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 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.

• Publication year

  2017

• Venue

  Bioinform.

• Publication date

  2017-01-19

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btx022PMID 28108450PMCID 5423452
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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