MP-GeneticSynth : inferring biological network regulations from time series
© The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissionsoup.com..
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 implementation: 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.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2015 |
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| Erschienen: |
2015 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:31 |
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| Enthalten in: |
Bioinformatics (Oxford, England) - 31(2015), 5 vom: 01. März, Seite 785-7 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Castellini, Alberto [VerfasserIn] |
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| Links: |
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| Themen: |
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| Anmerkungen: |
Date Completed 18.09.2015 Date Revised 02.12.2018 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1093/bioinformatics/btu694 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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NLM243050976 |
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| 520 | |a © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissionsoup.com. | ||
| 520 | |a 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 implementation: 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 | ||
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