Ocean

Ocean is a plug-in-based framework designed and implemented to analyze biological models through HPC techniques. It manages biological models as networks (SBML, BlenX, plus other data formats) and allows the user to (i) statically analyze their characteristics (centrality, importance, clustering, sparseness, etc), (ii) run simulation on multicore and cluster architectures based (or not based) on logical formula verification and (iii) statistically analyze the simulation results (to infer knowledge about the initial parameters’ configuration).

Ranker

Ranker is an Ocean’s plug-in designed to rank webs’ (groups of) vertices according to well-grounded centrality/importance measures. It is programmed to run on mutlicore-cluster architectures. (C#, .Net 4, Rx Extensions, MS Cluster API)

SweepeR

Sweeper is an Ocean’s plug-in thought to: (i) manage parameters of biological models written in BlenX, (ii) simulate the ‘sweeped’ models on multicore-cluster architectures and (iii) collect and statistically analyze results. (C#, .Net 4, Rx Extensions, MS Cluster API)

spPeAn

spPeAn is a standalone software package designed to simulate the budding yeast cell-cycle model in a stochastic environment and in a maximally parallel manner. It performs pedigree analysis of a mother cell up to her n-th generation. Consistency and viability checks are included in order to detect abnormal duplication and dead cells. (C#, .NET 4, RX Extensions, Cluster API)

Snazer

Snazer is a modular tool designed to manage the simulated outputs generated through the Beta WorkBench simulator. Moreover, it can parse the common CSV, SBML and GraphML file formats and store the loaded time course information into a standard XML data structure. Snazer performs many statistical routines on traces and visualizes the interaction graphs of the model which the traces are related to. (Java 6, JGraph API, XDOM, libSBML API).

Cyto-Sim

Cyto-Sim is a simulator of biological processes that involve compartments and membranes with peripheral and integral proteins. (Java 6, JFreeChart API) MS Analyzer Mass spectrometry-based proteomics requires the collection, pre-processing and analysis of data produced in remote laboratories. In such a scenario, MS-Analyzer has been designed and equipped with a set of distributed proteomics facilities: a software tool designed to load, pre-process and analyze MALDI/SELDI-TOF data. (Java 5, JGraph, OWL API, WebService API, WSDL4Java API).

SpecDB

Due to the large number of (m/z) pairs, the analysis of Mass Spectra by manual inspection is not feasible. Particularly, when experiments involve even few hundreds spectra, the effort in manipulating and handling such data is more and more onerous. Towards this direction, I developed a first prototype of a relational database.

SPECDB, UNICZ, University of Catanzaro

Spider Paper

Spider Paper is a web application that allows the academic community to publish, retrieve and manage its research publications. This project was born with the aim to maintain up to date publications, to share them with all the community members and to make easier the research evaluation on behalf of the proper academic organism. (JSP, HTML, JavaScript, Servlet, Cookies).

Spider Paper, UNICZ, University of Catanzaro