A Python program for drawing spontaneously emerging paths in Waddington's Epigenetic Landscape by Monte Carlo estimation

Description of MCLand

MCLand is a graphical user interface software tool [1] that allows user to model and visualize Waddington's epigenetic landscape for gene regulatory network. MCLand is a user friendly software tool based on Monte Carlo method to calculate and visualize quasi-potential landscape. MCLand is designed with graphical user interface to enable user to model gene regulatory network in the format of XPPAUT .ode file. Model equations are in ordinary differential equations with rate constants or parameter values. An editor is provided to user to edit their model equations in XPPAUT ode. Users who are familiar with XPPAUT will find MCLand very compatible as MCLand development is following the design of XPPAUT. User may change a parameter value and plot the Waddington’s epigenetic landscape. Users can save their model in ode file and simulated Waddington’s epigenetic landscape in MCLand file format (Python pickle .pckl). MCLand also supports SBML model file.

MCLand can be run in Windows, Linux or Mac. Users are required to install Anaconda 3 and python-libsbml package in order to run MCLand SBML models to visualize Waddington’s epigenetic landscape and attractors. MCLand is developed using the Anaconda 3: Python 3.6 (version 4.3.1). Anaconda 3 is chosen as the development environment due to the popularity and convenience of using Python package dependencies as all the required dependencies such as numpy, scipy and matplotlib are included in Anaconda 3.