BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/9092?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 232 KB
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"supervisor": "andrew",
"allowedToRead": [
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"hasTSData": "true",
"desc": {
"experiment_type": "Luciferase exp",
"id": "2629",
"status": "finished",
"name": "080115H1",
"purpose": "Comparison of Light:Shady night versus standard lights ON/OFF to dissect the role of photoreceptors and photosynthesis in the circadian clock.",
"description": "Plants entrained in 12L 12D white light.\n\nExperimental conditions (Red and Blue)\n12 hours light (90umolm-2s-1): 12 hours shady dark (6 umolm-2s-1) x4, constant light x3.\nDawn is at ZT0 and dusk (shady dark) is at ZT12.",
"comments": "Pedro is not able to record changes in intensity during an experiment, so please refer to the description & experimental conditions comment for true experimental conditions.\n\nPartner Experiment: 080115H2",
"provenance": {
"site": "Edinburgh",
"author": "Yvette Wilson",
"start_date": "2014-04-23"
},
"growth_condition": {
"name": "12L:12D",
"medium": "Agar 1.2% MS 0.5",
"incubation": "7 days at 4C",
"growth_space": "Percival",
"duration": "7.0",
"comment": "Plants were entrained at light intensity 90 umolm-2s-1 to correspond to the light intensity of the experiment.",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "7",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "7",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
"light_conditions": {
"label": "W: LD 12:00:12:00",
"light_channel": {
"spectrum": "white",
"intensity": "90",
"source": "tube",
"env_conditions": {
"type": "diurnal_light",
"label": "LD 12:00:12:00",
"duration": "7",
"env_day": {
"type": "diurnal_light",
"label": "diurnal light",
"duration": "7",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "12:00"
}
}
}
}
}
},
"experimental_condition": {
"name": "12L:12ShD x4 LL x3",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7.0",
"comment": "12 hours of bright light (90 umolm-2s-2) followed by 12 hours of 'shady dark' (6 umolm-2s-2) for four days and then 3 days of continuous light.\n\nThe first dawn starts at ZT0\n\nThe light intensities are controlled by the arduino.\n\nAt max light intensity red = 51 umolm-2s-1 and blue light intensity is 32 umol-2s-1.\n\nplants were transferred to experimental condiditons at ZT3",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "7",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "7",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
"light_conditions": {
"label": "B+R: 4*LD 12:00:12:00; 3*LL",
"light_channel": [
{
"spectrum": "blue",
"intensity": "32",
"source": "LED",
"env_conditions": {
"type": "light_complex",
"label": "4*LD 12:00:12:00; 3*LL",
"duration": "7",
"env_day": [
{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "4",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "12:00"
}
},
{
"type": "constant_light",
"label": "constant light",
"duration": "3",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "24:00"
}
}
]
}
},
{
"spectrum": "red",
"intensity": "51",
"source": "LED",
"env_conditions": {
"type": "light_complex",
"label": "4*LD 12:00:12:00; 3*LL",
"duration": "7",
"env_day": [
{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "4",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "12:00"
}
},
{
"type": "constant_light",
"label": "constant light",
"duration": "3",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "24:00"
}
}
]
}
}
]
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 1",
"parameters": "Imaging script started 1 hr 25 minutes after ZT0\n55mins wait, 5mins lights off, 30mins capture",
"description": "Seedlings were treated on 7th day with Luciferin. They were then transferred Experimental conditions. Imaging was started on d8."
},
"sample_preparation": {
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},
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{
"sample_id": "1",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Img Background",
"line": "unknown",
"provenance": "Robust stock"
},
"marker": "Actin",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
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"age": "7",
"genetic_info": {
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"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0007",
"provenance": "Robust stock"
},
"marker": "CCA1",
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"@value": "Luc"
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},
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},
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"sample_id": "140",
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},
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}
},
{
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}
},
{
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}
},
{
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},
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}
},
{
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},
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}
},
{
"sample_id": "146",
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},
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}
},
{
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},
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}
},
{
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}
},
{
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},
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}
},
{
"sample_id": "151",
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},
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}
},
{
"sample_id": "152",
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}
},
{
"sample_id": "153",
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"growth_stage": "seedling",
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},
"marker": "GI",
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"param": {
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}
},
{
"sample_id": "154",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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},
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"param": {
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}
},
{
"sample_id": "155",
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"age": "7",
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},
"marker": "GI",
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"param": {
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"@value": "Luc"
}
},
{
"sample_id": "156",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
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},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "157",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
"marker": "GI",
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"ignored": "false",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "158",
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"origin": "seedling",
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"age": "7",
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"species": "Arabidopsis thaliana",
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},
"marker": "GI",
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"ignored": "false",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "159",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
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"ignored": "false",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "160",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
"marker": "GI",
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"ignored": "false",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "161",
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"origin": "seedling",
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"age": "7",
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"species": "Arabidopsis thaliana",
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},
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"param": {
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"@value": "Luc"
}
},
{
"sample_id": "162",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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"genotype": "cca1;lhy",
"line": "M0064",
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},
"marker": "GI",
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"ignored": "false",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "163",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
"marker": "GI",
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"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "164",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "165",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
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"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "166",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
"marker": "GI",
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"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "167",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
"marker": "GI",
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"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "168",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
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"ignored": "false",
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"@value": "Luc"
}
},
{
"sample_id": "169",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
"marker": "GI",
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"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "170",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/W:/communal/DataDescription/models/luc/model/newluc_model.xsd",
"id": "will be updated by the system",
"status": "finished",
"name": "080115H1",
"purpose": "Comparison of Light:Shady night versus standard lights ON/OFF to dissect the role of photoreceptors and photosynthesis in the circadian clock.",
"description": "Plants entrained in 12L 12D white light.\n\nExperimental conditions (Red and Blue)\n12 hours light (90umolm-2s-1): 12 hours shady dark (6 umolm-2s-1) x4, constant light x3.\nDawn is at ZT0 and dusk (shady dark) is at ZT12.",
"comments": "Pedro is not able to record changes in intensity during an experiment, so please refer to the description & experimental conditions comment for true experimental conditions.\n\nPartner Experiment: 080115H2",
"provenance": {
"site": "Edinburgh",
"author": "Yvette Wilson",
"start_date": "2014-04-23"
},
"growth_condition": {
"name": "12L:12D",
"medium": "Agar 1.2% MS 0.5",
"incubation": "7 days at 4C",
"growth_space": "Percival",
"duration": "7",
"comment": "Plants were entrained at light intensity 90 umolm-2s-1 to correspond to the light intensity of the experiment.",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "90",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
}
},
"experimental_condition": {
"name": "12L:12ShD x4 LL x3",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7",
"comment": "12 hours of bright light (90 umolm-2s-2) followed by 12 hours of 'shady dark' (6 umolm-2s-2) for four days and then 3 days of continuous light.\n\nThe first dawn starts at ZT0\n\nThe light intensities are controlled by the arduino.\n\nAt max light intensity red = 51 umolm-2s-1 and blue light intensity is 32 umol-2s-1.\n\nplants were transferred to experimental condiditons at ZT3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": [
{
"spectrum": "blue",
"intensity": "32",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "4",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
},
{
"start_day": "5",
"duration": "3",
"constant_light": {
"cycle_length": "24"
}
}
]
}
},
{
"spectrum": "red",
"intensity": "51",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "4",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
},
{
"start_day": "5",
"duration": "3",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
]
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 1",
"parameters": "Imaging script started 1 hr 25 minutes after ZT0\n55mins wait, 5mins lights off, 30mins capture",
"description": "Seedlings were treated on 7th day with Luciferin. They were then transferred Experimental conditions. Imaging was started on d8."
},
"sample_preparation": {
"method": "Plants sprayed with luciferin on day 6 of growth conditions and transferred to experimental conditions. Imaging was started on day 7."
},
"samples": {
"sample": [
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"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "167",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "168",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "169",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "170",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "M0064",
"provenance": "Robust stock"
},
"marker": "GI",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12ShD x4 LL x3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
}
]
}
},
"biblio": {}
}
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Created: 18th Jun 2026 at 15:13
Last updated: 18th Jun 2026 at 15:13
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Version 1 (earliest) Created 18th Jun 2026 at 15:13 by Daniel Thedie
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https://orcid.org/0000-0002-1352-7245Research Software Engineer in the Biological Research Data Management team (BioRDM) at the University of Edinburgh.
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The Centre for Engineering Biology is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2023 as the successor to SynthSys, itself founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE). CSBE was newly founded in 2007. The Centre for Engineering Biology is a hub organisation that links across multiple, major funding awards, including an Engineering Biology Mission Hub, and EPSRC C-loop.
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository, BioDare1
Web page: https://biology.ed.ac.uk/centre-engineering-biology
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Experiment data previously hosted on the original version of BioDare (biodare.ed.ac.uk).
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: Not specified
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Collection of experiments created by Millar Andrew on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Millar et al. (2015), TiMet double dawns, TiMet shady nights
Assays: 010514H1, 010514H2, 030413H3: 12B-12Dx4 BB3, 030714H1, 030714H2, 060213H3: 12B-12Dx4 BBx3, 060313H1: 5L15Dx4 LLx3 (T-20), 060313H2: 12F-12Dx4 FFx3, 070814H1, 070814H2, 080115H1, 080115H2, 100414H1, 100414H2, 130212H1: 5L15Dx4 LLx3 (T-20), 130213H3: 12R-12Dx4 RRx3, 130313H1: 14L14D x 4 LL x 3 (T-28), 130313H2: 12F-12Dx4 FFx3, 140515H1, 140515H2, 140814H1, 140814H2, 190614H1, 190614H2, 200213H1: 15L5D x4 LL x3 (T-20), 200213H3: 12B-12Dx4 BB3, 200313H2: 7L 21Dx4 LLx3 (T-28), 200313H3: 12L-12Dx4 LLx3, 210814H1, 210814H2, 240414H1, 240414H2, 270213H1: 10L10Dx4 LLx3 (T-20), 270213H3: 12R-12Dx4 RRx3, 270313H1: 21L 7Dx4 LLx3 (T-28), 270313H3: 12L-12Dx4 LLx3, 280814H1, 280814H2, 290313H2: 15L 5Dx4 LLx3, AT0043: 4x 12:12-DD, AT0048 4x 18:6-DD, AT0078: 4x6:18-DD, AT0080: 4x18:6-DD
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080115H1
| Property | Value |
|---|---|
| BioDare ID | 2629 |
| Author | Yvette Wilson |
| Institution | |
| License |
Description
Plants entrained in 12L 12D white light.
Experimental conditions (Red and Blue) 12 hours light (90umolm-2s-1): 12 hours shady dark (6 umolm-2s-1) x4, constant light x3. Dawn is at ZT0 and dusk (shady dark) is at ZT12.
Purpose
Comparison of Light:Shady night versus standard lights ON/OFF to dissect the role of photoreceptors and ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Millar Andrew
Study: TiMet shady nights
