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A Software Tool for Quantitative Modeling and Visualization of Waddington’s Epigenetic Landscape

Version 1.0.0  |  Requires Java

NetLand is intended for modeling, simulation and visualization of gene regulatory networks (GRNs) and their corresponding quasi-potential landscapes. Users can import models of GRNs from a file in formats such as TSV, SBML, etc., and manually edit the network structure. Then, NetLand will automatically encode differential equations for modeling the kinetics of transcriptional regulations. Model equations and parameters can also be modified by users. As such, a computational model is constructed and can be used to simulate the dynamics of the input networks.

To display the 3D landscape for a network of more than two genes, NetLand allows users to either project the landscape to a state space of two chosen marker genes, or project to a latent space using a dimensionality reduction method called the Gaussian process dynamical model (GPDM). Therefore, NetLand can provide a global picture of cellular dynamics for a user-specified GRN. Although we designed the NetLand software originally for modeling stem cell fate transitions, it can also be used to study other cellular phenotypes, such as cancer cell death, cellular ageing, etc.

The software NetLand is written in Java, with a graphical user interface (GUI). The source code and additional resources are available at GitHub.

  • Dynamic modeling
  • Time-course simulation
  • Visualization of system dynamics in Waddington's epigenetic landscape



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