The DCB group has developed several software tools that can be used to analyze and simulate several datasets. We use our tools to work mostly on cancer, although more recently we have applied them to analysis of SARS-CoV-2 sequences.
pyTSA is a Python tool to make time-series analysis as intuitive as possible.
Its scripts can be pipelined with any simulation tool outputting time-series, and intuitive commands allow to perform complex analyses in a intuitive way.
CABERNET is a Cytoscape app for the generation, the simulation, the analysis and the visualization of Boolean models of gene regulatory networks, particularly focused on the investigation of their robustness.
GESTODifferent – a plugin for Cytoscape for the identification of Boolean gene regulatory networks describing the stochastic differentiation process. Please use CABERNET (it is an evolution of GESTODifferent).
You can find the description of GESTODifferent and the link for download here.