Modeling time-dependent transcription effects of HER2 oncogene in breast cancer cell-matrix adhesion Download   

Description: This is a set of MATLAB scripts and functions reproducing all the modeling steps reported in the paper: "Modeling time-dependent transcription effects of HER2 oncogene and discovery of a role for E2F2 in breast cancer cell-matrix adhesion". Experimental RAW data are provided together with the software.

Supervisors: Dr. Luca Marchetti, Prof. Vincenzo Manca.
License: GNU Lesser General Public License

BeQuanti Link   

Description: BeQuanti is a bioinformatics software designed to detect and quantify complex aspects of lymphocyte behavior undertow conditions simulating in vivo interactions and migration in blood vessels (see also Designed and validated by Laudanna's lab in collaboration with eVS.

Supervisors: Prof. Carlo Laudanna, Dr. Lara Toffali.
License: eVS Licence

MpTheory Java Library Link   

Description: MpTheory Java Library is an open-source project released under GNU Lesser General Public License (LGPL) Version 3. The library collects a set of Java objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a discrete mathematical theory based on P systems, introduced by Prof. Vincenzo Manca in 2004 for modeling biological dynamics. By means of the library, it is possible to model dynamical systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations.

Supervisors: Prof. Vincenzo Manca, Dr. Luca Marchetti.
License: GNU Lesser General Public License

Interference: A tool for virtual experimental network topological analysis Link   

Description: Centrality indexes allow categorizing nodes in complex networks according to their topological relevance (see CentiScaPe plugin). In a node-oriented perspective, centralities are very useful topological parameters to compute in order to quantify the effect of individual node(s) alteration. We have introduced the notion of interference and developed the Cytoscape plugin Interference to evaluate the topological effects of single or multiple nodes removal from a network. In this perspective, interference allows virtual node knock-out experiments: it is possible to remove one or more nodes from a network and analyze the consequences on network structure, by looking to the variations of the node centralities values. As the centrality value of a node is strictly dependent on the network structure and on the properties of other nodes in the network, the consequences of a node deletion are well captured by the variation on the centrality values of all the other nodes.

Supervisors: Dr. Giovanni Scardoni, Prof. Carlo Laudanna.
License: GNU General Public Licence

HOMECAT: homology and functional genomics mapping for Cytoscape Link   

Description: HOMECAT (HOmology Mapper for Enrichment and Comparative Analysis with Translation) is a Cytoscape plugin allowing cross-species data comparison with a particular emphasis on functional genomic data (i.e. microarrays and other high throughput biological data sources). The aim at the basis of this software is to ease knowledge transfer from different species. Networks can be enriched with orthologs from other species, in the desired format. Orthology assessment is a complex task, user can combine different sources of homology prediction, with different specificity and sensitivity, to allow achieving the desired level of precision and coverage. The data integration is eased by the possibility of choosing between nearly 30 identifiers formats (Uniprot, RefSeq, Ensembl, etc.) and 71 microarrays platforms identifiers (including Affymetrix, Illumina and Agilent) designed for the 30 organisms supported by the current version. Homology data can be used to enrich existing networks or to create new data visualization that improve external data loading and mapping. A specific interface allows the download of curated data directly from Array Express ATLAS database, and several functionalities ease the comparison of data from different networks. Once data is integrated in the user networks any Cytoscape functionality can be used to analyse, visualize and process the data.

Supervisors: Dr. Simone Zorzan.
License: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

CentiScaPe: Centralities for Cytoscape Link   

Description: Complex biological networks, such as intracellular signaling networks, are modeled by the evolution to accomplish a variety of different regulatory functions. This is achieved by controlling the overall topology of the network which, then, affects its dynamic behavior. Biological networks are hierarchichal, scale-free, modular structure in which few nodes, the hubs, play a particularly relevant topological role and this may reflect a critical role at biological level. However, also nodes with no or lower hub role may have critical regulatory role in certain biological phenomena. This could reflect node-specific topological properties. Thus, it is of interest to categorize every nodes in a network by means of topological parameters allowing scoring of the nodes according to their individual topological relevance. Computation of centrality indexes may accomplish this goal. The centrality indexes are topological parameters allowing a node-by-node quantification of the reciprocal relationship between the nodes. This provides a classification of the nodes according to their capability to influence the function of other nodes in the network. Combination of this analysis with experimental data (node attributes) may help to identify critical nodes and regulatory circuits in a context-specific manner.

Supervisors: Dr. Giovanni Scardoni, Prof. Carlo Laudanna.
License: GNU General Public Licence

MetaPlab virtual laboratory Link   

Description: MetaPlab is a virtual laboratory which aims at assisting modelers both to understand the internal mechanisms of biological systems and to forecast, in silico, their response to external stimuli, environmental condition alterations or structural changes. MetaPlab framework is based on a core module which enables to design and manage biological models, and an extensible set of plugins by which MP models can be generated, optimized, simulated and analyzed.

Supervisors: Prof. Vincenzo Manca, Dr. Alberto Castellini, Dr. Luca Marchetti.
License: GNU General Public Licence