MP-GeneticSynth: inferring biological network regulations from time series
- 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.
| Author details: | Alberto Castellini, Daniele Paltrinieri, Vincenzo Manca |
|---|---|
| DOI: | https://doi.org/10.1093/bioinformatics/btu694 |
| ISSN: | 1367-4803 |
| ISSN: | 1460-2059 |
| Pubmed ID: | https://pubmed.ncbi.nlm.nih.gov/25344496 |
| Title of parent work (English): | Bioinformatics |
| Publisher: | Oxford Univ. Press |
| Place of publishing: | Oxford |
| Publication type: | Article |
| Language: | English |
| Year of first publication: | 2015 |
| Publication year: | 2015 |
| Release date: | 2017/03/27 |
| Volume: | 31 |
| Issue: | 5 |
| Number of pages: | 3 |
| First page: | 785 |
| Last Page: | 787 |
| Funding institution: | CBMC (Center for Biomedical Computing), University of Verona |
| Organizational units: | Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie |
| Peer review: | Referiert |
