BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/8823?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 293 KB
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"param": {
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}
},
{
"sample_id": "209",
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"age": "7",
"genetic_info": {
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},
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},
{
"sample_id": "210",
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},
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}
},
{
"sample_id": "211",
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"age": "7",
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}
},
{
"sample_id": "212",
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"param": {
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}
},
{
"sample_id": "213",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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},
"marker": "ELF4",
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"ignored": "false",
"param": {
"@name": "TAG",
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}
},
{
"sample_id": "214",
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},
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}
},
{
"sample_id": "215",
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},
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"param": {
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}
},
{
"sample_id": "216",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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"line": "M0013",
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},
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"experiment_cond_name": "12B:12Dx4 BBx3",
"ignored": "false",
"param": {
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}
}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/C:/Honours Project/DataDescription/models/luc/model/newluc_model.xsd",
"id": "060213H3",
"status": "finished",
"name": "060213H3: 12B-12Dx4 BBx3",
"purpose": "Test how the cryptochromes interact with the circadian clock (WT, lhy/cca1 double mutant and lhy/cca1/gi triple mutant)",
"description": "Plants entrained in 12L 12D white light\nExperimental conditions: 12L-12Dx4 LLx3 (Blue)",
"comments": "Imaging script started at ZT+7mins, therefore each light period cut short by 30mins (11.3L 12.3Dx4 LLx3)",
"provenance": {
"site": "Edinburgh",
"author": "Jamie Carrington",
"start_date": "2013-02-06"
},
"growth_condition": {
"name": "12L 12D",
"medium": "Agar 1.2% MS 0.5",
"incubation": "4 days at 4C",
"growth_space": "Sanyo",
"duration": "6",
"comment": "Plants transferred to imaging cabinet during 7th day",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "110",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
}
},
"experimental_condition": {
"name": "12B:12Dx4 BBx3",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7",
"comment": "Plants sprayed with luciferin on 7th day of growth conditions and then transferred to imaging cabinet",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "blue",
"intensity": "25",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "3",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
},
{
"start_day": "4",
"duration": "3",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 3",
"parameters": "Imaging script started 7 minutes after ZT\n55mins wait, 5mins lights off, 30mins capture"
},
"sample_preparation": {
"method": "Plants sprayed with luciferin on day 7 of growth conditions and transferred to imaging cabinet under experimental conditions"
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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"background": "Wasilewski (WS)",
"genotype": "Img Background",
"provenance": "Robust stock"
},
"marker": "Actin",
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"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "2",
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"age": "7",
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"line": "M0006",
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},
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}
},
{
"sample_id": "3",
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"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
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},
"marker": "TOC1",
"growth_cond_name": "12L 12D",
"experiment_cond_name": "12B:12Dx4 BBx3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "4",
"sample_type": "seedling",
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"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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"line": "M0006",
"provenance": "Robust stock"
},
"marker": "TOC1",
"growth_cond_name": "12L 12D",
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"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
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"growth_stage": "seedling",
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"param": {
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}
},
{
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}
},
{
"sample_id": "7",
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"age": "7",
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},
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"param": {
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}
},
{
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"param": {
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}
},
{
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},
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"experiment_cond_name": "12B:12Dx4 BBx3",
"param": {
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}
},
{
"sample_id": "10",
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"age": "7",
"genetic_info": {
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},
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"param": {
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"@value": "Luc"
}
},
{
"sample_id": "11",
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},
"marker": "TOC1",
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"param": {
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}
},
{
"sample_id": "12",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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},
"marker": "TOC1",
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"experiment_cond_name": "12B:12Dx4 BBx3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "13",
"sample_type": "seedling",
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},
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"param": {
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}
},
{
"sample_id": "14",
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},
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"param": {
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}
},
{
"sample_id": "15",
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"age": "7",
"genetic_info": {
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"provenance": "Robust stock"
},
"marker": "TOC1",
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"experiment_cond_name": "12B:12Dx4 BBx3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "16",
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},
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}
},
{
"sample_id": "17",
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},
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}
},
{
"sample_id": "18",
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"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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},
"marker": "TOC1",
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"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "19",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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},
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"param": {
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}
},
{
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"param": {
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}
},
{
"sample_id": "21",
"sample_type": "seedling",
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"age": "7",
"genetic_info": {
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},
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"param": {
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}
},
{
"sample_id": "22",
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},
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"param": {
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}
},
{
"sample_id": "23",
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},
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"param": {
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}
},
{
"sample_id": "24",
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},
"marker": "TOC1",
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"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "25",
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}
},
{
"sample_id": "26",
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},
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"experiment_cond_name": "12B:12Dx4 BBx3",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "27",
"sample_type": "seedling",
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"age": "7",
"genetic_info": {
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},
"marker": "TOC1",
"growth_cond_name": "12L 12D",
"experiment_cond_name": "12B:12Dx4 BBx3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "28",
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"age": "7",
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},
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"experiment_cond_name": "12B:12Dx4 BBx3",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "29",
"sample_type": "seedling",
"origin": "seedling",
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{
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},
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},
{
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},
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"param": {
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}
}
]
}
},
"biblio": {
"principal": "Andrew Millar",
"institution": "University of Edinburgh",
"author": [
"Jamie Carrington",
"Sarah Hodge"
]
}
}
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Created: 18th Jun 2026 at 13:45
Last updated: 18th Jun 2026 at 13:45
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Version 1 (earliest) Created 18th Jun 2026 at 13:45 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
Advanced Projects list for this Data file with search and filtering
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
Advanced Investigations list for this Data file with search and filtering
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
Advanced Studies list for this Data file with search and filtering
Changing planetary rotation rescues the biological clock mutant lhy cca1 of Arabidopsis thaliana
Millar et al. (2015)
DOI: 10.1101/034629
Submitter: Daniel Thedie
Investigation: Millar Andrew
Assays: 030413H3: 12B-12Dx4 BB3, 060213H3: 12B-12Dx4 BBx3, 060313H1: 5L15Dx4 LLx3 (T-20), 060313H2: 12F-12Dx4 FFx3, 130212H1: 5L15Dx4 LLx3 (T-20), 130213H3: 12R-12Dx4 RRx3, 130313H1: 14L14D x 4 LL x 3 (T-28), 130313H2: 12F-12Dx4 FFx3, 200213H1: 15L5D x4 LL x3 (T-20), 200213H3: 12B-12Dx4 BB3, 200313H2: 7L 21Dx4 LLx3 (T-28), 200313H3: 12L-12Dx4 LLx3, 270213H1: 10L10Dx4 LLx3 (T-20), 270213H3: 12R-12Dx4 RRx3, 270313H1: 21L 7Dx4 LLx3 (T-28), 270313H3: 12L-12Dx4 LLx3, 290313H2: 15L 5Dx4 LLx3, AT0043: 4x 12:12-DD, AT0048 4x 18:6-DD, AT0078: 4x6:18-DD, AT0080: 4x18:6-DD
Advanced Assays list for this Data file with search and filtering
060213H3: 12B-12Dx4 BBx3
| Property | Value |
|---|---|
| BioDare ID | 13615365050841 |
| Author | Jamie Carrington |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Plants entrained in 12L 12D white light Experimental conditions: 12L-12Dx4 LLx3 (Blue)
Purpose
Test how the cryptochromes interact with the circadian clock (WT, lhy/cca1 double mutant and lhy/cca1/gi triple mutant)
Comments
Imaging script started at ZT+7mins, therefore ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Millar Andrew
Study: Millar et al. (2015)
