Literature DB >> 24078712

BooleSim: an interactive Boolean network simulator.

Matthias Bock1, Till Scharp, Chaitanya Talnikar, Edda Klipp.   

Abstract

SUMMARY: BooleSim (Boolean network simulator) is an open-source in-browser tool for simulation and manipulation of Boolean networks. It was developed mainly during Google's Summer of Code 2012 and uses the biographer project for network visualization. It can be used specifically for the modeling of gene regulatory or signal transduction networks.
AVAILABILITY AND IMPLEMENTATION: BooleSim is free software and can be downloaded from GitHub (https://github.com/matthiasbock/BooleSim). Online version available at http://rumo.biologie.hu-berlin.de/boolesim/.

Mesh:

Year:  2013        PMID: 24078712     DOI: 10.1093/bioinformatics/btt568

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  9 in total

1.  RMut: R package for a Boolean sensitivity analysis against various types of mutations.

Authors:  Hung-Cuong Trinh; Yung-Keun Kwon
Journal:  PLoS One       Date:  2019-03-19       Impact factor: 3.240

2.  Simulation and visualization of multiple KEGG pathways using BioNSi.

Authors:  Adva Yeheskel; Adam Reiter; Metsada Pasmanik-Chor; Amir Rubinstein
Journal:  F1000Res       Date:  2017-12-11

3.  Reverse Engineering of Genome-wide Gene Regulatory Networks from Gene Expression Data.

Authors:  Zhi-Ping Liu
Journal:  Curr Genomics       Date:  2015-02       Impact factor: 2.236

4.  Properties of Boolean dynamics by node classification using feedback loops in a network.

Authors:  Yung-Keun Kwon
Journal:  BMC Syst Biol       Date:  2016-08-24

5.  Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration.

Authors:  Alessandro Palma; Andrea Cerquone Perpetuini; Federica Ferrentino; Claudia Fuoco; Cesare Gargioli; Giulio Giuliani; Marta Iannuccelli; Luana Licata; Elisa Micarelli; Serena Paoluzi; Livia Perfetto; Lucia Lisa Petrilli; Alessio Reggio; Marco Rosina; Francesca Sacco; Simone Vumbaca; Alessandro Zuccotti; Luisa Castagnoli; Gianni Cesareni
Journal:  Front Physiol       Date:  2019-09-27       Impact factor: 4.566

Review 6.  An Integrated View of Virus-Triggered Cellular Plasticity Using Boolean Networks.

Authors:  Jenny Paola Alfaro-García; María Camila Granados-Alzate; Miguel Vicente-Manzanares; Juan Carlos Gallego-Gómez
Journal:  Cells       Date:  2021-10-24       Impact factor: 6.600

Review 7.  Review and assessment of Boolean approaches for inference of gene regulatory networks.

Authors:  Žiga Pušnik; Miha Mraz; Nikolaj Zimic; Miha Moškon
Journal:  Heliyon       Date:  2022-08-09

8.  Modelling with ANIMO: between fuzzy logic and differential equations.

Authors:  Stefano Schivo; Jetse Scholma; Paul E van der Vet; Marcel Karperien; Janine N Post; Jaco van de Pol; Rom Langerak
Journal:  BMC Syst Biol       Date:  2016-07-27

9.  CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.

Authors:  Andrea Paroni; Alex Graudenzi; Giulio Caravagna; Chiara Damiani; Giancarlo Mauri; Marco Antoniotti
Journal:  BMC Bioinformatics       Date:  2016-02-04       Impact factor: 3.169

  9 in total

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