The zip file contains model files and an experiment file. Unpack it in a directory and navigate with matlab to there. Use the 'matlab_execution_guide.m' for simulation and visualisation of the model. This file is written in matlab cell mode, so it is not a stand alone function.
Three models have been developed to test their capacity to reproduce the experimental data from Study: 'Controlled sigmaB induction in shake flask' with Assay: 'IPTG induction of sigmaB in BSA115'.
One model assumes a post-transcriptional inhibition (PTI) in the expression of the lacZ reporter gene. The PTI is either due to induced instability of lacZ mRNA or LacZ protein after activation of sigmaB. A hypothetical sigmaB dependent protein RegB is responsible for PTI. It is either a RNase or protease in this model.
One model assumes a transcription inhibitory effect on sigmaB dependent expression by a sigmaB dependent protein called RegB. This protein might bind to the sigma factor to decrease its efficacy in inducing transcription.
One model assumes that a protease called RegB acts specifically on sigmaB. This protease is also induced by sigmaB.
All models is based on mass-action (nearly so). Parameter for IPTG concentration is [100,200,1000], kbs, the expression parameter of Pspac-dependent sigmaB is fixed at 100. All other six parameters are estimated with two of the three experiments as training set (IPTG 0.1 and 0.2 mM) and one experiment as test set (IPTG 1mM). Parameter estimation is performed with SBToolbox2 using multiple rounds of particle swarm algorithm (pswarm).
Model image: No image specified
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Created: 16th Nov 2009 at 18:12
Last updated: 2nd May 2012 at 13:46
Last used: 17th Feb 2019 at 09:05