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

About NetLand NetLand is a software for quantitative modeling and visualization of Waddington’s epigenetic landscape. 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 (e.g. TSV, SBML format etc.), and manually edit the network structure. Then, NetLand will automatically encode differential equations for the kinetics of transcriptional regulations. The computational model will be used to simulate the dynamics of the input networks. Model equations and parameters can be easily modified. To display the 3D landscape for a network of more than two genes, NetLand allows users to either choose two marker genes, or project to a latent space using a dimensionality reduction method called GPDM (Gaussian process dynamical model). 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 be also used to study other cellular phenotypes, such as cancer cell death, cellular ageing, etc. Download The software NetLand is written in Java, with a graphical user interface (GUI). The user manual contains detailed instruction about installation and basic usage. It also includes running time and memory usage assessment and case studies. The source code and additional resources are available for downloading in this dataset record. They can also be downloaded at Github.