BioDare1

Overview

Experimental data that were previously hosted on the original version of BioDare (biodare.ed.ac.uk), which opened in 2009, please see https://doi.org/10.1007/978-1-4939-0700-7_2. BioDare was designed as a repository of rhythmic biological data, especially for 24-hour circadian rhythms, with specialised analytical routines for period, phase and amplitude estimation on each data timeseries. Most rhythms tested were measured using gene expression, either directly as RNA levels, or indirectly using luciferase or other reporter genes.

Here call the resource BioDare1 to emphasise the distinction from its successor, BioDare2 (https://biodare2.ed.ac.uk), which opened in 2017, please see https://doi.org/10.1007/978-1-0716-1912-4_2. The basic unit in BioDare was an 'Experiment', each of which usually had an XML metadata file (originally prepared in a customised standalone application, Pedro) and a spreadsheet of numerical data. The data were also read into an internal database; for experiments that were migrated to BioDare2 in 2017, only the internal data migrated so the BioDare2 versions have no file attachments.

Mapping to the SEEK ISA hierarchy

Investigation - the name of the creator of the BioDare experiment. Study - a publication from that researcher, as first author surname (year); or 'unpublished' for all of that author's other experiments. Assay - an experiment name from BioDare1

Files attached to each Assay

All the files from the BioDare1 experiment are then attached to the Assay, along with

  • a Readme file in markdown format, created from the subset of metadata that were displayed in BioDare1
  • a Metadata file with the experimental conditions from the Pedro metadata file
  • a Samples file with the biological samples from the Pedro metadata file

Other metadata

Dr. Daniel Thedie performed the migration in 2026 and is identified as the Submitter of each object in FDHub.

Programme: Centre for Engineering Biology (prev. SynthSys)

SEEK ID: https://fairdomhub.org/projects/534

Public web page: https://biodare2.ed.ac.uk

Organisms: Arabidopsis thaliana, Neurospora crassa

FAIRDOM PALs: No PALs for this Project

Project start date: 7th Jul 2006

Project end date: 21st Dec 2017

Annotated Properties
Topic annotations
Scientific disciplines
Biochemistry, Genetics and Molecular Biology
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