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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Vincent Noël, Marco Ruscone, Gautier Stoll, Eric Viara, Andrei Zinovyev, Emmanuel Barillot, Laurence Calzone
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	Boolean modelling stochastic simulation web interface SBML-qual automatic mutations sensitivity analysis Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c73a9529cc74419b8da3665900c401e7
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:c73a9529cc74419b8da3665900c401e7
record_format	dspace
spelling	oai:doaj.org-article:c73a9529cc74419b8da3665900c401e72021-11-30T14:55:37ZWebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically2296-889X10.3389/fmolb.2021.754444https://doaj.org/article/c73a9529cc74419b8da3665900c401e72021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fmolb.2021.754444/fullhttps://doaj.org/toc/2296-889XWebMaBoSS 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.Vincent NoëlVincent NoëlVincent NoëlMarco RusconeMarco RusconeMarco RusconeGautier StollEric ViaraAndrei ZinovyevAndrei ZinovyevAndrei ZinovyevEmmanuel BarillotEmmanuel BarillotEmmanuel BarillotLaurence CalzoneLaurence CalzoneLaurence CalzoneFrontiers Media S.A.articleBoolean modellingstochastic simulationweb interfaceSBML-qualautomatic mutationssensitivity analysisBiology (General)QH301-705.5ENFrontiers in Molecular Biosciences, Vol 8 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Boolean modelling stochastic simulation web interface SBML-qual automatic mutations sensitivity analysis Biology (General) QH301-705.5
spellingShingle	Boolean modelling stochastic simulation web interface SBML-qual automatic mutations sensitivity analysis Biology (General) QH301-705.5 Vincent Noël Vincent Noël Vincent Noël Marco Ruscone Marco Ruscone Marco Ruscone Gautier Stoll Eric Viara Andrei Zinovyev Andrei Zinovyev Andrei Zinovyev Emmanuel Barillot Emmanuel Barillot Emmanuel Barillot Laurence Calzone Laurence Calzone Laurence Calzone WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
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.
format	article
author	Vincent Noël Vincent Noël Vincent Noël Marco Ruscone Marco Ruscone Marco Ruscone Gautier Stoll Eric Viara Andrei Zinovyev Andrei Zinovyev Andrei Zinovyev Emmanuel Barillot Emmanuel Barillot Emmanuel Barillot Laurence Calzone Laurence Calzone Laurence Calzone
author_facet	Vincent Noël Vincent Noël Vincent Noël Marco Ruscone Marco Ruscone Marco Ruscone Gautier Stoll Eric Viara Andrei Zinovyev Andrei Zinovyev Andrei Zinovyev Emmanuel Barillot Emmanuel Barillot Emmanuel Barillot Laurence Calzone Laurence Calzone Laurence Calzone
author_sort	Vincent Noël
title	WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically
title_short	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_sort	webmaboss: a web interface for simulating boolean models stochastically
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/c73a9529cc74419b8da3665900c401e7
work_keys_str_mv	AT vincentnoel webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT vincentnoel webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT vincentnoel webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT marcoruscone webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT marcoruscone webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT marcoruscone webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT gautierstoll webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT ericviara webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT andreizinovyev webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT andreizinovyev webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT andreizinovyev webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT emmanuelbarillot webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT emmanuelbarillot webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT emmanuelbarillot webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT laurencecalzone webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT laurencecalzone webmabossawebinterfaceforsimulatingbooleanmodelsstochastically AT laurencecalzone webmabossawebinterfaceforsimulatingbooleanmodelsstochastically
_version_	1718406530979594240

WebMaBoSS: A Web Interface for Simulating Boolean Models Stochastically

Ejemplares similares