-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathtime_series_schema.json
595 lines (595 loc) · 24.6 KB
/
time_series_schema.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
{
"exp_info": {
"type": "group",
"label": "Sample Sources & Incubation Temperature",
"description": "Specify samples and temperatures to run an experiment at.",
"inputs": {
"src_samples": {
"type": "aliquot+",
"label": "Source Wells",
"description": "Select samples to run."
},
"inc_temp": {
"type": "choice",
"label": "Incubation Temperature",
"description": "Select the incubation temperature.",
"default": "warm_30",
"options": [
{
"value": "warm_30",
"name": "30 degrees Celsius"
},
{
"value": "warm_35",
"name": "35 degrees Celsius"
},
{
"value": "warm_37",
"name": "37 degrees Celsius"
}
]
},
"media_well_strings": {
"type": "string",
"label": "Media Wells",
"default": "",
"description": "Specify wells to be used as media blanks as comma-separated humanized well indices. Leave blank if you would prefer to use the default Strateos media blanks."
}
}
},
"inoc_info": {
"type": "group",
"label": "Inoculation Parameters",
"description": "Select culture and media volumes for inoculation",
"inputs": {
"inoc_vol": {
"type": "volume",
"default": "10:microliter",
"required": true,
"label": "Glycerol Stock Volume"
},
"inoc_media_vol": {
"type": "volume",
"default": "700:microliter",
"required": true,
"label": "Media Volume"
},
"inoculation_media": {
"type": "choice",
"label": "Growth Media",
"description": "Select media",
"default": "Modified M9 Media",
"options": [
{
"value": "Modified M9 Media",
"name": "M9 Media, Modified for Bacillus"
},
{
"value": "M9 Minimal Media",
"name": "M9 Minimal Media"
},
{
"value": "S750 Minimal Media",
"name": "S750 Minimal Media"
},
{
"value": "LB Cam",
"name": "LB Cam"
},
{
"value": "LB Miller",
"name": "LB Miller"
},
{
"value": "LB Chlor 5",
"name": "LB + 5ug/mL Chlor"
},
{
"value": "SC Media",
"name": "SC Media"
},
{
"value": "YAPD",
"name": "YAPD Media"
},
{
"value": "rich_media",
"name": "Rich Media"
},
{
"value": "slow_media",
"name": "Slow Media"
},
{
"value": "high_osm_media",
"name": "High Osmolarity Media"
}
]
},
"inc_time_1": {
"type": "time",
"label": "Initial Outgrowth Time",
"description": "Select the incubation time, must be between 8 and 24.",
"default": "16:hour"
}
}
},
"recovery_info": {
"type": "group+",
"label": "Recovery Parameters",
"description": "Select culture and media volumes for recovery",
"inputs": {
"recovery_sample_vol": {
"type": "volume",
"default": "10:microliter",
"required": true,
"label": "Culture Volume"
},
"recovery_media_vol": {
"type": "volume",
"default": "1000:microliter",
"required": true,
"label": "Media Volume"
},
"recovery_media": {
"type": "choice",
"label": "Recovery Media",
"description": "Select media",
"default": "Modified M9 Media",
"options": [
{
"value": "Modified M9 Media",
"name": "M9 Media, Modified for Bacillus"
},
{
"value": "M9 Minimal Media",
"name": "M9 Minimal Media"
},
{
"value": "S750 Minimal Media",
"name": "S750 Minimal Media"
},
{
"value": "LB Cam",
"name": "LB Cam"
},
{
"value": "LB Miller",
"name": "LB Miller"
},
{
"value": "LB Chlor 5",
"name": "LB + 5ug/mL Chlor"
},
{
"value": "SC Media",
"name": "SC Media"
},
{
"value": "YAPD",
"name": "YAPD Media"
},
{
"value": "rich_media",
"name": "Rich Media"
},
{
"value": "slow_media",
"name": "Slow Media"
},
{
"value": "high_osm_media",
"name": "High Osmolarity Media"
}
]
},
"inc_time_2": {
"type": "time",
"label": "Recovery Incubation Time",
"description": "Select the incubation time, must be between 1 and 12.",
"default": "6.00:hour"
}
}
},
"induction_info": {
"type": "group",
"label": "Induction Parameters",
"description": "Select culture and media volumes for induction loops",
"inputs": {
"induction_time": {
"type": "group",
"label": "Induction Timing",
"description": "Specify total induction duration and at what interval to sample at.",
"inputs": {
"sample_points": {
"type": "string",
"label": "Sampling Times",
"description": "Specify a comma-separated list of integers, representing hours to sample at. A maximum of 6 can be specified.",
"default": "3,4,5,6"
},
"induction_plate_info": {
"type": "choice",
"label": "Induction Plate Info",
"description": "Specify whether to create a new induction plate each cycle or use existing plate.",
"default": "same-induction-plate",
"options": [
{
"name": "Create New Induction Plate Each Cycle",
"value": "new-induction-plate"
},
{
"name": "Sample From Same Induction Plate",
"value": "same-induction-plate"
}
]
}
}
},
"induction_reagents": {
"type": "group",
"description": "Specify base media and inducer to be used.",
"label": "Induction Reagents",
"inputs": {
"ind_cult_vol": {
"type": "volume",
"default": "10:microliter",
"required": true,
"label": "Culture Volume",
"description": "Specify volume of culture from preceding plate to transfer into each new induction plate."
},
"induction_base_media": {
"type": "choice",
"label": "Induction Base Media",
"description": "Select media",
"default": "Modified M9 Media",
"options": [
{
"value": "Modified M9 Media",
"name": "M9 Media, Modified for Bacillus"
},
{
"value": "M9 Minimal Media",
"name": "M9 Minimal Media"
},
{
"value": "S750 Minimal Media",
"name": "S750 Minimal Media"
},
{
"value": "LB Cam",
"name": "LB Cam"
},
{
"value": "LB Miller",
"name": "LB Miller"
},
{
"value": "LB Chlor 5",
"name": "LB + 5ug/mL Chlor"
},
{
"value": "SC Media",
"name": "SC Media"
},
{
"value": "YAPD",
"name": "YAPD Media"
},
{
"value": "rich_media",
"name": "Rich Media"
},
{
"value": "slow_media",
"name": "Slow Media"
},
{
"value": "high_osm_media",
"name": "High Osmolarity Media"
}
]
},
"media_vol": {
"type": "volume",
"default": "1000:microliter",
"required": true,
"label": "Media Volume",
"description": "Specify volume of media for induction plate."
},
"inducer": {
"type": "aliquot",
"label": "Select Inducer",
"description": "Choose inducer from inventory to use. Aliquot must have a `concentration` property associated with it."
},
"inducer_layout": {
"type": "group-choice",
"description": "Full Plate or Columnwise Layout",
"label": "Select Columns to Transfer Inducer",
"default": "full_plate",
"options": [
{
"name": "Full Plate",
"value": "full_plate",
"inputs": {
"inducer_conc": {
"type": "decimal",
"default": 10.0,
"required": true,
"label": "Inducer Concentration",
"description": "Concentration of inducer to use in all wells in a plate. Last column (12) will be without inducer."
},
"inducer_unit": {
"type": "choice",
"label": "Concentration Units",
"description": "Specify units of concentration for inducer",
"default": "millimolar",
"options": [
{
"value": "percent",
"name": "percent"
},
{
"value": "millimolar",
"name": "mM"
},
{
"value": "micromolar",
"name": "uM"
},
{
"value": "nanomolar",
"name": "nM"
},
{
"value": "nanogram/milliliter",
"name": "ng/mL"
},
{
"value": "microgram/milliliter",
"name": "ug/mL"
}
]
}
}
},
{
"name": "Select Columns",
"value": "select_cols",
"inputs": {
"inducer_unit": {
"type": "choice",
"label": "Concentration Units",
"description": "Specify units of concentration for inducer",
"default": "millimolar",
"options": [
{
"value": "percent",
"name": "percent"
},
{
"value": "millimolar",
"name": "mM"
},
{
"value": "micromolar",
"name": "uM"
},
{
"value": "nanomolar",
"name": "nM"
},
{
"value": "nanogram/milliliter",
"name": "ng/mL"
},
{
"value": "microgram/milliliter",
"name": "ug/mL"
}
]
},
"col_and_conc": {
"type": "group+",
"label": "Column and Concentration",
"inputs": {
"col_num": {
"type": "integer",
"label": "Column Number",
"description": "Specify column number for this ethanol concentration (1-indexed)",
"default": 4
},
"conc": {
"type": "decimal",
"label": "Concentration",
"description": "Specify concentration.",
"default": 15.0
}
}
}
}
}
]
}
}
},
"sampling_info": {
"type": "group",
"label": "Measurement Plate Parameters",
"description": "Specify volume, solvent, and stain for read and flow",
"inputs": {
"read_cult_vol": {
"type": "volume",
"default": "100:microliter",
"required": true,
"label": "Plate Read Culture Volume"
},
"read_solv_vol": {
"type": "volume",
"default": "0:microliter",
"required": true,
"label": "Plate Read Solvent Volume"
},
"read_solv": {
"type": "choice",
"label": "Plate Read Solvent",
"description": "Select Solvent to Dilute Cells in for Plate Read",
"default": "None",
"options": [
{
"value": "PBS 2 mg per mL Kan",
"name": "PBS w/ 2mg/mL Kan"
},
{
"value": "PBS",
"name": "PBS"
},
{
"value": "None",
"name": "None"
}
]
},
"flow_cult_vol": {
"type": "volume",
"default": "100:microliter",
"required": true,
"label": "Flow Plate Culture Volume"
},
"flow_solv_vol": {
"type": "volume",
"default": "0:microliter",
"required": true,
"label": "Flow Plate Solvent Volume"
},
"flow_solv": {
"type": "choice",
"label": "Flow Solvent",
"description": "Select Solvent to Resuspend Cells in for Flow",
"default": "None",
"options": [
{
"value": "PBS 2 mg per mL Kan",
"name": "PBS w/ 2mg/mL Kan"
},
{
"value": "PBS",
"name": "PBS"
},
{
"value": "None",
"name": "None"
}
]
},
"stain_before_flow": {
"type": "choice",
"label": "Stain Prior to Flow",
"description": "Choose whether to stain cells prior to flow",
"default": "None",
"options": [
{
"value": "None",
"name": "None"
},
{
"value": "Sytox",
"name": "Sytox"
}
]
}
}
}
}
},
"plate_reader_info": {
"type": "group",
"label": "Plate Reader Parameters",
"description": "Specify params for plate reading",
"inputs": {
"fluor_ex": {
"type": "length",
"label": "Fluorescence Excitation",
"description": "Ex",
"default": "588:nanometer"
},
"fluor_em": {
"type": "length",
"label": "Fluorescence Emission",
"description": "Em",
"default": "620:nanometer"
},
"gain": {
"type": "decimal",
"label": "Gain",
"description": "",
"default": 0.274
}
}
},
"run_info": {
"type": "group",
"label": "Additional Parameters",
"description": "Specify measurement options",
"inputs": {
"save_for_rnaseq": {
"type": "bool",
"label": "Save Plates for RNA Seq",
"description": "Choose whether to save a plate of cells for sequencing",
"default": false
},
"skip_first_flow": {
"type": "bool",
"label": "Skip First Induction Plate Flow",
"description": "Choose whether to omit first induction timepoint from flow",
"default": true
},
"only_endpoint_flow": {
"type": "bool",
"label": "Only Endpoint Flow",
"description": "Specifies to only run a single flow plate at end of induction period.",
"default": true
},
"read_each_recovery": {
"type": "bool",
"label": "Plate Read Each Recovery",
"description": "Choose whether to read a plate at the end of each recovery loop",
"default": true
},
"read_each_induction": {
"type": "bool",
"label": "Plate Read Each Induction",
"description": "Choose whether to read a plate at the end of each induction cycle.",
"default": true
}
}
},
"validate_samples": {
"type": "bool",
"default": true,
"label": "Validate Samples Contain ID",
"description": "Validates each source sample has a `sd2_common_name` or `sbh_uri` property."
},
"experimental_info": {
"type": "group",
"description": "",
"label": "Experimental Information",
"inputs": {
"experiment_id": {
"type": "string",
"label": "Experiment ID",
"default": " ",
"description": "Experimental Request ID to be associated with data generated."
},
"experiment_reference": {
"type": "string",
"label": "Experiment Reference",
"default": " "
},
"experiment_reference_url": {
"type": "string",
"label": "Experiment Reference URL",
"default": " "
}
}
}
}