Models

An ODE model of the gene regulation network governing sporulation initiation in Bacillus subtilis to be run in Matlab.

The network incorporates four sporulation-related signals: nutrient supply, DNA damage, the products of the competence genes and the bacterial population size.

Run execute_bacillus_sporulation_initiation.m to simulate the model. This file also contains the signal-related parameters which can be altered to investigate the effect of competing signals.

Some results for this model ...

The zip file contains two executable Matlab functions.

File named 'fnct_gen_tfcompmod.m' generates a Simbiology model based on the following interactions: R + X <-> RX -> R + X + Px R + Y <-> RY -> R + Y + Py R + Z <-> RZ -> R + Z + Pz Y + Pz -> Pz Px -> Py -> Pz ->

We assume much higher reaction speeds of sigma factor RNApol binding/unbinding compared to protein expression. Protein expression can therefore be represented by Michaelis-Menten like kinetic ...

only lacZ synthesis reduced by inhibitor in BSA115

The model file represents the expression of beta-gal from a sigB dependent promoter after sigb production was stimulated by IPTG. The model is based on an assumption that a hypothetical protein degrates the sigb factor.

This is a JWS model of the successful model for data representation. It realises regulation by a hypothetical sigB dependent protein that degrades beta-Gal.

The model represents a hypothetical situation in which an anti-sigmafactor reduces sigB efficacy.

The zip folder contains files that allow simulation of stressosome dynamics. The models are based on a cellular automaton approach. Each protein of RsbR and RsbS is located in the crystal structure of the stressosome. The proteins can be phosphorylated or not and these states determine the future of neighbouring proteins. To simulate the model open the file 'liebal_stressosome-model_12_workflow-matlab.m' in Matlab. It is written in the cell-model, put the cursor into a cell that you wish to ...

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 ...

The zip-folder contains files for execution in matlab that allow for the simulation of stressosome dynamics and reproduction of published data on the stressosome. The important file for execution is 'liebal_stressosome-model_12_workflow-matlab.m'.

The model can simulate the the dynamics of sigB dependent transcription at the transition to starvation. It is was developed along the comic in 'sigB-activation-comic_vol1'. Parameters were partly taken from Delumeau et al., 2002, J. Bact. and Igoshin et al., 2007, JMB. Parameter estimation was performed using experimental data from '0804_shake-flask'. Use the .m-file with matlab as: % reading initial conditions from the file: inic = sigb_model_liebal;

% performing the simulation: [t,y] = ...