Software

• Network Analyzer and Dynamics Simulator

Here you can find R code implementing a translation of a directed network into a set of mass action law equations. The repository contains also R code for network analysis, numerical integration of the equation and sensitivity analysis.

• Identification of genes responsive to treatments against Chronic Myeloid Leukemia

Here you can find R code implementing differential expression analysis and gene set enrichment analysis applied to the expression data of genes candidate to be involved in Chronic Myeloid Leukemia onset and development.

• Advection-diffusion equations simulation - project on GitHub

Here you can find Python code for the simulation of advection-diffusion equation in bubble columns bioreactor.

• Data regression - project on GitHub

Here you can find scripts in R for experimental data regression. This repository is constantly updated with new scripts relating to specific ongoing projects in computational biology.

• TD-WGcluster (Time Dependent Weighted Graphs Clustering)

Time Delayed Weighted Edge Clustering (TD-WGcluster) integrates static interaction networks with time series data in order to detect modules of nodes between which the information flows at similar time delays and intensities.

Reference paper here.

• TO-DAG (Timed Oncogenetic Direct Acyclic Graphs)

TO-DAG infers the graph of the causal dependencies and the waiting times among mutational events from cross-sectional data of genetic alterations in independent human tumor samples. The use of TO-DAG is relevant to three crucial aspects of computational modeling of tumor progression, i.e.

• • data organization,

  • data interpretation

  • and inference of new knowledge in cancer genomics.

Reference paper here.

• WG-Cluster (Weighted Graphs Clustering)

WG-Cluster (Weighted Graph CLUSTERing). is a tool to detect communities in biological network.

Principal features of the tool are:

• • efficient clustering by edge weights

  • efficient (fast-greedy based) community detection

  • assessment of statistical significance for detected communities.

Reference paper available here.

Software available here.

• KInfer (Kinetics Infernece, see COSBI LAB)

KInfer is a tool for estimating rate constants of systems of chemical reactions from experimental time series of reagents concentrations.

Principal features of the tool are:

• • automatic generation of generalized mass action model from the chemical equations of the reactions involved in the system

  • automatic estimation of the initial guesses and bounds for the parameter values

  • estimate of the propagation of the experimental errors from the input data to the parameter estimates

  • estimation of the level of noise in the input data.

  • Reference paper available here.

• Redi (Reaction-diffusion, see COSBI LAB)

Redi is a simulator of stochastic reaction-diffusion systems. It implements a new model of diffusion of molecules in non-homogenoues media and incorporates this model into a Gillespie-like simulation algorithm of biochemical reactions. In the new model of diffusion, diffusion coefficient are not fixed, but computed dynamically in a state-dependent way, as function of local concentration of soulte and solvent, local frictional forces and local temperature. The diffusion model is inspired to the Maxwell-Stephen model of transport phenomena.

Reference paper available here.

• COSBI LAB Infer (not available for download)

COSBI LAB Infer infers the topological and causal structure of a gene and metabolic network from time-series data of the amount of aboundance of networks components (expression levels, metabolites and enzymes concetrations, respectively).

Reference paper available here.