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WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically

WebMaBoSS is an easy-to-use web interface for conversion, storage, simulation and analysis of Boolean models that allows to get insight from these models without any specific knowledge of modeling or coding. It relies on an existing software, MaBoSS, which simulates Boolean models using a stochastic...

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Detalles Bibliográficos
Autores principales: Noël, Vincent, Ruscone, Marco, Stoll, Gautier, Viara, Eric, Zinovyev, Andrei, Barillot, Emmanuel, Calzone, Laurence
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8651056/
https://www.ncbi.nlm.nih.gov/pubmed/34888352
http://dx.doi.org/10.3389/fmolb.2021.754444
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author Noël, Vincent
Ruscone, Marco
Stoll, Gautier
Viara, Eric
Zinovyev, Andrei
Barillot, Emmanuel
Calzone, Laurence
author_facet Noël, Vincent
Ruscone, Marco
Stoll, Gautier
Viara, Eric
Zinovyev, Andrei
Barillot, Emmanuel
Calzone, Laurence
author_sort Noël, Vincent
collection PubMed
description WebMaBoSS is an easy-to-use web interface for conversion, storage, simulation and analysis of Boolean models that allows to get insight from these models without any specific knowledge of modeling or coding. It relies on an existing software, MaBoSS, which simulates Boolean models using a stochastic approach: it applies continuous time Markov processes over the Boolean network. It was initially built to fill the gap between Boolean and continuous formalisms, i.e., providing semi-quantitative results using a simple representation with a minimum number of parameters to fit. The goal of WebMaBoSS is to simplify the use and the analysis of Boolean models coping with two main issues: 1) the simulation of Boolean models of intracellular processes with MaBoSS, or any modeling tool, may appear as non-intuitive for non-experts; 2) the simulation of already-published models available in current model databases (e.g., Cell Collective, BioModels) may require some extra steps to ensure compatibility with modeling tools such as MaBoSS. With WebMaBoSS, new models can be created or imported directly from existing databases. They can then be simulated, modified and stored in personal folders. Model simulations are performed easily, results visualized interactively, and figures can be exported in a preferred format. Extensive model analyses such as mutant screening or parameter sensitivity can also be performed. For all these tasks, results are stored and can be subsequently filtered to look for specific outputs. This web interface can be accessed at the address: https://maboss.curie.fr/webmaboss/ and deployed locally using docker. This application is open-source under LGPL license, and available at https://github.com/sysbio-curie/WebMaBoSS.
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spelling pubmed-86510562021-12-08 WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically Noël, Vincent Ruscone, Marco Stoll, Gautier Viara, Eric Zinovyev, Andrei Barillot, Emmanuel Calzone, Laurence Front Mol Biosci Molecular Biosciences WebMaBoSS is an easy-to-use web interface for conversion, storage, simulation and analysis of Boolean models that allows to get insight from these models without any specific knowledge of modeling or coding. It relies on an existing software, MaBoSS, which simulates Boolean models using a stochastic approach: it applies continuous time Markov processes over the Boolean network. It was initially built to fill the gap between Boolean and continuous formalisms, i.e., providing semi-quantitative results using a simple representation with a minimum number of parameters to fit. The goal of WebMaBoSS is to simplify the use and the analysis of Boolean models coping with two main issues: 1) the simulation of Boolean models of intracellular processes with MaBoSS, or any modeling tool, may appear as non-intuitive for non-experts; 2) the simulation of already-published models available in current model databases (e.g., Cell Collective, BioModels) may require some extra steps to ensure compatibility with modeling tools such as MaBoSS. With WebMaBoSS, new models can be created or imported directly from existing databases. They can then be simulated, modified and stored in personal folders. Model simulations are performed easily, results visualized interactively, and figures can be exported in a preferred format. Extensive model analyses such as mutant screening or parameter sensitivity can also be performed. For all these tasks, results are stored and can be subsequently filtered to look for specific outputs. This web interface can be accessed at the address: https://maboss.curie.fr/webmaboss/ and deployed locally using docker. This application is open-source under LGPL license, and available at https://github.com/sysbio-curie/WebMaBoSS. Frontiers Media S.A. 2021-11-15 /pmc/articles/PMC8651056/ /pubmed/34888352 http://dx.doi.org/10.3389/fmolb.2021.754444 Text en Copyright © 2021 Noël, Ruscone, Stoll, Viara, Zinovyev, Barillot and Calzone. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Noël, Vincent
Ruscone, Marco
Stoll, Gautier
Viara, Eric
Zinovyev, Andrei
Barillot, Emmanuel
Calzone, Laurence
WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
title WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
title_full WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
title_fullStr WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
title_full_unstemmed WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
title_short WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
title_sort webmaboss: a web interface for simulating boolean models stochastically
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8651056/
https://www.ncbi.nlm.nih.gov/pubmed/34888352
http://dx.doi.org/10.3389/fmolb.2021.754444
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