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MP-GeneticSynth: inferring biological network regulations from time series.
- Source :
-
Bioinformatics . Mar2015, Vol. 31 Issue 5, p785-787. 3p. - Publication Year :
- 2015
-
Abstract
- Summary: MP-GeneticSynth is a Java tool for discovering the logic and regulation mechanisms responsible for observed biological dynamics in terms of finite difference recurrent equations. The software makes use of: (i) metabolic P systems as a modeling framework, (ii) an evolutionary approach to discover flux regulation functions as linear combinations of given primitive functions, (iii) a suitable reformulation of the least squares method to estimate function parameters considering simultaneously all the reactions involved in complex dynamics. The tool is available as a plugin for the virtual laboratory MetaPlab. It has graphical and interactive interfaces for data preparation, a priori knowledge integration, and flux regulator analysis.Availability and implemention: Source code, binaries, documentation (including quick start guide and videos) and case studies are freely available at http://mplab.sci.univr.it/plugins/mpgs/index.html.Contact: castellini@mpimp-golm.mpg.de [ABSTRACT FROM PUBLISHER]
Details
- Language :
- English
- ISSN :
- 13674803
- Volume :
- 31
- Issue :
- 5
- Database :
- Academic Search Index
- Journal :
- Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 101371636
- Full Text :
- https://doi.org/10.1093/bioinformatics/btu694