Solid	137.99 g mol⁻¹	–	516949
`sodium_pyruvate`	Solid	110.04 g mol⁻¹	–	23662274
`sodium_selenite`	Solid	172.95 g mol⁻¹	3.1 g mL⁻¹	24934
`sodium_succinate_hexahydrate`	Solid	270.14 g mol⁻¹	–	3083938
`sodium_tungstate`	Solid	329.85 g mol⁻¹	3.25 g mL⁻¹	150191
`soluble_starch`	Solid	–	–	–
`sorbitol`	Solid	182.17 g mol⁻¹	1.49 g mL⁻¹	5780
`spectinomycin`	Solid	332.35 g mol⁻¹	–	15541
`spermidine`	Solid	145.25 g mol⁻¹	–	1102
`streptomycin`	Solid	581.58 g mol⁻¹	–	19649
`succinic_acid`	Solid	118.09 g mol⁻¹	1.57 g mL⁻¹	1110
`sucrose`	Solid	342.3 g mol⁻¹	1.59 g mL⁻¹	5988
`sulfadiazine`	Solid	250.28 g mol⁻¹	–	5215
`sulfamethazine`	Solid	278.33 g mol⁻¹	1.47 g mL⁻¹	5327
`sulfathiazole`	Solid	255.31 g mol⁻¹	–	5340
`tartrate`	Solid	230.08 g mol⁻¹	–	12598458
`taurine`	Solid	125.14 g mol⁻¹	–	1123
`tetracycline`	Solid	480.9 g mol⁻¹	–	54704426
`thb`	Solid	–	–	–
`thiamine`	Solid	337.26 g mol⁻¹	–	6202
`thiourea`	Solid	76.12 g mol⁻¹	1.4 g mL⁻¹	2723790
`threonine`	Solid	119.12 g mol⁻¹	–	6288
`thymine`	Solid	126.12 g mol⁻¹	–	1135
`tin_fluoride`	Solid	156.71 g mol⁻¹	2.79 g mL⁻¹	24550
`tobramycin`	Solid	467.52 g mol⁻¹	–	36294
`trehalose`	Solid	378.33 g mol⁻¹	–	181978
`triclosan`	Solid	289.54 g mol⁻¹	–	5564
`tryptic_soy_broth`	Solid	–	–	–
`tryptone`	Solid	–	–	–
`tryptophan`	Solid	204.23 g mol⁻¹	–	6305
`tryptose`	Solid	–	–	–
`tyrosine`	Solid	181.19 g mol⁻¹	–	6057
`uracil`	Solid	112.09 g mol⁻¹	–	1174
`urea`	Solid	60.06 g mol⁻¹	1.34 g mL⁻¹	1176
`uridine`	Solid	244.2 g mol⁻¹	–	6029
`valine`	Solid	117.15 g mol⁻¹	1.23 g mL⁻¹	6287
`vancomycin`	Solid	1449.26 g mol⁻¹	–	14969
`vitamin_b12`	Solid	1355.39 g mol⁻¹	–	165339223
`vitamin_k1`	Solid	450.71 g mol⁻¹	0.96 g mL⁻¹	5284607
`water`	Liquid	18.02 g mol⁻¹	1.0 g mL⁻¹	962
`xanthine`	Solid	152.11 g mol⁻¹	–	1188
`xanthosine`	Solid	284.23 g mol⁻¹	–	64959
`xylitol`	Solid	278.35 g mol⁻¹	–	581285
`xylose`	Solid	150.13 g mol⁻¹	1.52 g mL⁻¹	135191
`yeast_extract`	Solid	–	–	–
`zinc_chloride`	Solid	136.28 g mol⁻¹	2.91 g mL⁻¹	5727
`zinc_sulfate`	Solid	287.54 g mol⁻¹	1.97 g mL⁻¹	62640

Acid/base systems

Reagent	Species (fully-protonated → fully-deprotonated)	pKa
`acetic_acid`	Acetic Acid → Acetate	4.76
`agmatine`	Agmatine(dication) → Agmatine(cation) → Agmatine	9.4, 12.5
`alanine`	Alanine(cation) → DL-alanine → Alanine(anion)	2.34, 9.69
`alpha_ketoglutaric_acid`	Alpha Ketoglutaric Acid (2-Oxoglutaric Acid) → HAlphaKetoglutarate- → AlphaKetoglutarate2-	1.85, 4.68
`amitrole`	Amitrole(cation) → amitrole (3-amino-1,2,4-triazole)	4.2
`ammonium_chloride`	NH4+ → NH3	9.25
`ammonium_nitrate`	NH4+ → NH3	9.25
`ammonium_sulfate`	NH4+ → NH3	9.25
`amoxicillin`	Amoxicillin(cation) → amoxicillin → Amoxicillin(anion) → Amoxicillin(dianion)	2.4, 7.4, 9.6
`ampicillin`	Ampicillin(cation) → ampicllin → Ampicillin(anion)	2.5, 7.3
`arginine`	Arginine(dication) → Arginine(cation) → L-arginine → Arginine(anion)	2.17, 9.04, 12.48
`ascorbate`	L-Ascorbic Acid → Ascorbate(anion) → Ascorbate(dianion)	4.1, 11.6
`asparagine`	Asparagine(cation) → L-asparagine → Asparagine(anion)	2.02, 8.8
`aspartic_acid`	Aspartate(cation) → L-aspartic acid → Aspartate(anion) → Aspartate(dianion)	1.99, 3.9, 9.9
`benzamadine`	Benzamidine(cation) → benzamadine	11.6
`biotin`	biotin → Biotin(anion)	4.5
`boric_acid`	Boric Acid → B(OH)4-	9.24
`butyric_acid`	Butyric Acid → Butyrate(anion)	4.82
`carbenicillin`	carbenicillin → Carbenicillin(anion)	2.6
`carnitine`	Carnitine(cation) → D,L-Carnitine	3.8
`chlortetracycline`	Chlortetracycline(cation) → Chlortetracycline(zwitterion) → Chlortetracycline(anion) → Chlortetracycline(dianion)	3.3, 7.7, 9.7
`ciprofloxacin`	Ciprofloxacin(cation) → ciprofloxacin → Ciprofloxacin(anion)	6.1, 8.7
`citric_acid`	Citric Acid → H2Citrate- → HCitrate2- → Citrate3-	3.13, 4.76, 6.4
`citruline`	Citruline(cation) → L-citruline → Citruline(anion)	2.43, 9.41
`cycloserine`	Cycloserine(cation) → cycloserine → Cycloserine(anion)	4.5, 7.4
`cysteine`	Cysteine(cation) → Cysteine(zwitterion) → Cysteine(anion) → Cysteine(dianion)	1.96, 8.3, 10.28
`cystine`	Cystine(dication) → Cystine(cation) → L-cystine → Cystine(anion) → Cystine(dianion)	1.0, 2.1, 7.9, 9.9
`d_alanine`	Alanine(cation) → D-Alanine → Alanine(anion)	2.34, 9.69
`d_malic_acid`	D-Malic Acid → HMalate- → Malate2-	3.4, 5.2
`doxycycline`	Doxycycline(cation) → Doxycycline(zwitterion) → Doxycycline(anion) → Doxycycline(dianion)	3.3, 7.7, 9.7
`edta`	EDTA → EDTA(anion) → EDTA(dianion) → EDTA(trianion) → EDTA(tetraanion)	2.0, 2.68, 6.11, 10.17
`erythromycin`	Erythromycin(cation) → erythromycin	8.8
`ethanolamine`	Ethanolamine(cation) → Ethanolamine	9.5
`formic_acid`	Formic Acid → Formate-	3.75
`glutamic_acid`	Glutamate(cation) → L-glutamic_acid → Glutamate(anion) → Glutamate(dianion)	2.19, 4.25, 9.67
`glutamine`	Glutamine(cation) → L-glutamine → Glutamine(anion)	2.17, 9.13
`glutathione`	Glutathione(cation) → L-Glutathione (reduced) → Glutathione(anion) → Glutathione(dianion) → Glutathione(trianion)	2.05, 3.53, 8.66, 9.42
`glycine`	Glycine(cation) → glycine → Glycine(anion)	2.34, 9.6
`guanidine`	Guanidine(cation) → guanidine	13.6
`histidine`	Histidine(dication) → Histidine(cation) → L-histidine → Histidine(anion)	1.8, 6.04, 9.33
`hypoxanthine`	Hypoxanthine → Hypoxanthine(anion)	8.94
`iron_chloride`	Fe3+ → FeOH2+	2.2
`iron_nitrate`	Fe3+ → FeOH2+	2.2
`iron_sulfate`	Fe2+ → FeOH+	9.5
`isoleucine`	Isoleucine(cation) → L-isoleucine → Isoleucine(anion)	2.36, 9.68
`l_malic_acid`	L-Malic Acid → HMalate- → Malate2-	3.4, 5.2
`lactic_acid`	Lactic Acid (88% w/w solution) → Lactate-	3.86
`leucine`	Leucine(cation) → L-leucine → Leucine(anion)	2.36, 9.6
`lincomycin`	Lincomycin(cation) → lincomycin	7.6
`lipoic_acid`	lipoic_acid → Lipoate(anion)	4.8
`lysine`	Lysine(dication) → Lysine(cation) → Lysine(zwitterion) → Lysine(anion)	2.18, 8.95, 10.5
`malic_acid`	Malic Acid → HMalate- → Malate2-	3.4, 5.2
`methionine`	Methionine(cation) → L-methionine → Methionine(anion)	2.28, 9.21
`minocycline`	Minocycline(cation) → Minocycline(zwitterion) → Minocycline(anion) → Minocycline(dianion)	3.3, 7.7, 9.7
`mops`	MOPS → MOPS-	7.2
`ofloxacin`	Ofloxacin(cation) → ofloxacin → Ofloxacin(anion)	6.1, 8.7
`ornithine`	Ornithine(dication) → Ornithine(cation) → L-Ornithine → Ornithine(anion)	1.94, 8.65, 10.76
`oxacillin`	oxacillin → Oxacillin(anion)	2.7
`oxalic_acid`	Oxalic Acid → HOxalate- → Oxalate2-	1.25, 4.14
`paba`	PABA(cation) → 4-aminobenzoic acid → PABA(anion)	2.5, 4.85
`penicillin_g`	penicillin_g → PenicillinG(anion)	2.75
`phenylalanine`	Phenylalanine(cation) → L-phenylalanine → Phenylalanine(anion)	1.83, 9.13
`potassium_phosphate_di`	H3PO4 → H2PO4- → HPO4 2- → PO4 3-	2.15, 7.2, 12.38
`potassium_phosphate_mono`	H3PO4 → H2PO4- → HPO4 2- → PO4 3-	2.15, 7.2, 12.38
`proline`	Proline(cation) → L-proline → Proline(anion)	1.99, 10.6
`promethazine`	Promethazine(cation) → promethazine	9.1
`propionic_acid`	Propionic Acid → Propionate-	4.87
`putrescine`	Putrescine(dication) → Putrescine(cation) → Putrescine	9.35, 10.8
`serine`	Serine(cation) → L-serine → Serine(anion)	2.21, 9.15
`shikimic_acid`	Shikimic Acid → Shikimate-	4.15
`sodium_acetate_anhydrous`	Acetic Acid → Acetate	4.76
`sodium_acetate_trihydrate`	Acetic Acid → Acetate	4.76
`sodium_bicarbonate`	H2CO3 → HCO3- → CO3 2-	6.35, 10.33
`sodium_butyrate`	Butyric acid → Butyrate(anion)	4.82
`sodium_carbonate`	H2CO3 → HCO3- → CO3 2-	6.35, 10.33
`sodium_citrate_dihydrate`	Citric Acid → H2Citrate- → HCitrate2- → Citrate3-	3.13, 4.76, 6.4
`sodium_phosphate_di`	H3PO4 → H2PO4- → HPO4 2- → PO4 3-	2.15, 7.2, 12.38
`sodium_phosphate_di_anhydrous`	H3PO4 → H2PO4- → HPO4 2- → PO4 3-	2.15, 7.2, 12.38
`sodium_phosphate_mono`	H3PO4 → H2PO4- → HPO4 2- → PO4 3-	2.15, 7.2, 12.38
`sodium_pyruvate`	Pyruvic acid → Pyruvate(anion)	2.5
`sodium_succinate_hexahydrate`	Succinic acid → Succinate(monoanion) → Succinate	4.21, 5.64
`succinic_acid`	Succinic Acid → Succinate(monoanion) → Succinate	4.21, 5.64
`sulfadiazine`	Sulfadiazine(cation) → sulfadiazine → Sulfadiazine(anion)	1.6, 6.5
`sulfamethazine`	Sulfamethazine(cation) → sulfamethazine → Sulfamethazine(anion)	2.3, 7.4
`sulfathiazole`	Sulfathiazole(cation) → sulfathiazole → Sulfathiazole(anion)	2.1, 7.2
`tartrate`	Tartaric acid → Tartrate(monoanion) → Tartrate(dianion)	3.0, 4.4
`taurine`	Taurine → Taurine(anion)	9.06
`tetracycline`	Tetracycline(cation) → Tetracycline(zwitterion) → Tetracycline(anion) → Tetracycline(dianion)	3.3, 7.7, 9.7
`threonine`	Threonine(cation) → L-threonine → Threonine(anion)	2.09, 9.1
`tryptophan`	Tryptophan(cation) → L-tryptophan → Tryptophan(anion)	2.38, 9.39
`tyrosine`	Tyrosine(cation) → L-tyrosine → Tyrosine(anion) → Tyrosine(dianion)	2.2, 9.11, 10.07
`valine`	Valine(cation) → L-valine → Valine(anion)	2.32, 9.62

Organisms

Name	Genus	Species	Strain
`BSU_168`	Bacillus	subtilis	168
`EC_K12`	Escherichia	coli	K-12
`SGO_CH1`	Streptococcus	gordonii	Challis
`SMU_LAR01`	Streptococcus	mutans	LAR01
`SMU_T8`	Streptococcus	mutans	T8
`SMU_UA140`	Streptococcus	mutans	UA140
`SMU_UA159`	Streptococcus	mutans	UA159
`SSA_SK36`	Streptococcus	sanguinis	SK36
`SSO_6715`	Streptococcus	sobrinus	6715

Location kinds

Name	Categories	Shape	Capacity
`AltemisBox`	Box	(8, 12)	–
`AltemisTube`	CryoTube, Tube	(1, 1)	–
`Bench`	–	–	–
`BioSpaDrawer`	Rack	(1, 2)	–
`Bottle1L`	ScrewBottle, Bottle	(1, 1)	–
`Bottle250mL`	ScrewBottle, Bottle	(1, 1)	–
`Bottle500mL`	ScrewBottle, Bottle	(1, 1)	–
`BreakawayPCRPlate`	PCRLabware	(1, 3)	–
`BreakawayPCRWafer`	PCRLabware	(8, 4)	–
`CobraSlot`	Slot	–	–
`Conical15`	Conical, Tube	(1, 1)	–
`Conical50`	Conical, Tube	(1, 1)	–
`CryoTubeSlot`	Slot	–	–
`CultureTube10mL`	CultureTube, Tube	(1, 1)	–
`DeepReservoir`	DeepWell, WellPlate	(1, 1)	–
`DeepWP96`	DeepWell, WellPlate	(8, 12)	–
`DeepWellColumn`	DeepWell, WellPlate	(1, 12)	–
`DeepWellRow`	DeepWell, WellPlate	(8, 1)	–
`DemoPlate`	Plate	(8, 12)	–
`DemoWell`	–	–	200.0 μL
`FilterBottle1L`	FilterBottle, Bottle	(1, 1)	–
`Flask`	–	–	–
`GilsonSlot`	Slot	–	–
`HudsonStack`	Rack	(15, 1)	–
`IncubatorShelf`	Slot	–	–
`LC3`	–	(24, 1)	–
`LC3Slot`	Slot	–	–
`Lab`	–	–	–
`MagPlate`	PCRLocation	–	–
`MantisBottle`	Bottle	(1, 1)	–
`MantisConicalHolder`	Deck	(4, 1)	–
`MantisConicalSlot`	Slot	–	–
`MantisSlot`	Slot	–	–
`MatrixBox`	Box	(8, 12)	–
`MatrixTube`	CryoTube, Tube	(1, 1)	–
`MicroPlateSlot`	Slot	–	–
`NimbusConical15Rack`	NimbusRack, Rack	(4, 6)	–
`NimbusConical15Slot`	Slot	–	–
`NimbusConical50Rack`	NimbusRack, Rack	(2, 3)	–
`NimbusConical50Slot`	Slot	–	–
`NimbusPlateRack`	NimbusRack, Rack	–	–
`NimbusPosition`	Slot	–	–
`PCR8Strip`	PCRLabware	(8, 1)	–
`PCRRack`	Rack	–	–
`PCRTube`	PCRLabware	(1, 1)	–
`ProFlexSlot`	Slot	–	–
`QPCRPlate96`	PCRLabware	(8, 12)	–
`QuantStudioSlot`	Slot	–	–
`Reservior25mL`	Reservior	(1, 1)	–
`Reservoir100mL`	Reservior	(1, 1)	–
`Room`	–	–	–
`Shelf`	–	–	–
`SimpliAmpSlot`	Slot	–	–
`SmallIncubator`	–	–	–
`TempestHolder`	Rack	(1, 6)	–
`TempestMagazine`	Slot	–	–
`TempestSlot`	Slot	–	–
`TipReservior`	–	(1, 1)	–
`WP384`	MicroPlate, WellPlate	(16, 24)	–
`WP96`	MicroPlate, WellPlate	(8, 12)	–
`Well100`	–	–	100.0 μL
`Well1000`	–	–	1000.0 μL
`Well10000`	–	–	10000.0 μL
`Well100000`	–	–	100000.0 μL
`Well1000000`	–	–	1.0e6 μL
`Well1400`	–	–	1400.0 μL
`Well15000`	–	–	15000.0 μL
`Well150000`	–	–	150000.0 μL
`Well200`	–	–	200.0 μL
`Well2000`	–	–	2000.0 μL
`Well20000`	–	–	20000.0 μL
`Well25000`	–	–	25000.0 μL
`Well250000`	–	–	250000.0 μL
`Well400`	–	–	400.0 μL
`Well50000`	–	–	50000.0 μL
`Well500000`	–	–	500000.0 μL
`brPCR96`	PCRLabware	(8, 12)	–

Instruments

Name	Categories
`Autoclave`	Incubator, Instrument
`BioSpa`	Incubator, Instrument
`CarouselBase`	Instrument
`Cobra`	LiquidHandler, Instrument
`Cytation10`	PlateReader, Instrument
`Cytation5`	PlateReader, Instrument
`Epoch2`	PlateReader, Instrument
`Freezer`	Incubator, Instrument
`Gilson`	LiquidHandler, Instrument
`Incubator`	Incubator, Instrument
`Mantis`	LiquidHandler, Instrument
`Nimbus`	LiquidHandler, Instrument
`Panopticon`	Incubator
`PlateCrane`	Instrument
`ProFlex`	ThermalCycler, Incubator, Instrument
`QuantStudio`	ThermalCycler, Incubator, Instrument
`Refrigerator`	Incubator, Instrument
`SimpliAmp`	ThermalCycler, Incubator, Instrument
`StackBase`	Instrument
`SynergyH1`	PlateReader, Instrument
`Tempest`	LiquidHandler, Instrument

Standard stock recipes

Name	Type
`amino_acids_50x_500mL`	Solution
`atcc_thy_1000mL`	Solution
`atcc_thy_agar_1000mL`	Solution
`bases_100x_200mL`	Solution
`brain_heart_infusion_agar_1000mL`	Solution
`brain_heart_infusion_broth_1000mL`	Solution
`calcium_chloride_1000x_50mL`	Solution
`cdm_glucose_500mL`	Solution
`cysteine_500x_50mL`	Solution
`gifu_anaerobic_agar_1000mL`	Solution
`gifu_anaerobic_broth_1000mL`	Solution
`iron_1000x_50mL`	Solution
`lb_1000mL`	Solution
`lb_agar_1000mL`	Solution
`m9_agar_1000mL`	Solution
`m9_broth_1000mL`	Solution
`m9_calcium_chloride`	Solution
`m9_glucose`	Solution
`m9_magnesium_sulfate`	Solution
`m9_salts`	Solution
`m9_supplement`	Solution
`m9_thiamine`	Solution
`magnesium_500x_250mL`	Solution
`manganese_1000x_250mL`	Solution
`marine_agar_1000mL`	Solution
`marine_broth_1000mL`	Solution
`modified_reinforced_clostridial_1000mL`	Solution
`modified_reinforced_clostridial__agar_1000mL`	Solution
`mrs_agar_1000mL`	Solution
`mrs_broth_1000mL`	Solution
`nutrient_agar_1000mL`	Solution
`nutrient_broth_1000mL`	Solution
`phosphates_25x_1L`	Solution
`sodium_acetate_50x_500mL`	Solution
`sodium_bicarbonate_20x_1L`	Solution
`thy_350mL`	Solution
`thy_agar_350mL`	Solution
`tryptic_soy_agar_1000mL`	Solution
`tryptic_soy_broth_1000mL`	Solution
`tryptic_soy_sheep_blood_1000mL`	Solution
`tryptic_soy_sheep_blood_agar_1000mL`	Solution
`vitamins_1000x_50mL`	Solution