TRONCO (TRanslational ONCOlogy) / PiCnIc

An R tool for cancer progression inference from heterogeneous genomic data. 
TRONCO/PiCnIc has an official website.

Gaussian Processes Correction Maps

Statistical correction of models' outputs via heteroscedastic Gaussian Process regression.
Matlab/Python sources: Github repository.

CoGNaC (Chaste and Gene Networks for Cancer)

A Chaste plugin for the multi-scale simulation of Gene Regulatory Networks driving the spatial dynamics of tissues and cancer. A tutorial webpage on COGNAC is available at Chaste webpage.

NoisySIM (Noisy Simulation)

Simulation of chemically reacting systems with intrinsic and extrinsic bounded noises, with a compiler to generate Java source code from model's specification.


pyTSA (Python Time-Series Analyzer)

A Python tool for the statistical analysis of time-series that can process standard CSV formats and plot heatmaps of distributions, phase spaces, 3D surfaces etc. 


CABERNET (Augmented Boolean Gene Regulatory Networks)

This is a follow up of our earlier works on GESTODifferent. This new tool extends the former by including:
  • further capabilities of networks generation, simulation and visualization;
  • new routines for robustness and network analysis;
  • a better integration with Cytoscape.
This tool has an official website.

GESTODifferent (Genes and Stochastic Differentiation)

Cytoscape plugin to generate Noisy Random Boolean models of Gene Regulatory Networks to describe hierarchical, stochastic or deterministic differentiation processes as well as induced pluripotency. 
GESTODifferent has an official website.                        
Follow up: CABERNET.