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Circadian Clock Model Visualisation Tools

23 Oct 2006 (Updated 23 Oct 2006)

Code covered by the BSD License

Moving 2/3D plots and network diagram of an ode model of the circadian clock gene network

File Information
Description	This program presents the solution to an ode model of the circadian clock, published by Locke et al (2005) 'http://www.nature.com/msb/journal/v1/n1/full/msb4100018.html', in two different ways. A moving plot can show either time series or a limit cycle in 2D or 3D mode, with the user able to select which of the model outputs is represented on each axis. A dynamic moving network diagram of the model can also be displayed. In this case, the blocks representing the model species and the arrows representing species interactions vary in size periodically, corresponding to the varying species levels as the model oscillates. A corresponding time series plot appears alongside the network. GUI controls allow the user to alter model parameters during a simulation in order to immediately observe the effect on model behaviour. It is possible for the user to record their own avi files of simulations. This program should prove particulary useful in the teaching of circadian biology, but should also be useful for gaining a greater understanding of model dynamics and the effect of perturbations.
MATLAB release	MATLAB 7.0.1 (R14SP1)
Zip File Content
Other Files	locke_05b.prm, Settings.set, locke_05b.sts, ReadMe.txt, Default.env, Default.pv, Using the Network Tool.pdf, Using the Plot Tool.pdf, locke_05b_network.m, locke_05b_plot.m

Tags for This File
Everyone's Tags	biosimulation, circadian, clock, gene network, medical, ode, visualisation
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Tag Activity for this File
Tag	Applied By	Date/Time
medical	Paul Brown	22 Oct 2008 08:45:14
biosimulation	Paul Brown	22 Oct 2008 08:45:14
ode	Paul Brown	22 Oct 2008 08:45:14
visualisation	Paul Brown	22 Oct 2008 08:45:14
gene network	Paul Brown	22 Oct 2008 08:45:14
circadian	Paul Brown	22 Oct 2008 08:45:14
clock	Paul Brown	22 Oct 2008 08:45:14

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