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Your search keyword '"Gianluigi Zanetti"' showing total 3 results
Start Over Author "Gianluigi Zanetti" Publisher oxford university press (oup)
3 results on '"Gianluigi Zanetti"'

1. BioBlend.objects: metacomputing with Galaxy

Author

Nicola Soranzo, Enis Afgan, Gianluigi Zanetti, Luca Pireddu, Luca Lianas, Gianmauro Cuccuru, and Simone Leo

Subjects
Statistics and Probability, Bioblend, Galaxy, Metacomputing, ComputerSystemsOrganization_COMPUTERSYSTEMIMPLEMENTATION, Computer science, Interface (Java), computer.software_genre, Biochemistry, Computer graphics, Automation, User-Computer Interface, 03 medical and health sciences, Software, Computer Systems, Component (UML), Computer Graphics, Molecular Biology, 030304 developmental biology, 0303 health sciences, Application programming interface, Database, business.industry, 05 social sciences, Computational Biology, 050301 education, Applications Notes, Computer Science Applications, Computational Mathematics, Workflow, Computational Theory and Mathematics, Operating system, Programming Languages, business, Sequence Analysis, 0503 education, computer, Algorithms
Abstract

Summary: BioBlend.objects is a new component of the BioBlend package, adding an object-oriented interface for the Galaxy REST-based application programming interface. It improves support for metacomputing on Galaxy entities by providing higher-level functionality and allowing users to more easily create programs to explore, query and create Galaxy datasets and workflows. Availability and implementation: BioBlend.objects is available online at https://github.com/afgane/bioblend . The new object-oriented API is implemented by the galaxy/objects subpackage. Contact: simone.leo@crs4.it

Published
2014
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2. Orione, a web-based framework for NGS analysis in microbiology

Author

Andrea Pinna, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti, Gianmauro Cuccuru, Giorgio Fotia, Nicola Soranzo, Andrea Sbardellati, and Massimiliano Orsini

Subjects
Microbiological Techniques, Statistics and Probability, Interoperability, Sequence assembly, Biology, Biochemistry, Microbiology, Software, Web application, Molecular Biology, Internet, business.industry, Data manipulation language, High-Throughput Nucleotide Sequencing, Reproducibility of Results, Gene Annotation, Applications Notes, Computer Science Applications, Computational Mathematics, Workflow, Computational Theory and Mathematics, Metagenomics, business, Sequence Analysis
Abstract

Summary: End-to-end next-generation sequencing microbiology data analysis requires a diversity of tools covering bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-Seq, gene annotation and metagenomics. However, the construction of computational pipelines that use different software packages is difficult owing to a lack of interoperability, reproducibility and transparency. To overcome these limitations we present Orione, a Galaxy-based framework consisting of publicly available research software and specifically designed pipelines to build complex, reproducible workflows for next-generation sequencing microbiology data analysis. Enabling microbiology researchers to conduct their own custom analysis and data manipulation without software installation or programming, Orione provides new opportunities for data-intensive computational analyses in microbiology and metagenomics. Availability and implementation: Orione is available online at http://orione.crs4.it . Contact: gianmauro.cuccuru@crs4.it Supplementary information: Supplementary data are available at Bioinformatics online.

Published
2014
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3. SEAL: a distributed short read mapping and duplicate removal tool

Author

Luca Pireddu, Gianluigi Zanetti, and Simone Leo

Subjects
Statistics and Probability, Database, Computer science, business.industry, Computational Biology, Sequence Analysis, DNA, Short read, computer.software_genre, Biochemistry, Seal (mechanical), Computer Science Applications, Applications Note, Computational Mathematics, Mode (computer interface), Computational Theory and Mathematics, Scalability, business, Sequence Alignment, Sequence Analysis, Molecular Biology, Throughput (business), computer, Algorithms, Software, Computer hardware
Abstract

Summary: SEAL is a scalable tool for short read pair mapping and duplicate removal. It computes mappings that are consistent with those produced by BWA and removes duplicates according to the same criteria employed by Picard MarkDuplicates. On a 16-node Hadoop cluster, it is capable of processing about 13 GB per hour in map+rmdup mode, while reaching a throughput of 19 GB per hour in mapping-only mode. Availability: SEAL is available online at http://biodoop-seal.sourceforge.net/. Contact: luca.pireddu@crs4.it

Published
2011
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