LiNA -- A graphical MATLAB tool for analyzing intrinsic noise in biochemical reaction networks

LiNA provides a simple, but easy-to-use, GUI from within MATLAB running under R2010b or higher. In its current form it comprises the following features:

• calculates the variance-covariance matrix for mass-action networks under steady state conditions based on the linear noise approximation of the chemical master equation
• automatically detects and takes care of conservation relations in the network
• parameter scans for the mean values and stochastic quantities such as the Fano factor, the coefficient of variation and correlation coefficients
• allows to define parameter combinations as new parameters (e.g. to analyze the Fano factor as a function of a dissociation constant rather than separately for forward and backward rates)
• allows to calculate stochastic quantities along different stable branches in bistable systems
• easy export of plots as MATLAB figure for further processing

News

• 12/2014: New version of LiNA (v1.1) has been released which contains minor bug fixes.
  (Thanks to Qurat-Ul-Ain Azim for his bug report.)

Downloads (03/12/2014)

• LiNA v1.1 (changelog)
• Tutorial

Credits

LiNA has been developed by Bastian Hagel, Axel von Kamp and Ronny Straube.

Installation

Unzip the Lina_v1.1.zip archive to your HOME directory which will create the directory LiNA_v1.1
Startup MATLAB and change to the LiNA directory. Type 'startlina' at the console.
Note that LiNA requires the 'Symbolic Toolbox' of MATLAB.

License Conditions

LiNA is free software, i.e. it can be redistributed and/or modified under the terms
of the GNU General Public License as published by the Free Software Foundation.
For a detailed version of the License conditions, please see http://www.gnu.org/licenses/.

Comments, suggestions and bug reports can be sent to lina@mpi-magdeburg.mpg.de.