The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology

Summary: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compa...

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Detalles Bibliográficos
Autores principales: Blakes, Jonathan, Twycross, Jamie, Romero−Campero, Francisco Jose, Krasnogor, Natalio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2011
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3223367/
https://www.ncbi.nlm.nih.gov/pubmed/21994219
http://dx.doi.org/10.1093/bioinformatics/btr571
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author Blakes, Jonathan
Twycross, Jamie
Romero−Campero, Francisco Jose
Krasnogor, Natalio
author_facet Blakes, Jonathan
Twycross, Jamie
Romero−Campero, Francisco Jose
Krasnogor, Natalio
author_sort Blakes, Jonathan
collection PubMed
description Summary: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking. Availability: Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3. Contact: Natalio.Krasnogor@nottingham.ac.uk
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spelling pubmed-32233672011-11-25 The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology Blakes, Jonathan Twycross, Jamie Romero−Campero, Francisco Jose Krasnogor, Natalio Bioinformatics Applications Note Summary: The Infobiotics Workbench is an integrated software suite incorporating model specification, simulation, parameter optimization and model checking for Systems and Synthetic Biology. A modular model specification allows for straightforward creation of large-scale models containing many compartments and reactions. Models are simulated either using stochastic simulation or numerical integration, and visualized in time and space. Model parameters and structure can be optimized with evolutionary algorithms, and model properties calculated using probabilistic model checking. Availability: Source code and binaries for Linux, Mac and Windows are available at http://www.infobiotics.org/infobiotics-workbench/; released under the GNU General Public License (GPL) version 3. Contact: Natalio.Krasnogor@nottingham.ac.uk Oxford University Press 2011-12-01 2011-10-12 /pmc/articles/PMC3223367/ /pubmed/21994219 http://dx.doi.org/10.1093/bioinformatics/btr571 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Blakes, Jonathan
Twycross, Jamie
Romero−Campero, Francisco Jose
Krasnogor, Natalio
The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
title The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
title_full The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
title_fullStr The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
title_full_unstemmed The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
title_short The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology
title_sort infobiotics workbench: an integrated in silico modelling platform for systems and synthetic biology
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3223367/
https://www.ncbi.nlm.nih.gov/pubmed/21994219
http://dx.doi.org/10.1093/bioinformatics/btr571
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