icona researchSoftware

GreatMod: GreatSPN + EPIMOD

Developers: Paolo Castagno, Simone Pernice, Matteo Sereno and Marco Beccuti

A modeling framework for the analysis of epidemiological and biological systems, which exploits Petri Net graphical formalism, R environment, and Docker containerization to derive a tool easily accessible by any researcher even without advanced mathematical and computational skills.

Download GreatMod code.

rCASC: Cluster Analysis of Single Cells.

Developers: Marco Beccuti, Luca Alessandri, Raffaele A. Calogero and Francesca Cordero.

rCASC, Cluster Analysis of Single Cells, is part of the reproducible-bioinformatics.org project and provides single cell analysis functionalities within the reproducible rules described by Sandve et al. [PLoS Comp Biol. 2013]. rCASC is designed to provide a complete workflow (Figure 1) for cell-subpopulation discovery.

Download rCASC code.

SeqBox: RNAseq/ChIPseq reproducible analysis on a consumer game computer.

Developers: Marco Beccuti, Raffaele A. Calogero and Francesca Cordero.

SeqBox was developed to facilitate the use of computing demanding applications in the field of NGS data analysis.
SeqBox uses docker containers that embed demanding computing tasks (e.g. short reads mapping) into isolated containers. This approach provides multiple advantages: (i)user does not need to install all the software on its local server; (ii)results generated by different containers can be organized in pipelines; (iii)reproducible research is guarantee by the possibility of sharing the docker images used for the analysis.
SeqBox comes with the R engine, docker4seq, its graphical interface, 4SeqGUI, and all dockers images installed in the NUC6I7KYK, Intel mini-computer equipped with 32GB GB RAM and 250GB/500GB Internal SSD.

Download SeqBox code.

HashClone: a new tool to quantify the minimal residual disease in B-cell lymphoma from deep sequencing data.

Developers: Marco Beccuti, Francesca Cordero and Greta Romano.

The HashClone strategy-based is composed of three steps: the first and second steps implement an alignment-free prediction method that identifies a set of putative clones belonging to the repertoire of the patient under study. In the third step the IGH variable E region, diversity region, and joining region identification is obtained by the alignment of rearrangements with respect to the international ImMunoGenetics information system database. Moreover, a provided graphical user interface for HashClone execution and clonality visualization over time facilitate the tool use and the results interpretation.

Download HashClone.

Kidney exchange simulator: a tool to simulate and evaluate almost myopic exchange policies.

Developers: Marco Beccuti, Giuliana Franceschinis and Silvia Villa.

It is a parametric simulator that allows to study almost myopic kidney exchange policies considering multiple characteristics of both donors and recipients, different degrees of compatibility (quantifying the quality of the exchange) and different cost factors concurring to the definition of the reward function.

Download the simulator source code.

MDWNsolver: a framework to design and solve Markov Decision Petri Nets and Markov Decision well-formed Nets.

Developers: Marco Beccuti, Giuliana Franceschinis and Serge Haddad.

MDWNsolver is a framework for system modeling and optimization of performability measures based on Markov Decision Petri Net (MDPN) and Markov Decision Well-formed Net (MDWN) formalisms, two Petri Net extensions for high level specification of Markov Decision Processes (MDP). It is integrated in the GreatSPN suite which provides a GUI to design MDPN/MDWN models. From the analysis point of view, MDWNsolver uses efficient algorithms that take advantage of system symmetries, thus reducing the analysis complexity.

Official GreatSPN web page.

ESRGsolver: a framework to efficiently analysis asymmetric systems in GreatSPN.

Developers: Soheib Baarir, Marco Beccuti and Giuliana Franceschinis.

ESRGsolver is a framework which exploits the Extended Symbolic Reachability method to efficiently analysis asymmetric systems described through the Stochastic Well-formed Net formalism. The tool is currently integrated in the GreatSPN suite.

Official GreatSPN web page.

RGMEDD: a CTL model checker based on symbolic data structures.

Developers: Elvio Amparore, Marco Beccuti, Susanna Donatelli and Erica Turin.

RGMEDD is a symbolic model checker for Petri Net models, which is also able to provide the generation of counter-examples and witnesses. Its implementation is based on the DD library Meddly, developed at Iowa State University. The tool is currently integrated in the GreatSPN suite.

Official GreatSPN web page.

Chimera: a Bioconductor package for secondary analysis of fusion products.

Developers: Raffaele A. Calogero, Matteo Carrara, Marco Beccuti and Francesca Cordero.

Chimera is a Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools; current implementation can deal with output from, bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion, and STAR. The core of Chimera is a fusion data structure that can store fusion events detected with any of the above mentioned tools. Fu- sions are then easily manipulated with standard R functions or through the set of functionalities specifically developed in Chimera with the aim of supporting the user in managing fusions and discriminating false positives.

Official Chimera web page.

HashFilter: a tool for supporting read de-convolution.

Developers: Marco Beccuti, Gianfranco Ciardo, Francesca Cordero and Stefano Leonardi.

HashFilter is C++ tool implementing an innovative read de-convolution algorithm based on hash table. It was used to obtain the physical, genetic and functional sequence assembly of the barley genome in the project Advancing the Barley Genome (CRIS NUMBER: 0218967).

Official HashFilter web page.

Hashcheker: a tool for supporting read comparison

Developers: Marco Beccuti and Francesca Cordero.

Hashcheker is C++ tool implementing an innovative read comparison based on hash table. It was used to study the difference among transcriptional profiling of patients with colorectal cancer.

More infomation are availble on request (mail:mbeccuti@di.unto.it)