Projects per year
Abstract
by Zielinski, Moore, Troup, Beaton, Adams, Halliday, Millar.
2016 overview: BioDare returns immediate value to any user who uploads data, directly justifying the time that they spend in describing and organising their data. This makes BioDare unusual among biological data management systems. It is entirely typical that this immediate value is highly targeted, to users who require specialised analysis of rhythmic data. In addition, it facilitates data sharing and public dissemination, which give value in the much longer term.
2011 summary: BioDare, was developed to store, share and analyse rhythmic time series data. Currently it stores more than 70000 time series with over 9 million time points. The repository supports the description and processing of data from various experimental techniques, as well as literature data. It allows searching and aggregation of data from independent experiments and subsequent visualisation of not only original data but also processed data (averaged, normalized, detrended). BioDare also performs data analysis by executing period analysis routines via web services, including FFT-NLLS, mFourfit and the ROBuST spectrum resampling method. BioDare was designed initially to support the ROBuST project [opening to ROBuST users in 2009], and was extended for SynthSys and TiMet projects. It is highly relevant to other similar research, worldwide. The data infrastructure team is following a staged process to open the data repository and associated web services for analysis of rhythmic data to external users. Six potential beta-testing locations were recruited and visited in Jan-Feb 2011. Requirements specified by these betatesters have been progressively included in the system, in some cases over multiple rounds of interaction. Further beta-test users were recruited in the summer of 2011. We expect to open the system to additional users in the Spring of 2012, and to make the system public within the year.
2016 update.
BioDare was made public as proposed and additional external users were recruited at scientific conferences in 2012-2014, including the UK circadian clock clubs, Gordon conferences on Chronobiology and GARNET data management workshops.
BioDare's data analysis was transformed to support public use. First SynthSys, then in 2015 the UK Centre for Mammalian Synthetic Biology provided upgraded computer servers. Both the original analysis methods and four further rhythm analysis methods were refactored to native Java, greatly enhancing compute speed and stability, in part through a collaborative project with Edinburgh's supercomputing centre EPCC (see Zielinski et al. 2014 for detailed method evaluation and user guidance).
The detailed experimental metadata required from users now supports a very powerful search method, which aggregates data from multiple labs and experiments.
Data visualisation is more flexible, with many secondary data series (normalised, de-trended, averages, error bars, etc) pre-computed for rapid graphical display.
Any data displayed can be downloaded as a numerical spreadsheet, to reproduce exactly the online graphs.
As of February 2015, BioDare held over 41 million data points, in 232,844 timeseries, from 2,344 experiments. The 10 largest user labs were from UK, USA, Chile and Sweden. The largest single user lab by experiments works on circadian clocks in mouse cell and tissue cultures, at MRC LMB, Cambridge UK. The largest user lab by timeseries is from the original ROBuST project, working on plant circadian clocks. (see Flis et al. 2015).
Partial cost recovery started in 2014: heavy users of data analysis functions pay an annual subscription. To encourage data sharing, users who release their BioDare data for public dissemination gain "analysis credits", which can fully support their usage costs.
Original language | English |
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Type | BioDare Data Repository |
Publication status | Published - 2011 |
Fingerprint
Dive into the research topics of 'The Biodare Data Repository'. Together they form a unique fingerprint.Projects
- 4 Finished
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SynthSys-Mammalian: Edinburgh Mammalian Synthetic Biology Research Centre
Rosser, S. (Principal Investigator), Bird, A. (Co-investigator), Cai, Y. (Co-investigator), Earnshaw, B. (Co-investigator), Millar, A. (Co-investigator), Molina, N. (Co-investigator), Pilizota, T. (Co-investigator), Swain, P. (Co-investigator) & Waites, W. (Researcher)
14/11/14 → 31/03/22
Project: Research
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TiMet: Linking the clock to metabolism
Millar, A. (Principal Investigator)
1/03/10 → 28/02/15
Project: Research
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Regulation of biological signalling by temperature (ROBUST)
Halliday, K. (Principal Investigator), Gilmore, S. (Co-investigator) & Millar, A. (Co-investigator)
14/04/08 → 13/10/13
Project: Research
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Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
Flis, A., Fernández, A. P., Zielinski, T., Mengin, V., Sulpice, R., Stratford, K., Hume, A., Pokhilko, A., Southern, M. M., Seaton, D. D., McWatters, H. G., Stitt, M., Halliday, K. J. & Millar, A. J., 14 Oct 2015, In: Open Biology. 5, 10, 150042.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
Light and circadian regulation of clock components aids flexible responses to environmental signals
Dixon, L. E., Hodge, S. K., van Ooijen, G., Troein, C., Akman, O. E. & Millar, A. J., 20 May 2014, In: New Phytologist.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure
Moore, A., Zielinski, T. & Millar, A., 8 Apr 2014, (E-pub ahead of print) Plant Circadian Networks: Methods and Protocols. Staiger, D. (ed.). Springer, Vol. 1158. p. 13-44 32 p. (Methods in Molecular Biology; vol. 1158).Research output: Chapter in Book/Report/Conference proceeding › Chapter
Datasets
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Data, Code and Models for Flis et al. RS Open Biology 2015
Millar, A. (Creator), Zielinski, T. (Data Manager), Flis, A. (Creator), Mengin, V. (Creator), Stitt, M. (Creator), Fernández, A. P. (Creator), McWatters, H. G. (Creator) & Halliday, K. (Creator), The Royal Society, 2015
https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12820611467827 and 30 more links, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12820610743262, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12820611319996, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12820611188065, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12820611587928, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12820606741450, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12820610913763, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13228354371807, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12962296599986, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=12962294335805, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=2841, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=2842, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=2843 , https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13228298288040, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13227619871305, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13228357183121, http://sourceforge.net/projects/biodare/, http://www.biodare.ed.ac.uk, http://sourceforge.net/projects/sbsi/, http://www.sbsi.ed.ac.uk, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_71&version=1, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_71&version=2, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_1041&version=1, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_1042&version=1, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_1043&version=1, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_1044&version=1, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13227622661196, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13228357183121, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=3488, https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=3492, http://www.plasmo.ed.ac.uk/plasmo/models/model.shtml?accession=PLM_1045&version=1 (show fewer)
Dataset