Online Period Estimation and Determination of Rhythmicity in Circadian Data, Using the BioDare Data Infrastructure
Circadian biology is a major area of research in many species. One of the key objectives of data analysis in this field is to quantify the rhythmic properties of the experimental data. Standalone software such as our earlier Biological Rhythm Analysis Software Suite (BRASS) is widely used. Different parts of the community have settled on different software packages, sometimes for historical reasons. Recent advances in experimental techniques and available computing power have led to an almost exponential growth in the size of the experimental data sets being generated. This, together with the trend towards multinational, multidisciplinary projects and public data dissemination, has led to a requirement to be able to store and share these large data sets. BioDare (Biological Data repository) is an online system which encompasses data storage, data sharing, and processing and analysis. This chapter outlines the description of an experiment for BioDare, how to upload and share the experiment and associated data, and how to process and analyze the data. Functions of BRASS that are not supported in BioDare are also briefly summarized.
Key wordsCircadian clock Period estimation Data repository Data sharing
We are grateful for much helpful discussion, feedback and programming input from Drs. Martin Beaton and Eilidh Troup (Edinburgh), Paul Brown (Warwick), from members of our collaborating projects listed below, and from the community via the UK Circadian Clock Club. BioDare development was funded by the BBSRC and EPSRC systems biology projects ROBuST (award BB/F005237) and SynthSys (award BB/D019621), and by the EU FP7 Integrated Project TiMet (award 245143).
- 5.Bujdoso N, Davis SJ (2013) Mathematical modelling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana. Frontiers Plant Syst Biol 4:2013.00003Google Scholar
- 10.Gould PD et al (2013) Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. Mol Syst Biol 9:650Google Scholar
- 20.Costa MJ et al (2013) Inference on periodicity of circadian time series. Biostatistics 2013:1–15Google Scholar
- 21.Zielinski T, Moore A et al (2014) Strengths and limitations of period estimation methods for circadian data. PLoS ONE (in press)Google Scholar