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NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential

SUMMARY: Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s...

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Autores principales: Guo, Jing, Lin, Feng, Zhang, Xiaomeng, Tanavde, Vivek, Zheng, Jie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423452/
https://www.ncbi.nlm.nih.gov/pubmed/28108450
http://dx.doi.org/10.1093/bioinformatics/btx022
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author Guo, Jing
Lin, Feng
Zhang, Xiaomeng
Tanavde, Vivek
Zheng, Jie
author_facet Guo, Jing
Lin, Feng
Zhang, Xiaomeng
Tanavde, Vivek
Zheng, Jie
author_sort Guo, Jing
collection PubMed
description SUMMARY: Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of GRNs, and visualizing the corresponding Waddington’s epigenetic landscape in three dimensions without restriction on the number of genes in a GRN. With an interactive and graphical user interface, NetLand can facilitate the knowledge discovery and experimental design in the study of cell fate regulation (e.g. stem cell differentiation and reprogramming). AVAILABILITY AND IMPLEMENTATION: NetLand can run under operating systems including Windows, Linux and OS X. The executive files and source code of NetLand as well as a user manual, example models etc. can be downloaded from http://netland-ntu.github.io/NetLand/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-54234522017-05-11 NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential Guo, Jing Lin, Feng Zhang, Xiaomeng Tanavde, Vivek Zheng, Jie Bioinformatics Applications Notes SUMMARY: Waddington’s epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks (GRNs). Its quantitative modeling and visualization, however, remains a challenge, especially when there are more than two genes in the network. A software tool for Waddington’s landscape has not been available in the literature. We present NetLand, an open-source software tool for modeling and simulating the kinetic dynamics of GRNs, and visualizing the corresponding Waddington’s epigenetic landscape in three dimensions without restriction on the number of genes in a GRN. With an interactive and graphical user interface, NetLand can facilitate the knowledge discovery and experimental design in the study of cell fate regulation (e.g. stem cell differentiation and reprogramming). AVAILABILITY AND IMPLEMENTATION: NetLand can run under operating systems including Windows, Linux and OS X. The executive files and source code of NetLand as well as a user manual, example models etc. can be downloaded from http://netland-ntu.github.io/NetLand/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2017-05-15 2017-01-20 /pmc/articles/PMC5423452/ /pubmed/28108450 http://dx.doi.org/10.1093/bioinformatics/btx022 Text en © The Author 2017. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Guo, Jing
Lin, Feng
Zhang, Xiaomeng
Tanavde, Vivek
Zheng, Jie
NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
title NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
title_full NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
title_fullStr NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
title_full_unstemmed NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
title_short NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential
title_sort netland: quantitative modeling and visualization of waddington’s epigenetic landscape using probabilistic potential
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423452/
https://www.ncbi.nlm.nih.gov/pubmed/28108450
http://dx.doi.org/10.1093/bioinformatics/btx022
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