presentation/251 1st BioSim Conference - Presentation

1st BioSim Conference


The Development of Data Analysis and Simulation Software Tools for the Circadian Biology Community

Author: Paul Brown, Warwick Systems Biology Centre, Coventry House, University of Warwick, Coventry, CV4 7AL, UK.

Names and affiliation of other authors:
Isabelle A. Carré, Department of Biological Sciences, University of Warwick, Coventry, CV4 7AL, UK
David A. Rand, Warwick Systems Biology Centre, Coventry House, University of Warwick, Coventry, CV4 7AL, UK
Andrew J. Millar, School of Biological Sciences, Daniel Rutherford Building, Kings Buildings, University of Edinburgh, EH9 3JH, UK

Oral or poster: Poster

Modelling is invaluable for studying the complex gene networks comprising the circadian system, but it is under exploited by experimentalists due to difficulties in modifying published models to suit a particular research interest. Thus we have developed Circadian Modelling, a user-friendly modelling interface. Parameters are presented in a biologically relevant way, and mutations, environmental regimes and experimental protocols can be easily simulated. Results are presented in an Excel workbook. Users can fine-tune simulations to suit their own interests.
We have developed a network visualisation tool for Matlab. Users can view a moving image of an oscillating network representing changing RNA and protein levels and interactions, and dynamically alter model parameters to immediately observe the effect on the network.
We have also developed Biological Rhythms Analysis Software System (BRASS), an Excel workbook for analysis of circadian experimental data. BRASS can import data from a range of acquisition systems. Data is then sorted and analysis of period, phase and amplitude performed. BRASS contains tools for detrending and plotting of time series data, and the plotting of statistics from the analysis.
Our ultimate aim is to link our simulation and analysis software so simulated and experimental data can be analysed together and compared. This will both validate models and make experimental predictions.
Our software is available from

1st BioSim Conference. October 6th to October 8th, 2005. Palma de Mallorca, Spain.