Within

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

, intrinsic Noise Analyzer (iNA) is an open source software for studying reaction kinetics in living cells. The software analyzes mathematical models of intracellular reaction kinetics such as gene expression, regulatory networks or signaling pathways to quantify concentration fluctuations due to the random nature of chemical reactions.

Background

Under well-mixed conditions, the concentrations in living cells are often modeled by a set of deterministic reaction

rate equation In chemistry, the rate law or rate equation for a reaction is an equation that links the initial or forward reaction rate with the concentrations or pressures of the reactants and constant parameters (normally rate coefficients and partial reacti ...

s. This approach frequently becomes inaccurate when some molecular species are present in low molecule numbers per cell because of the randomness inherent in chemical reaction kinetics. This randomness leads to fluctuations in intracellular molecule numbers and hence to cell-to-cell variability. The more accurate stochastic description of these systems is given by the Chemical Master Equation. The latter can be easily simulated by means of Monte Carlo methods such as the stochastic simulation algorithm. This method, however, often becomes computationally inefficient due to the large amount of sampling needed for accurate statistics. iNA provides a more efficient way to obtain the desired statistics via the

system size expansion The system size expansion, also known as van Kampen's expansion or the Ω-expansion, is a technique pioneered by Nico van Kampenvan Kampen, N. G. (2007) "Stochastic Processes in Physics and Chemistry", North-Holland Personal Library used in the anal ...

of the Chemical Master Equation, a systematic analytical approximation method.

References

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External links

iNA home page

iNA (Windows)

iNA (MacOSX)
Bioinformatics software