2017
DOI: 10.1093/bioinformatics/btx123
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MaBoSS 2.0: an environment for stochastic Boolean modeling

Abstract: Supplementary data are available at Bioinformatics online.

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Cited by 125 publications
(144 citation statements)
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“…Taking advantage of the multiple export formats supported by GINsim, it is also possible to use complementary tools, including stochastic simulations software (e.g. MaBoSS, see Stoll et al [42]), model checking tools (e.g. NuSMV, see Abou-Jaoudé et al [1,3], Traynard et al [48], or yet various graph visualisation and analysis packages (see Note 5 for a list of export options).…”
Section: Discussionmentioning
confidence: 99%
“…Taking advantage of the multiple export formats supported by GINsim, it is also possible to use complementary tools, including stochastic simulations software (e.g. MaBoSS, see Stoll et al [42]), model checking tools (e.g. NuSMV, see Abou-Jaoudé et al [1,3], Traynard et al [48], or yet various graph visualisation and analysis packages (see Note 5 for a list of export options).…”
Section: Discussionmentioning
confidence: 99%
“…This modeling framework does not require the knowledge of biochemical constants that are often unavailable for most cellular processes. An extension of asynchronously (stochastically) updated, discrete time logical models emerged in recent years (Stoll et al, 2017(Stoll et al, , 2012 using timescale parameters (transition rates) for the model's variables to generate continuous time Monte Carlo simulations. This approach produces continuous values (probabilities of activation) for a model's variables, enabling more quantitative analysis and comparison with continuous biological data.…”
Section: Resultsmentioning
confidence: 99%
“…In recent years, efforts were made to bridge the gap between qualitative and quantitative modeling by a continuous time stochastic version of Boolean modeling (Stoll et al, 2012(Stoll et al, , 2017. With this approach, the temporal evolution of a system is described as a continuous time Markov process on a Boolean state space.…”
Section: Introductionmentioning
confidence: 99%
“…MaBoSS [13] is a C++ software that performs stochastic simulations of a Boolean network by translating it into a continuous time Markov processes. Each node activation and inactivation is associated with an up and a down rate, which specify the propensity of the corresponding transition.…”
Section: Assessing the Probabilities To Reach Alternative Attractors mentioning
confidence: 99%
“…To support the development and analysis of logical models, a series of software tools have been proposed, often with specific assets [7,9,12,13].…”
mentioning
confidence: 99%