**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