{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,16]],"date-time":"2025-10-16T10:00:18Z","timestamp":1760608818228},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,3,1]]},"abstract":"<jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Contact: \u00a0castellini@mpimp-golm.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu694","type":"journal-article","created":{"date-parts":[[2014,10,25]],"date-time":"2014-10-25T03:54:31Z","timestamp":1414209271000},"page":"785-787","source":"Crossref","is-referenced-by-count":12,"title":["MP-GeneticSynth: inferring biological network regulations from time series"],"prefix":"10.1093","volume":"31","author":[{"given":"Alberto","family":"Castellini","sequence":"first","affiliation":[{"name":"1 \u00a01Center for BioMedical Computing, Verona University, 37134 Verona, Italy, 2Max Planck Institute for Molecular Plant Physiology-Syst Bio & Math Modelling Group, 14476, Germany, 3University of Potsdam, Institute for Biochemistry and Biology - Bioinformatics Group, 14476, Germany and 4Department of Computer Science, Verona University, 37134 Verona, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniele","family":"Paltrinieri","sequence":"additional","affiliation":[{"name":"1 \u00a01Center for BioMedical Computing, Verona University, 37134 Verona, Italy, 2Max Planck Institute for Molecular Plant Physiology-Syst Bio & Math Modelling Group, 14476, Germany, 3University of Potsdam, Institute for Biochemistry and Biology - Bioinformatics Group, 14476, Germany and 4Department of Computer Science, Verona University, 37134 Verona, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincenzo","family":"Manca","sequence":"additional","affiliation":[{"name":"1 \u00a01Center for BioMedical Computing, Verona University, 37134 Verona, Italy, 2Max Planck Institute for Molecular Plant Physiology-Syst Bio & Math Modelling Group, 14476, Germany, 3University of Potsdam, Institute for Biochemistry and Biology - Bioinformatics Group, 14476, Germany and 4Department of Computer Science, Verona University, 37134 Verona, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,10,24]]},"reference":[{"key":"2023020116163141900_btu694-B1","first-page":"116","article-title":"A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems","volume":"5483","author":"Besozzi","year":"2009","journal-title":"LNCS"},{"key":"2023020116163141900_btu694-B2","doi-asserted-by":"crossref","first-page":"3036","DOI":"10.1093\/bioinformatics\/btu400","article-title":"Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion","volume":"30","author":"Bollig-Fischer","year":"2014","journal-title":"Bioinformatics"},{"key":"2023020116163141900_btu694-B3","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/s11693-009-9050-7","article-title":"Evolving cell models for systems and synthetic biology","volume":"4","author":"Cao","year":"2010","journal-title":"Syst. 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