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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Bibliographic Details
Main Authors: Guo, Jing, Lin, Feng, Zhang, Xiaomeng, Tanavde, Vivek, Zheng, Jie
Other Authors: School of Computer Science and Engineering
Format: Article
Language:English
Published: 2017
Online Access:https://hdl.handle.net/10356/85842
http://hdl.handle.net/10220/43851
https://doi.org/10.21979/N9/IP6DBD
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Institution: Nanyang Technological University
Language: English
Description
Summary: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/.