:Intrinsic Noise Analyzer
{{lowercase title}}
{{one source|date=July 2012}}
{{Infobox software
| name = intrinsic Noise Analyzer
| logo =
| screenshot =
| caption =
| collapsible =
| author =
| developer =
| released = {{Start date and age|2012|04|12}}
| latest release version = 0.4.3
| latest release date = {{Start date and age|2014|03|13}}
| programming language = C++
| operating system = Linux, macOS and Microsoft Windows
| platform = Qt
| size =
| language =
| status =
| genre =
| license = GPL
| website = {{URL|http://www.ina.bio.ed.ac.uk}}
}}
Within bioinformatics, intrinsic Noise Analyzer (iNA) is an open source software for studying reaction kinetics in living cells.{{cite journal |vauthors= Thomas P, Matuschek H, Grima R |year= 2012 |title=intrinsic Noise Analyzer: A Software Package for the Exploration of Stochastic Biochemical Kinetics Using the System Size Expansion |journal=PLOS ONE |volume=7 |pages=e38518 |doi=10.1371/journal.pone.0038518 |issue= 6 |pmid= 22723865 |pmc= 3373587 |editor1-last= Peccoud |editor1-first= Jean|bibcode=2012PLoSO...738518T |doi-access= free }} 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.{{cite web |url=http://www.softpedia.com/get/Science-CAD/Intrinsic-Noise-Analyzer.shtml |title=Softpedia article |accessdate=25 Jan 2013 }}
Background
Under well-mixed conditions, the concentrations in living cells are often modeled by a set of deterministic reaction rate equations. 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.{{cite journal |author= Gillespie, D.T. |year= 1992 |title=A rigorous derivation of the chemical master equation |journal=Physica A: Statistical Mechanics and Its Applications |volume=188 |pages=404–425 |doi=10.1016/0378-4371(92)90283-V |issue= 1|bibcode=1992PhyA..188..404G |citeseerx= 10.1.1.159.5220 }} The latter can be easily simulated by means of Monte Carlo methods such as the stochastic simulation algorithm.{{cite journal |author= Gillespie, D.T. |year= 1976 |title=A general method for numerically simulating the stochastic time evolution of coupled chemical reactions |journal=Journal of Computational Physics |volume=22 |pages=403–434 |issue= 4 |bibcode= 1976JCoPh..22..403G |doi= 10.1016/0021-9991(76)90041-3}} 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 of the Chemical Master Equation, a systematic analytical approximation method.
References
{{reflist}}
External links
- [https://web.archive.org/web/20140301081129/http://www.ina.bio.ed.ac.uk/ iNA home page]
- [https://doi.org/10.6084/m9.figshare.8153813 iNA (Windows)]
- [https://doi.org/10.6084/m9.figshare.8280926 iNA (MacOSX)]