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

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

Bioinformatics. 2017 Jan 19;:

Authors: Guo J, Lin F, Zhang X, Tanavde V, Zheng J

Abstract
Waddington's epigenetic landscape is a powerful metaphor for cellular dynamics driven by gene regulatory networks. 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 gene regulatory networks (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: 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 and example models, etc. can be downloaded from http://ift.tt/2j0cEN4 CONTACT: zhengjie@ntu.edu.sg.

PMID: 28108450 [PubMed - as supplied by publisher]

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