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.
Implements:
Dynamic modeling
Time-course simulation
Visualization of system dynamics in Waddington's epigenetic landscape
Example:
Screencast:
If you have trouble to view the video, please try Youku link.
