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time_series_schema.json
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time_series_schema.json
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{
"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": " "
}
}
}
}