Supplementary MATLAB Files

Alexander V. Ratushny, Ilya Shmulevich, John D. Aitchison

"Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues"

This page provides a link to the supplementary MATLAB files for the Ratushny et al. 2010 manuscript on the generalized time-frequency analysis (TFA) of the OLE, GAL and LPS-induced network models. The files are provided in a ZIP archive, along with a text file that describes how to run models and TFA scripts (readme.txt).

tfaMatlabCodes.zip (1538 kb)

Generation of random stimuli

Random stimuli were generated using precalcInputSignals MATLAB function available in the 'inputs' folder of the tfaMatlabCodes package.

Mathematical models

Kinetic model of the OLE network

OLE network model responses (the target gene expression profiles) to random noisy stimuli were calculated using oleModelMulpRun MATLAB function available in the 'oleModel' folder of the tfaMatlabCodes package.

Kinetic model of the GAL network

GAL network model responses (the target gene expression profiles) to random noisy stimuli were calculated using galModelMulpRun MATLAB function available in the 'galModel' folder of the tfaMatlabCodes package.

Kinetic model of the LPS-induced regulatory network

LPS-induced network model responses (the target gene expression profiles) to random noisy stimuli were calculated using cebpdModelMulpRun MATLAB function available in the 'cebpdModel' folder of the tfaMatlabCodes package.

Generalized time-frequency analysis

The responsiveness and noise suppression statistics were calculated using the getHMforAllVarPrms MATLAB function available in the 'tfa' folder of the tfaMatlabCodes package.


Last modified: April 2011