Dataset Information

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

ABSTRACT:

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/ .

Contact

zhengjie@ntu.edu.sg.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Guo J

PROVIDER: S-EPMC5423452 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Guo Jing J Lin Feng F Zhang Xiaomeng X Tanavde Vivek V Zheng Jie J

Bioinformatics (Oxford, England) 20170501 10

<h4>Summary</h4>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 ...[more]

PMID: 28108450

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Dataset Information

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

Summary

Availability and implementation

Contact

Supplementary information

Publications

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

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