SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks

Summary: SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records th...

Descripción completa

Detalles Bibliográficos
Autores principales: Zheng, Jie, Zhang, David, Przytycki, Pawel F., Zielinski, Rafal, Capala, Jacek, Przytycka, Teresa M.
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796819/
https://www.ncbi.nlm.nih.gov/pubmed/19887508
http://dx.doi.org/10.1093/bioinformatics/btp617
_version_ 1782175565782974464
author Zheng, Jie
Zhang, David
Przytycki, Pawel F.
Zielinski, Rafal
Capala, Jacek
Przytycka, Teresa M.
author_facet Zheng, Jie
Zhang, David
Przytycki, Pawel F.
Zielinski, Rafal
Capala, Jacek
Przytycka, Teresa M.
author_sort Zheng, Jie
collection PubMed
description Summary: SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network. It can be used to generate hypotheses and facilitate experimental studies about causal relations and crosstalk among cellular signaling pathways. Availability: SimBoolNet package (with manual) is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet Contact: przytyck@ncbi.nlm.nih.gov; zhengj@ncbi.nlm.nih.gov
format Text
id pubmed-2796819
institution National Center for Biotechnology Information
language English
publishDate 2010
publisher Oxford University Press
record_format MEDLINE/PubMed
spelling pubmed-27968192009-12-23 SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks Zheng, Jie Zhang, David Przytycki, Pawel F. Zielinski, Rafal Capala, Jacek Przytycka, Teresa M. Bioinformatics Applications Note Summary: SimBoolNet is an open source Cytoscape plugin that simulates the dynamics of signaling transduction using Boolean networks. Given a user-specified level of stimulation to signal receptors, SimBoolNet simulates the response of downstream molecules and visualizes with animation and records the dynamic changes of the network. It can be used to generate hypotheses and facilitate experimental studies about causal relations and crosstalk among cellular signaling pathways. Availability: SimBoolNet package (with manual) is freely available at http://www.ncbi.nlm.nih.gov/CBBresearch/Przytycka/SimBoolNet Contact: przytyck@ncbi.nlm.nih.gov; zhengj@ncbi.nlm.nih.gov Oxford University Press 2010-01-01 2009-11-03 /pmc/articles/PMC2796819/ /pubmed/19887508 http://dx.doi.org/10.1093/bioinformatics/btp617 Text en © The Author(s) 2009. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Note
Zheng, Jie
Zhang, David
Przytycki, Pawel F.
Zielinski, Rafal
Capala, Jacek
Przytycka, Teresa M.
SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks
title SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks
title_full SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks
title_fullStr SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks
title_full_unstemmed SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks
title_short SimBoolNet—a Cytoscape plugin for dynamic simulation of signaling networks
title_sort simboolnet—a cytoscape plugin for dynamic simulation of signaling networks
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796819/
https://www.ncbi.nlm.nih.gov/pubmed/19887508
http://dx.doi.org/10.1093/bioinformatics/btp617
work_keys_str_mv AT zhengjie simboolnetacytoscapepluginfordynamicsimulationofsignalingnetworks
AT zhangdavid simboolnetacytoscapepluginfordynamicsimulationofsignalingnetworks
AT przytyckipawelf simboolnetacytoscapepluginfordynamicsimulationofsignalingnetworks
AT zielinskirafal simboolnetacytoscapepluginfordynamicsimulationofsignalingnetworks
AT capalajacek simboolnetacytoscapepluginfordynamicsimulationofsignalingnetworks
AT przytyckateresam simboolnetacytoscapepluginfordynamicsimulationofsignalingnetworks

Ejemplares similares