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 an

SUBMITTER: Guo J 

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

REPOSITORIES: biostudies-literature