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1. Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

Author

Marco Antonio Tangaro, Pietro Mandreoli, Matteo Chiara, Giacinto Donvito, Marica Antonacci, Antonio Parisi, Angelica Bianco, Angelo Romano, Daniela Manila Bianchi, Davide Cangelosi, Paolo Uva, Ivan Molineris, Vladimir Nosi, Raffaele A. Calogero, Luca Alessandri, Elena Pedrini, Marina Mordenti, Emanuele Bonetti, Luca Sangiorgi, Graziano Pesole, and Federico Zambelli

Subjects
Galaxy, Cloud computing, Bioinformatics, Laniakea, Software environment, NGS, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server’s initial configuration and deployment. Results “Laniakea@ReCaS”, the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. Conclusions During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers’ work.

Published
2021
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2. ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

Author

Tiziana Castrignanò, Silvia Gioiosa, Tiziano Flati, Mirko Cestari, Ernesto Picardi, Matteo Chiara, Maddalena Fratelli, Stefano Amente, Marco Cirilli, Marco Antonio Tangaro, Giovanni Chillemi, Graziano Pesole, and Federico Zambelli

Subjects
HPC, Compute service, Bioinformatics, Software environment, NGS data analysis, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5
Abstract

Abstract Background The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the “Big Data” era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians. Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center. Results Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call “ELIXIR-IT HPC@CINECA”, offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of ~ 8 Millions of CPU/hours and, for data storage, ~ 100 TB of permanent and ~ 300 TB of temporary space. Conclusions Three years after the beginning of the ELIXIR-IT HPC@CINECA program, we can appreciate its impact over the Italian bioinformatics community and draw some considerations. Several Italian researchers who applied to the program have gained access to one of the top-ranking public scientific supercomputing facilities in Europe. Those investigators had the opportunity to sensibly reduce computational turnaround times in their research projects and to process massive amounts of data, pursuing research approaches that would have been otherwise difficult or impossible to undertake. Moreover, by taking advantage of the wealth of documentation and training material provided by CINECA, participants had the opportunity to improve their skills in the usage of HPC systems and be better positioned to apply to similar EU programs of greater scale, such as PRACE. To illustrate the effective usage and impact of the resources awarded by the program - in different research applications - we report five successful use cases, which have already published their findings in peer-reviewed journals.

Published
2020
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5. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update.

Author

Enis Afgan, Anton Nekrutenko, Björn A. Grüning, Daniel J. Blankenberg, Jeremy Goecks, Michael C. Schatz, Alexander E. Ostrovsky, Alexandru Mahmoud, Andrew J. Lonie, Anna Syme, Anne Fouilloux, Anthony Bretaudeau, Anup Kumar, Arthur C. Eschenlauer, Assunta D. Desanto, Aysam Guerler, Beatriz Serrano-Solano, Bérénice Batut, Bradley W. Langhorst, Bridget Carr, Bryan A. Raubenolt, Cameron J. Hyde, Catherine J. Bromhead, Christopher B. Barnett, Coline Royaux, Cristóbal Gallardo, Daniel J. Fornika, Dannon Baker, Dave Bouvier, Dave Clements, David A. de Lima Morais, David Lopez Tabernero, Delphine Larivière, Engy Nasr, Federico Zambelli, Florian Heyl, Fotis E. Psomopoulos, Frederik Coppens, Gareth R. Price, Gianmauro Cuccuru, Gildas Le Corguillé, Gregory Von Kuster, Gulsum Gudukbay, Helena Rasche, Hans-Rudolf Hotz, Ignacio Eguinoa, Igor V. Makunin, Isuru Ranawaka, James Taylor 0001, Jayadev Joshi, Jennifer Hillman-Jackson, John Chilton, Kaivan Kamali, Keith Suderman, Krzysztof Poterlowicz, Yvan Le Bras, Lucille Lopez-Delisle, Luke Sargent, Madeline E. Bassetti, Marco Antonio Tangaro, Marius van den Beek, Martin Cech, Matthias Bernt, Matthias Fahrner, Mehmet Tekman, Melanie Christine Föll, Michael R. Crusoe, Miguel Roncoroni, Natalie Kucher, Nate Coraor, Nicholas Stoler, Nick Rhodes, Nicola Soranzo, Niko Pinter, Nuwan Goonasekera, Pablo A. Moreno, Pavankumar Videm, Petera Melanie, Pietro Mandreoli, Pratik D. Jagtap, Qiang Gu, Ralf J. M. Weber, Ross Lazarus, Ruben H. P. Vorderman, Saskia D. Hiltemann, Sergey Golitsynskiy, Shilpa Garg, Simon A. Bray, Simon L. Gladman, Simone Leo, Subina P. Mehta, Timothy J. Griffin, Vahid Jalili, Yves Vandenbrouck, Victor Wen, Vijay K. Nagampalli, Wendi A. Bacon, Willem L. De Koning, Wolfgang Maier 0003, and Peter J. Briggs

Published
2022
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8. INDIGO-DataCloud: a Platform to Facilitate Seamless Access to E-Infrastructures.

Author

Davide Salomoni, Isabel Campos Plasencia, Luciano Gaido, Jesús E. Marco de Lucas, P. Solagna, Jorge Gomes 0001, Ludek Matyska, P. Fuhrman, Marcus Hardt, Giacinto Donvito, Lukasz Dutka, Marcin Plóciennik, Roberto Barbera, Ignacio Blanquer, Andrea Ceccanti, Eva Cetinic, Mário David, Doina Cristina Duma, álvaro López García, Germán Moltó, Pablo Orviz Fernández, Zdenek Sustr, Matthew Viljoen, Fernando Aguilar, Luís Alves, Marica Antonacci, Lucio Angelo Antonelli, Stefano Bagnasco, A. Bonving, Riccardo Bruno, Y. Chen, Alessandro Costa, Davor Davidovic, Benjamin Ertl, Marco Fargetta, Sandro Fiore, S. Gallozzi, Z. Kurkcuoglu, Lara Lloret Iglesias, J. Martins, Alessandra Nuzzo, Paola Nassisi, Cosimo Palazzo, João Murta Pina, Eva Sciacca, Daniele Spiga, Marco Antonio Tangaro, Michal Urbaniak, Sara Vallero, Bas Wegh, Valentina Zaccolo, Federico Zambelli, and Tomasz Zok

Published
2018
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14. Using 'Galaxy-rCASC': A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis

Author

Pietro, Mandreoli, Luca, Alessandri, Raffaele A, Calogero, Marco Antonio, Tangaro, and Federico, Zambelli

Abstract

rCASC is a modular workflow providing an integrated environment for single-cell RNA-seq (scRNA-Seq) data analysis exploiting Docker containers to achieve functional and computational reproducibility. It was initially developed as an R package usable also through a Java GUI. However, the Java frontend cannot be employed when running rCASC on a remote server, a typical setup due to the significant computational resources commonly needed to analyze scRNA-Seq data.To allow the use of rCASC through a graphical user interface on the client side and to harness the many advantages provided by the Galaxy platform, we have made rCASC available as a Galaxy set of tools, also providing a dedicated public instance of Galaxy named "Galaxy-rCASC." To integrate rCASC into Galaxy, all its functions, originally implemented as a set of Docker containers to maximize reproducibility, have been extensively reworked to become independent from the R package functions that launch them in the original implementation. Furthermore, suitable Galaxy wrappers have been developed for most functions of rCASC. We provide a detailed reference document to the use of Galaxy-rCASC with insights and explanations on the platform functionalities, parameters, and output while guiding the reader through the typical rCASC analysis workflow of a scRNA-Seq dataset.

Published
2022

15. INDIGO-DataCloud: A data and computing platform to facilitate seamless access to e-infrastructures.

Author

Davide Salomoni, Luciano Gaido, Isabel Campos Plasencia, Jesús E. Marco de Lucas, P. Solagna, Jorge Gomes 0001, Ludek Matyska, P. Fuhrman, Marcus Hardt, Giacinto Donvito, Lukasz Dutka, Marcin Plóciennik, Roberto Barbera, Cristina Aiftimiei, Ignacio Blanquer, Andrea Ceccanti, Mário David, álvaro López García, Germán Moltó, Pablo Orviz Fernández, Zdenek Sustr, Matthew Viljoen, Fernando Aguilar, Luís Alves, A. Bonving, Riccardo Bruno, Davor Davidovic, Marco Fargetta, Y. Chen, Sandro Fiore, Z. Kurkcuoglu, Lara Lloret Iglesias, J. Martins, Alessandra Nuzzo, Paola Nassisi, João Murta Pina, Eva Sciacca, Daniele Spiga, Marco Antonio Tangaro, Michal Urbaniak, Bas Wegh, and Tomasz Zok

Published
2017

16. Legal Framework for the use and re-use of health data for scientific purposes

Author

Nadina Foggetti, Giacinto Donvito, and Marco Antonio Tangaro

Subjects
Open Access, Open Science, Health Data, GDPR, FAIR
Abstract

Subtask T6.6.4 – “Health data security aspects” concerns Legal and ethics requirements on the storage and handling of health data are becoming stricter (e.g. GDPR). In some cases, legal gaps can create obstacles to data sharing and interoperability. This subtask will look at how proposed solutions can be put in place while meeting those strong security requirements.

Published
2022
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17. Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

Author

Angelica Bianco, Elena Pedrini, Federico Zambelli, Vladimir Nosi, Ivan Molineris, Giacinto Donvito, Marco Antonio Tangaro, Pietro Mandreoli, Graziano Pesole, Luca Alessandrì, Marina Mordenti, Raffaele A. Calogero, Luca Sangiorgi, Daniela Bianchi, Angelo Romano, Marica Antonacci, Emanuele Bonetti, Paolo Uva, Matteo Chiara, Antonio Parisi, and Davide Cangelosi

Subjects
Web server, Service (systems architecture), QH301-705.5, Bioinformatics, Computer science, Computer applications to medicine. Medical informatics, R858-859.7, Software environment, Cloud computing, Covid-19, ELIXIR, Galaxy, Laniakea, NGS, SARS-Cov-2, Computational Biology, Humans, SARS-CoV-2, Software, COVID-19, Cloud Computing, computer.software_genre, Biochemistry, World Wide Web, 03 medical and health sciences, Structural Biology, Use case, Biology (General), Molecular Biology, 030304 developmental biology, 0303 health sciences, 030306 microbiology, business.industry, Applied Mathematics, Usability, Computer Science Applications, Workflow, Software deployment, User interface, business, computer
Abstract

Background Improving the availability and usability of data and analytical tools is a critical precondition for further advancing modern biological and biomedical research. For instance, one of the many ramifications of the COVID-19 global pandemic has been to make even more evident the importance of having bioinformatics tools and data readily actionable by researchers through convenient access points and supported by adequate IT infrastructures. One of the most successful efforts in improving the availability and usability of bioinformatics tools and data is represented by the Galaxy workflow manager and its thriving community. In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of “on-demand” Galaxy instances over the cloud. By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses. The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server’s initial configuration and deployment. Results “Laniakea@ReCaS”, the first instance of a Laniakea-based service, is managed by ELIXIR-IT and was officially launched in February 2020, after about one year of development and testing that involved several users. Researchers can request access to Laniakea@ReCaS through an open-ended call for use-cases. Ten project proposals have been accepted since then, totalling 18 Galaxy on-demand virtual servers that employ ~ 100 CPUs, ~ 250 GB of RAM and ~ 5 TB of storage and serve several different communities and purposes. Herein, we present eight use cases demonstrating the versatility of the platform. Conclusions During this first year of activity, the Laniakea-based service emerged as a flexible platform that facilitated the rapid development of bioinformatics tools, the efficient delivery of training activities, and the provision of public bioinformatics services in different settings, including food safety and clinical research. Laniakea@ReCaS provides a proof of concept of how enabling access to appropriate, reliable IT resources and ready-to-use bioinformatics tools can considerably streamline researchers’ work.

Published
2021

18. ITSoneWB: profiling global taxonomic diversity of eukaryotic communities on Galaxy

Author

Enrico Lavezzo, Graziano Pesole, Bruno Fosso, Giorgio Grillo, Marco Antonio Tangaro, Giacinto Donvito, Giacomo Baruzzo, Giuseppe Defazio, Monica Santamaria, and Vito Flavio Licciulli

Subjects
Statistics and Probability, Profiling (computer programming), Supplementary data, 0303 health sciences, Service (systems architecture), business.industry, Computer science, media_common.quotation_subject, 030302 biochemistry & molecular biology, Cloud computing, Biochemistry, Galaxy, Computer Science Applications, World Wide Web, 03 medical and health sciences, Computational Mathematics, Reference data, Computational Theory and Mathematics, Workbench, business, Molecular Biology, 030304 developmental biology, Diversity (politics), media_common
Abstract

Summary ITSoneWB (ITSone WorkBench) is a Galaxy-based bioinformatic environment where comprehensive and high-quality reference data are connected with established pipelines and new tools in an automated and easy-to-use service targeted at global taxonomic analysis of eukaryotic communities based on Internal Transcribed Spacer 1 variants high-throughput sequencing. Availability and implementation ITSoneWB has been deployed on the INFN-Bari ReCaS cloud facility and is freely available on the web at http://itsonewb.cloud.ba.infn.it/galaxy. Supplementary information Supplementary data are available at Bioinformatics online.

Published
2021

19. REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

Author

Tiziano Flati, Claudio Lo Giudice, Amos A Schaffer, Giovanni Chillemi, Ernesto Picardi, Tiziana Castrignanò, Eli Kopel, Marco Antonio Tangaro, Luigi Mansi, and Graziano Pesole

Subjects
Proteomics, Proteome, AcademicSubjects/SCI00010, Computational biology, Biology, Transcriptome, Databases, Genetic, Genetics, Data Mining, Humans, Database Issue, Gene, Data Curation, Comparative genomics, Regulation of gene expression, Internet, Base Sequence, Gene Expression Profiling, Computational Biology, Genomics, Transcriptome Sequencing, Gene Expression Regulation, RNA editing, ADAR, RNA Editing
Abstract

RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html.

Published
2021
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20. Author Correction: DOME: recommendations for supervised machine learning validation in biology

Author

Gianluca Pollastri, Ian Walsh, Tom Lenaerts, Marco Antonio Tangaro, Vojtech Spiwok, Dario Garcia-Gasulla, Tiina Titma, David Salgado, and Jennifer Harrow

Subjects
Dome (geology), business.industry, Published Erratum, MEDLINE, Cell Biology, Artificial intelligence, computer.software_genre, business, Molecular Biology, Biochemistry, computer, Natural language processing, Biotechnology
Published
2021

21. aScan: A Novel Method for the Study of Allele Specific Expression in Single Individuals

Author

Federico Zambelli, Giulio Pavesi, Graziano Pesole, Pietro Mandreoli, Erika Ferrandi, Matteo Chiara, and Marco Antonio Tangaro

Subjects
Computer science, Value (computer science), Human genetic variation, Computational biology, DNA sequencing, 03 medical and health sciences, Annotation, 0302 clinical medicine, Structural Biology, Genotype, Databases, Genetic, Humans, Computer Simulation, Allele, Promoter Regions, Genetic, Molecular Biology, Alleles, 030304 developmental biology, 0303 health sciences, Polymorphism, Genetic, Identification (information), Gene Expression Regulation, Genes, Organ Specificity, Transcription (software), 030217 neurology & neurosurgery, Software
Abstract

In diploid organisms, two copies of each allele are normally inherited from parents. Paternal and maternal alleles can be regulated and expressed unequally, which is referred to as allele-specific expression (ASE). In this work, we present aScan, a novel method for the identification of ASE from the analysis of matched individual genomic and RNA sequencing data. By performing extensive analyses of both real and simulated data, we demonstrate that aScan can correctly identify ASE with high accuracy and sensitivity in different experimental settings. Additionally, by applying our method to a small cohort of individuals that are not included in publicly available databases of human genetic variation, we outline the value of possible applications of ASE analysis in single individuals for deriving a more accurate annotation of "private" low-frequency genetic variants associated with regulatory effects on transcription. All in all, we believe that aScan will represent a beneficial addition to the set of bioinformatics tools for the analysis of ASE. Finally, while our method was initially conceived for the analysis of RNA-seq data, it can in principle be applied to any quantitative NGS assay for which matched genotypic and expression data are available. AVAILABILITY: aScan is currently available in the form of an open source standalone software package at: https://github.com/Federico77z/aScan/. aScan version 1.0.3, available at https://github.com/Federico77z/aScan/releases/tag/1.0.3, has been used for all the analyses included in this manuscript. A Docker image of the tool has also been made available at https://github.com/pmandreoli/aScanDocker.

Published
2020

22. VINYL: Variant prIoritizatioN by survivaL analysis

Author

Sandro Sorrentino, David S. Horner, Marco Antonio Tangaro, Graziano Pesole, Pietro Mandreoli, Federico Zambelli, Anna Maria D'Erchia, Matteo Chiara, and Cinzia Forleo

Subjects
Statistics and Probability, Prioritization, 0303 health sciences, Clinical genomics, Computer science, Context (language use), Computational biology, Biochemistry, Genome, Computer Science Applications, Identification (information), 03 medical and health sciences, Computational Mathematics, 0302 clinical medicine, Computational Theory and Mathematics, 030220 oncology & carcinogenesis, Molecular Biology, Survival analysis, 030304 developmental biology
Abstract

MotivationClinical applications of genome re-sequencing technologies typically generate large amounts of data that need to be carefully annotated and interpreted to identify genetic variants potentially associated with pathological conditions. In this context, accurate and reproducible methods for the functional annotation and prioritization of genetic variants are of fundamental importance.ResultsIn this article, we present VINYL, a flexible and fully automated system for the functional annotation and prioritization of genetic variants. Extensive analyses of both real and simulated datasets suggest that VINYL can identify clinically relevant genetic variants in a more accurate manner compared to equivalent state of the art methods, allowing a more rapid and effective prioritization of genetic variants in different experimental settings. As such we believe that VINYL can establish itself as a valuable tool to assist healthcare operators and researchers in clinical genomics investigations.Availability and implementationVINYL is available at http://beaconlab.it/VINYL and https://github.com/matteo14c/VINYL.Supplementary informationSupplementary data are available at Bioinformatics online.

Published
2020

23. Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

Author

Claudio Lo Giudice, Marco Antonio Tangaro, Ernesto Picardi, and Graziano Pesole

Subjects
0303 health sciences, Computer science, Sequence analysis, Bioinformatics, Molecular biology, High-throughput screening, RNA, Computational biology, Software package, Genome, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Workflow, RNA editing, ADAR, Transcriptomics, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

RNA editing is a widespread post-transcriptional mechanism able to modify transcripts through insertions/deletions or base substitutions. It is prominent in mammals, in which millions of adenosines are deaminated to inosines by members of the ADAR family of enzymes. A-to-I RNA editing has a plethora of biological functions, but its detection in large-scale transcriptome datasets is still an unsolved computational task. To this aim, we developed REDItools, the first software package devoted to the RNA editing profiling in RNA-sequencing (RNAseq) data. It has been successfully used in human transcriptomes, proving the tissue and cell type specificity of RNA editing as well as its pervasive nature. Outcomes from large-scale REDItools analyses on human RNAseq data have been collected in our specialized REDIportal database, containing more than 4.5 million events. Here we describe in detail two bioinformatic procedures based on our computational resources, REDItools and REDIportal. In the first procedure, we outline a workflow to detect RNA editing in the human cell line NA12878, for which transcriptome and whole genome data are available. In the second procedure, we show how to identify dysregulated editing at specific recoding sites in post-mortem brain samples of Huntington disease donors. On a 64-bit computer running Linux with ≥32 GB of random-access memory (RAM), both procedures should take ~76 h, using 4 to 24 cores. Our protocols have been designed to investigate RNA editing in different organisms with available transcriptomic and/or genomic reads. Scripts to complete both procedures and a docker image are available at https://github.com/BioinfoUNIBA/REDItools. This protocol describes bioinformatics procedures to detect RNA editing in RNA-sequencing datasets using REDItools and REDIportal. REDItools is a software package to profile RNA editing, while known editing sites are collected in the REDIportal database.

Published
2020

24. ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

Author

Federico Zambelli, Graziano Pesole, Stefano Amente, Matteo Chiara, Ernesto Picardi, Tiziana Castrignanò, Silvia Gioiosa, Marco Antonio Tangaro, Maddalena Fratelli, Tiziano Flati, Giovanni Chillemi, Mirko Cestari, Marco Cirilli, Castrignano, T., Gioiosa, S., Flati, T., Cestari, M., Picardi, E., Chiara, M., Fratelli, M., Amente, S., Cirilli, M., Tangaro, M. A., Chillemi, G., Pesole, G., and Zambelli, F.

Subjects
Computer science, Bioinformatics, Big data, Software environment, lcsh:Computer applications to medicine. Medical informatics, Computing Methodologies, Biochemistry, DNA sequencing, Cell Line, 03 medical and health sciences, 0302 clinical medicine, Structural Biology, Databases, Genetic, Animals, Humans, Profiling (information science), lcsh:QH301-705.5, Molecular Biology, 030304 developmental biology, Prunus persica, Bioinformatic, 0303 health sciences, Biological data, Genome, business.industry, Applied Mathematics, Computational Biology, Provisioning, Supercomputer, Computer Science Applications, NGS data analysis, Workflow, lcsh:Biology (General), Swallows, 030220 oncology & carcinogenesis, HPC, lcsh:R858-859.7, RNA Editing, Gene Fusion, DNA microarray, business, Compute service, Algorithms, Software, NGS data analysi
Abstract

Background The advent of Next Generation Sequencing (NGS) technologies and the concomitant reduction in sequencing costs allows unprecedented high throughput profiling of biological systems in a cost-efficient manner. Modern biological experiments are increasingly becoming both data and computationally intensive and the wealth of publicly available biological data is introducing bioinformatics into the “Big Data” era. For these reasons, the effective application of High Performance Computing (HPC) architectures is becoming progressively more recognized also by bioinformaticians. Here we describe HPC resources provisioning pilot programs dedicated to bioinformaticians, run by the Italian Node of ELIXIR (ELIXIR-IT) in collaboration with CINECA, the main Italian supercomputing center. Results Starting from April 2016, CINECA and ELIXIR-IT launched the pilot Call “ELIXIR-IT HPC@CINECA”, offering streamlined access to HPC resources for bioinformatics. Resources are made available either through web front-ends to dedicated workflows developed at CINECA or by providing direct access to the High Performance Computing systems through a standard command-line interface tailored for bioinformatics data analysis. This allows to offer to the biomedical research community a production scale environment, continuously updated with the latest available versions of publicly available reference datasets and bioinformatic tools. Currently, 63 research projects have gained access to the HPC@CINECA program, for a total handout of ~ 8 Millions of CPU/hours and, for data storage, ~ 100 TB of permanent and ~ 300 TB of temporary space. Conclusions Three years after the beginning of the ELIXIR-IT HPC@CINECA program, we can appreciate its impact over the Italian bioinformatics community and draw some considerations. Several Italian researchers who applied to the program have gained access to one of the top-ranking public scientific supercomputing facilities in Europe. Those investigators had the opportunity to sensibly reduce computational turnaround times in their research projects and to process massive amounts of data, pursuing research approaches that would have been otherwise difficult or impossible to undertake. Moreover, by taking advantage of the wealth of documentation and training material provided by CINECA, participants had the opportunity to improve their skills in the usage of HPC systems and be better positioned to apply to similar EU programs of greater scale, such as PRACE. To illustrate the effective usage and impact of the resources awarded by the program - in different research applications - we report five successful use cases, which have already published their findings in peer-reviewed journals.

Published
2020

25. PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data

Author

Maria Carla Bosco, Martina Morini, Luigi Varesio, Marco Antonio Tangaro, Federico Zambelli, Nicolò Zanardi, Alessandra Eva, and Davide Cangelosi

Subjects
0301 basic medicine, Source code, Statistical methods, Computer science, media_common.quotation_subject, education, lcsh:Medicine, Gene Expression, Real-Time Polymerase Chain Reaction, computer.software_genre, Article, law.invention, 03 medical and health sciences, 0302 clinical medicine, Software, law, Gene expression, lcsh:Science, Transcriptomics, Polymerase chain reaction, media_common, Measure (data warehouse), Multidisciplinary, business.industry, cloud computing, lcsh:R, Computational Biology, Genomics, pipe-t, Laniakea, Galaxy, Reverse transcriptase, 030104 developmental biology, Expression data, Data Interpretation, Statistical, lcsh:Q, Data mining, Transcriptome, business, computer, 030217 neurology & neurosurgery
Abstract

Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) is an accurate and fast method to measure gene expression. Reproducibility of the analyses is the main limitation of RT-qPCR experiments. Galaxy is an open, web-based, genomic workbench for a reproducible, transparent, and accessible science. Our aim was developing a new Galaxy tool for the analysis of RT-qPCR expression data. Our tool was developed using Galaxy workbench version 19.01 and functions implemented in several R packages. We developed PIPE-T, a new Galaxy tool implementing a workflow, which offers several options for parsing, filtering, normalizing, imputing, and analyzing RT-qPCR data. PIPE-T requires two input files and returns seven output files. We tested the ability of PIPE-T to analyze RT-qPCR data on two example datasets available in the gene expression omnibus repository. In both cases, our tool successfully completed execution returning expected results. PIPE-T can be easily installed from the Galaxy main tool shed or from Docker. Source code, step-by-step instructions, and example files are available on GitHub to assist new users to install, execute, and test PIPE-T. PIPE-T is a new tool suitable for the reproducible, transparent, and accessible analysis of RT-qPCR expression data.

Published
2019

26. Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal

Author

Claudio, Lo Giudice, Marco Antonio, Tangaro, Graziano, Pesole, and Ernesto, Picardi

Subjects
Huntington Disease, Base Sequence, Genome, Human, Sequence Analysis, RNA, Databases, Genetic, Brain, Computational Biology, High-Throughput Nucleotide Sequencing, Humans, RNA Editing, Software
Abstract

RNA editing is a widespread post-transcriptional mechanism able to modify transcripts through insertions/deletions or base substitutions. It is prominent in mammals, in which millions of adenosines are deaminated to inosines by members of the ADAR family of enzymes. A-to-I RNA editing has a plethora of biological functions, but its detection in large-scale transcriptome datasets is still an unsolved computational task. To this aim, we developed REDItools, the first software package devoted to the RNA editing profiling in RNA-sequencing (RNAseq) data. It has been successfully used in human transcriptomes, proving the tissue and cell type specificity of RNA editing as well as its pervasive nature. Outcomes from large-scale REDItools analyses on human RNAseq data have been collected in our specialized REDIportal database, containing more than 4.5 million events. Here we describe in detail two bioinformatic procedures based on our computational resources, REDItools and REDIportal. In the first procedure, we outline a workflow to detect RNA editing in the human cell line NA12878, for which transcriptome and whole genome data are available. In the second procedure, we show how to identify dysregulated editing at specific recoding sites in post-mortem brain samples of Huntington disease donors. On a 64-bit computer running Linux with ≥32 GB of random-access memory (RAM), both procedures should take ~76 h, using 4 to 24 cores. Our protocols have been designed to investigate RNA editing in different organisms with available transcriptomic and/or genomic reads. Scripts to complete both procedures and a docker image are available at https://github.com/BioinfoUNIBA/REDItools.

Published
2019

27. Laniakea: an open solution to provide Galaxy 'on-demand' instances over heterogeneous cloud infrastructures

Author

Matteo Chiara, Marica Antonacci, Graziano Pesole, Pietro Mandreoli, Giacinto Donvito, Marco Antonio Tangaro, and Federico Zambelli

Subjects
Service (systems architecture), workflow, Computer science, Distributed computing, AcademicSubjects/SCI02254, Health Informatics, Cloud computing, 02 engineering and technology, computer.software_genre, on-demand, User-Computer Interface, 03 medical and health sciences, 0302 clinical medicine, Server, Technical Note, 0202 electrical engineering, electronic engineering, information engineering, cloud, PaaS, 030304 developmental biology, 0303 health sciences, Software suite, End user, business.industry, Computational Biology, Provisioning, Cloud Computing, Virtualization, Data science, Laniakea, Galaxy, Computer Science Applications, Workflow, Software deployment, Virtual machine, Middleware, Component-based software engineering, AcademicSubjects/SCI00960, 020201 artificial intelligence & image processing, galaxy, business, computer, 030217 neurology & neurosurgery, Software
Abstract

BackgroundGalaxy is rapidly becoming the de facto standard among workflow managers for bioinformatics. A rich feature set, its overall flexibility, and a thriving community of enthusiastic users are among the main factors contributing to the popularity of Galaxy and Galaxy based applications. One of the main advantages of Galaxy consists in providing access to sophisticated analysis pipelines, e.g., involving numerous steps and large data sets, even to users lacking computer proficiency, while at the same time improving reproducibility and facilitating teamwork and data sharing among researchers. Although several Galaxy public services are currently available, these resources are often overloaded with a large number of jobs and offer little or no customization options to end users. Moreover, there are scenarios where a private Galaxy instance still constitutes a more viable alternative, including, but not limited to, heavy workloads, data privacy concerns or particular needs of customization. In such cases, a cloud-based virtual Galaxy instance can represent a solution that overcomes the typical burdens of managing the local hardware and software infrastructure needed to run and maintain a production-grade Galaxy service.ResultsHere we present Laniakea, a robust and feature-rich software suite which can be deployed on any scientific or commercial Cloud infrastructure in order to provide a “Galaxy on demand” Platform as a Service (PaaS). Laying its foundations on the INDIGO-DataCloud middleware, which has been developed to accommodate the needs of a large number of scientific communities, Laniakea can be deployed and provisioned over multiple architectures by private or public e-infrastructures. The end user interacts with Laniakea through a front-end that allows a general setup of the Galaxy instance, then Laniakea takes charge of the deployment both of the virtual hardware and all the software components. At the end of the process the user has access to a private, production-grade, yet fully customizable, Galaxy virtual instance. Laniakea’s supports the deployment of plain or cluster backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours, that is Galaxy configurations tailored for specific tasks. As a proof of concept, we provide a demo Laniakea instance hosted at an ELIXIR-IT Cloud facility.ConclusionsThe migration of scientific computational services towards virtualization and e-infrastructures is one of the most visible trends of our times. Laniakea provides Cloud administrators with a ready-to-use software suite that enables them to offer Galaxy, a popular workflow manager for bioinformatics, as an on-demand PaaS to their users. We believe that Laniakea can concur in making the many advantages of using Galaxy more accessible to a broader user base by removing most of the burdens involved in running a private instance. Finally, Laniakea’s design is sufficiently general and modular that could be easily adapted to support different services and platforms beyond Galaxy.

Published
2018
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28. INDIGO-DataCloud: a platform to facilitate seamless access to e-infrastructures

Author

Sandro Fiore, João Martins, Daniele Spiga, Paola Nassisi, Giacinto Donvito, Alessandro Costa, J. Marco de Lucas, Marcin Plociennik, Tomasz Zok, Andrea Ceccanti, Isabel Campos, Cristina Duma, L. Alves, Marco Antonio Tangaro, João Murta Pina, M. Viljoen, Michal Urbaniak, Marcus Hardt, Luciano Gaido, Davide Salomoni, Y. Chen, Álvaro López-García, Federico Zambelli, Alexandre M. J. J. Bonvin, Louis Antonelli, Lukasz Dutka, Bas Wegh, P. Solagna, Cosimo Palazzo, Luděk Matyska, Eva Sciacca, Mario David, Zeynep Kurkcuoglu, B. Ertl, Davor Davidović, Eva Cetinic, S. Vallero, S. Gallozzi, Valentina Zaccolo, Marica Antonacci, Riccardo Bruno, Fernando Aguilar, P. Fuhrman, S. Bagnasco, Zdeněk Šustr, Germán Moltó, Jorge Gomes, Marco Fargetta, Ignacio Blanquer, Lara Lloret, Alessandra Nuzzo, Pablo Orviz, Roberto Barbera, and European Commission

Subjects
Advanced user interfaces, Computer science, Computer Networks and Communications, Platform as a service, Cloud computing, 02 engineering and technology, Authorization and authentication, Containers, Software, 0202 electrical engineering, electronic engineering, information engineering, Information system, CIENCIAS DE LA COMPUTACION E INTELIGENCIA ARTIFICIAL, Cloud Computing, Platform as a Service, Software Management, Advanced User Interfaces, Authorization and Authentication, 020203 distributed computing, business.industry, Software management, DATA processing & computer science, Computing, E infrastructure, Hardware and Architecture, 020201 artificial intelligence & image processing, ddc:004, business, Software engineering, Information Systems
Abstract

Journal of grid computing 16(3), 381 - 408 (2018). doi:10.1007/s10723-018-9453-3, This paper describes the achievements of the H2020 project INDIGO-DataCloud. The project has provided e-infrastructures with tools, applications and cloud framework enhancements to manage the demanding requirements of scientific communities, either locally or through enhanced interfaces. The middleware developed allows to federate hybrid resources, to easily write, port and run scientific applications to the cloud. In particular, we have extended existing PaaS (Platform as a Service) solutions, allowing public and private e-infrastructures, including those provided by EGI, EUDAT, and Helix Nebula, to integrate their existing services and make them available through AAI services compliant with GEANT interfederation policies, thus guaranteeing transparency and trust in the provisioning of such services. Our middleware facilitates the execution of applications using containers on Cloud and Grid based infrastructures, as well as on HPC clusters. Our developments are freely downloadable as open source components, and are already being integrated into many scientific applications., Published by Springer Nature, Dordrecht

Published
2018

29. Multipion Bose-Einstein correlations inpp,p-Pb, and Pb-Pb collisions at energies available at the CERN Large Hadron Collider

Author

Christian Klein-Boesing, Podist Kurashvili, Marek Bombara, Diego Stocco, Rinaldo Rui, Łukasz Kamil Graczykowski, Mauro Cosentino, Yvonne Pachmayer, Toru Sugitate, Paolo Bartalini, Subhasis Chattopadhyay, Ivan Kisel, Leonid Vinogradov, Martin Schulc, Victor Gonzalez, Janka Vrlakova, Juan Carlos Cabanillas Noris, Muhammad Umair Naru, Jihyun Bhom, Caio Alves Garcia Prado, Yaroslav Berdnikov, Christoph Blume, Lee Barnby, Alexandre Suaide, Amalia Pop, Alexey Kurepin, Pasquale Di Nezza, Dr. Biswarup Paul, Jesus Roberto Millan-Almaraz, Ali OKATAN, Salvatore De Pasquale, Sara Vallero, Boris Teyssier, Prabhat Ranjan Pujahari, Elena Rocco, Ketil Røed, Nikolay Zaviyalov, Jovan Milosevic, Sumit Basu, Mirko Planinic, Jiri A. Mares, Paola Gianotti, Ashim Roy, Janusz Oleniacz, Professor David Evans, Salvatore Aiola, Marco Antonio Tangaro, Ciprian Mihai MITU, Smbat Grigoryan, Sergey Nikolaev, Andrew Lowe, Claude Pruneau, Leticia Cunqueiro, Borge S Nielsen, Francesca Carnesecchi, Ramona Lea, Lilit Karayan, Renu Bala, Stefania Beole', Rafael Derradi de Souza, Valery Kondratiev, Fedor Guber, Vito Manzari, Maximiliano Puccio, Jeremy Wilkinson, Jens-Jorgen Gaardhoje, Mais Suleymanov, Christoph Mayer, Alexander Akindinov, Andres Gomez Ramirez, Igor Pshenichnov, Krzysztof Redlich, Thomas Peitzmann, Kristjan Gulbrandsen, Christine Nattrass, Elena Botta, Ranjit Nayak, Francesca Bellini, Vladimir Kovalenko, Antonio Ortiz, Debasish Das, Yuri Kharlov, Antonio Uras, Domenico Di Bari, Arild Velure, Pranjal Sarma, Mohd Danish Azmi, Tiziano Virgili, Indranil Das, Andrzej Rybicki, Andrea Festanti, Raphael Tieulent, Federico Ronchetti, David Silvermyr, Victor Riabov, Kai Schweda, Christian Christensen, Jan Figiel, Adrian Sevcenco, Paolo Giubellino, Kenneth Read, Ewa Gładysz-Dziaduś, Ashutosh Kumar Pandey, Jens Erik Brücken, Francesca Soramel, Thomas Dietel, Vladimir Vechernin, Lukas Nellen, Sang Un Ahn, Elena G. Ferreiro, Catia Maria Annunziata Petta, Panos Kostarakis, Nikola Poljak, Ayben Karasu Uysal, Gabriele Gaetano Fronzé, Ion-Sorin ZGURA, Wladyslaw Henryk Trzaska, Eleuterio Spiriti, Raimond Snellings, Markus Keil, Guillaume Batigne, Nirbhay Kumar Behera, Andrea Alici, Mikael Mieskolainen, Satyajit Jena, Carlos Eugenio Perez Lara, Michal Sumbera, Chinorat Kobdaj, Yury Melikyan, Luciano Ramello, Arturo Fernandez Tellez, Marielle Chartier, Sergey Fokin, Roy Lemmon, Roberto Barbera, Nicolò Jacazio, Sami Räsänen, Michael Winn, Grzegorz Stefanek, Daniele De Gruttola, Piero Giubilato, Marie Germain, Christian Bourjau, Sergey Gorbunov, Arturo Fernández Téllez, Marco Van Leeuwen, Livio BIANCHI, David Chinellato, Giacomo Margagliotti, Mario Iván Martínez Hernández, Dmitry Blau, Somnath Kar, Javier Castillo Castellanos, Anju Bhasin, Fiorella Maria Celeste Fionda, Petr Závada, Hector Bello Martinez, Anton Alkin, Roberto Preghenella, Elisa Meninno, Friederike Bock, Adam Kisiel, Grigory Feofilov, You Zhou, Stefano Bagnasco, In-Kwon Yoo, Jun Takahashi, Sandra Moretto, Tomas Vanat, Peter Christiansen, Gines Martinez Garcia, Oleg Grachov, Peter Hristov, Stefano Piano, Ivonne Alicia Maldonado Cervantes, Valentina Zaccolo, Mario Rodriguez Cahuantzi, Barbara Guerzoni, Paolo Camerini, A. J. Rubio-Montero, Cristina Terrevoli, Lidia Goerlich, Alessandro Grelli, Massimo Masera, Alberto Martín Gago Medina, Giacomo Volpe, Marek Kowalski, Otwinowski Jacek, Laurent Aphecetche, Mikhail Zhalov, DEEPIKA JENA, Michael Weber, Charalampos Kouzinopoulos, Sabyasachi Siddhanta, Sean Murray, Uzma Tabassam, Kenta Shigaki, Ian Bearden, Małgorzata Janik, Rahul Ramachandran Nair, Piotr Gasik, Adela Kravcakova, Francesco Riggi, Marcello Lunardon, Marta Verweij, and Francesco Prino

Subjects
Physics, Particle physics, Large Hadron Collider, 010308 nuclear & particles physics, Nuclear Theory, Bose–Einstein correlations, 01 natural sciences, law.invention, Nuclear physics, Pion, law, 0103 physical sciences, Quark–gluon plasma, Coulomb, Nuclear Experiment, 010306 general physics, Bose–Einstein condensate, Coherence (physics)
Abstract

Three- and four-pion Bose-Einstein correlations are presented in pp, p-Pb, and Pb-Pb collisions at the LHC. We compare our measured four-pion correlations to the expectation derived from two- and three-pion measurements. Such a comparison provides a method to search for coherent pion emission. We also present mixed-charge correlations in order to demonstrate the effectiveness of several analysis procedures such as Coulomb corrections. Same-charge four-pion correlations in pp and p-Pb appear consistent with the expectations from three-pion measurements. However, the presence of non- negligible background correlations in both systems prevent a conclusive statement. In Pb-Pb collisions, we observe a significant suppression of three- and four-pion Bose-Einstein correlations compared to expectations from two- pion measurements. There appears to be no centrality dependence of the suppression within the 0-50% centrality interval. The origin of the suppression is not clear. However, by postulating either coherent pion emission or large multibody Coulomb effects, the suppression may be explained.

Published
2016

30. Charge-dependent flow and the search for the chiral magnetic wave in Pb-Pb collisions atsNN=2.76TeV

Author

Christian Klein-Boesing, Podist Kurashvili, Marek Bombara, Diego Stocco, Rinaldo Rui, Łukasz Kamil Graczykowski, Yvonne Pachmayer, Toru Sugitate, Paolo Bartalini, Subhasis Chattopadhyay, Ivan Kisel, Leonid Vinogradov, Martin Schulc, Victor Gonzalez, Janka Vrlakova, Juan Carlos Cabanillas Noris, Muhammad Umair Naru, Jihyun Bhom, Caio Alves Garcia Prado, Yaroslav Berdnikov, Lee Barnby, Alexandre Suaide, Amalia Pop, Alexey Kurepin, Pasquale Di Nezza, Dr. Biswarup Paul, Jesus Roberto Millan-Almaraz, Ali OKATAN, Salvatore De Pasquale, Sara Vallero, Boris Teyssier, Prabhat Ranjan Pujahari, Elena Rocco, Ketil Røed, Nikolay Zaviyalov, Jovan Milosevic, Sumit Basu, Mirko Planinic, Jiri A. Mares, Paola Gianotti, Ashim Roy, Janusz Oleniacz, Professor David Evans, Salvatore Aiola, Marco Antonio Tangaro, Ciprian Mihai MITU, Smbat Grigoryan, Sergey Nikolaev, Andrew Lowe, Claude Pruneau, Leticia Cunqueiro, Borge S Nielsen, Francesca Carnesecchi, Ramona Lea, Lilit Karayan, Renu Bala, Stefania Beole', Rafael Derradi de Souza, Valery Kondratiev, Fedor Guber, Vito Manzari, Maximiliano Puccio, Jeremy Wilkinson, Jens-Jorgen Gaardhoje, Mais Suleymanov, Christoph Mayer, Alexander Akindinov, Andres Gomez Ramirez, Igor Pshenichnov, Krzysztof Redlich, Thomas Peitzmann, Kristjan Gulbrandsen, Christine Nattrass, Elena Botta, Ranjit Nayak, Francesca Bellini, Vladimir Kovalenko, Antonio Ortiz, Debasish Das, Yuri Kharlov, Antonio Uras, Domenico Di Bari, Arild Velure, Pranjal Sarma, Mohd Danish Azmi, Tiziano Virgili, Indranil Das, Andrzej Rybicki, Andrea Festanti, Raphael Tieulent, Federico Ronchetti, David Silvermyr, Victor Riabov, Kai Schweda, Christian Christensen, Jan Figiel, Adrian Sevcenco, Paolo Giubellino, Kenneth Read, Ewa Gładysz-Dziaduś, Ashutosh Kumar Pandey, Jens Erik Brücken, Francesca Soramel, Thomas Dietel, Vladimir Vechernin, Lukas Nellen, Sang Un Ahn, Elena G. Ferreiro, Catia Maria Annunziata Petta, Nikola Poljak, Ayben Karasu Uysal, Ion-Sorin ZGURA, Wladyslaw Henryk Trzaska, Eleuterio Spiriti, Raimond Snellings, Markus Keil, Guillaume Batigne, Nirbhay Kumar Behera, Andrea Alici, Mikael Mieskolainen, Satyajit Jena, Carlos Eugenio Perez Lara, Michal Sumbera, Chinorat Kobdaj, Luciano Ramello, Arturo Fernandez Tellez, Marielle Chartier, Sergey Fokin, Roy Lemmon, Roberto Barbera, Nicolò Jacazio, Sami Räsänen, Michael Winn, Grzegorz Stefanek, Daniele De Gruttola, Piero Giubilato, Marie Germain, Christian Bourjau, Sergey Gorbunov, Arturo Fernández Téllez, Marco Van Leeuwen, Giacomo Margagliotti, Dmitry Blau, Somnath Kar, Javier Castillo Castellanos, Anju Bhasin, Fiorella Maria Celeste Fionda, Petr Závada, Hector Bello Martinez, Anton Alkin, Roberto Preghenella, Elisa Meninno, Friederike Bock, Adam Kisiel, Grigory Feofilov, You Zhou, Stefano Bagnasco, In-Kwon Yoo, Jun Takahashi, Sandra Moretto, Tomas Vanat, Peter Christiansen, Gines Martinez Garcia, Oleg Grachov, Peter Hristov, Stefano Piano, Ivonne Alicia Maldonado Cervantes, Valentina Zaccolo, Mario Rodriguez Cahuantzi, Peter Papcun, Barbara Guerzoni, Paolo Camerini, A. J. Rubio-Montero, Cristina Terrevoli, Lidia Goerlich, Alessandro Grelli, Massimo Masera, Alberto Martín Gago Medina, Giacomo Volpe, Marek Kowalski, Otwinowski Jacek, Laurent Aphecetche, Mikhail Zhalov, DEEPIKA JENA, Michael Weber, Charalampos Kouzinopoulos, Sabyasachi Siddhanta, Sean Murray, Uzma Tabassam, Kenta Shigaki, Ian Bearden, Małgorzata Janik, Rahul Ramachandran Nair, Piotr Gasik, Adela Kravcakova, Francesco Riggi, Marcello Lunardon, Marta Verweij, and Francesco Prino

Subjects
Physics, Charge conservation, Particle physics, Large Hadron Collider, 010308 nuclear & particles physics, media_common.quotation_subject, Hadron, Elementary particle, Parity (physics), 01 natural sciences, Asymmetry, Nuclear physics, Pseudorapidity, 0103 physical sciences, Rapidity, Nuclear Experiment, 010306 general physics, media_common
Abstract

We report on measurements of a charge-dependent flow using a novel three-particle correlator with ALICE in Pb-Pb collisions at the CERN Large Hadron Collider (LHC), and discuss the implications for observation of local parity violation and the chiral magnetic wave (CMW) in heavy-ion collisions. Charge-dependent flow is reported for different collision centralities as a function of the event charge asymmetry. While our results are in qualitative agreement with expectations based on the CMW, the nonzero signal observed in higher harmonics correlations indicates a possible significant background contribution. We also present results on a differential correlator, where the flow of positive and negative charges is reported as a function of the mean charge of the particles and their pseudorapidity separation. We argue that this differential correlator is better suited to distinguish the differences in positive and negative charges expected due to the CMW and the background effects, such as local charge conservation coupled with strong radial and anisotropic flow.

Published
2016

31. Centrality dependence of pion freeze-out radii in Pb-Pb collisions atsNN=2.76 TeV

Author

Christian Klein-Boesing, Podist Kurashvili, Marek Bombara, Diego Stocco, Rinaldo Rui, Łukasz Kamil Graczykowski, Mauro Cosentino, Yvonne Pachmayer, Toru Sugitate, Paolo Bartalini, Subhasis Chattopadhyay, Ivan Kisel, Leonid Vinogradov, Martin Schulc, Ron Soltz, Janka Vrlakova, Juan Carlos Cabanillas Noris, Muhammad Umair Naru, Jihyun Bhom, Caio Alves Garcia Prado, Yaroslav Berdnikov, Lee Barnby, Alexandre Suaide, Amalia Pop, Alexey Kurepin, Pasquale Di Nezza, Alessandro Feliciello, Dr. Biswarup Paul, Jesus Roberto Millan-Almaraz, Salvatore De Pasquale, Sara Vallero, Boris Teyssier, Prabhat Ranjan Pujahari, Elena Rocco, Ketil Røed, Nikolay Zaviyalov, Michal Křelina, Daniel Felea, Jovan Milosevic, Sumit Basu, Mirko Planinic, Jiri A. Mares, Paola Gianotti, Ashim Roy, Janusz Oleniacz, Professor David Evans, Salvatore Aiola, Marco Antonio Tangaro, Ciprian Mihai MITU, Smbat Grigoryan, Sergey Nikolaev, Andrew Lowe, Claude Pruneau, Leticia Cunqueiro, Borge S Nielsen, Francesca Carnesecchi, Ramona Lea, Lilit Karayan, Renu Bala, Stefania Beole', Valery Kondratiev, Fedor Guber, Vito Manzari, Maximiliano Puccio, Jeremy Wilkinson, Jens-Jorgen Gaardhoje, Mais Suleymanov, Christoph Mayer, Alexander Akindinov, Andres Gomez Ramirez, Igor Pshenichnov, Krzysztof Redlich, Thomas Peitzmann, Kristjan Gulbrandsen, Christine Nattrass, Daniel Tapia Takaki, Elena Botta, Francesca Bellini, Vladimir Kovalenko, Antonio Ortiz, Debasish Das, Carlos A. Salgado, Yuri Kharlov, Antonio Uras, Domenico Di Bari, Arild Velure, Mohd Danish Azmi, Tiziano Virgili, Jan Čepila, Indranil Das, Andrzej Rybicki, Andrea Festanti, Raphael Tieulent, Fernando Scarlassara, Federico Ronchetti, David Silvermyr, Victor Riabov, Kai Schweda, Christian Christensen, Jan Figiel, Adrian Sevcenco, Paolo Giubellino, Kenneth Read, Ewa Gładysz-Dziaduś, Ashutosh Kumar Pandey, Jens Erik Brücken, Francesca Soramel, Timo Hilden, Vladimir Vechernin, Lukas Nellen, Sang Un Ahn, Elena G. Ferreiro, Catia Maria Annunziata Petta, Nikola Poljak, Ayben Karasu Uysal, Ion-Sorin ZGURA, Eleuterio Spiriti, Raimond Snellings, Markus Keil, Guillaume Batigne, Nirbhay Kumar Behera, Andrea Alici, Mikael Mieskolainen, Satyajit Jena, Carlos Eugenio Perez Lara, Michal Sumbera, Chinorat Kobdaj, Yury Melikyan, Luciano Ramello, Arturo Fernandez Tellez, Marielle Chartier, Sergey Fokin, Roy Lemmon, Roberto Barbera, Sami Räsänen, Michael Winn, Grzegorz Stefanek, Daniele De Gruttola, Piero Giubilato, Marie Germain, Christian Bourjau, Michele Floris, Sergey Gorbunov, Arturo Fernández Téllez, Gianluca Usai, Marco Van Leeuwen, Muhammad Ajaz, Giacomo Margagliotti, Mario Iván Martínez Hernández, Dmitry Blau, Somnath Kar, Javier Castillo Castellanos, Néstor Armesto, Enrico Scomparin, Yevgen Martynov, Anju Bhasin, Petr Závada, Hector Bello Martinez, Anton Alkin, Roberto Preghenella, Elisa Meninno, Friederike Bock, Adam Kisiel, Grigory Feofilov, You Zhou, Stefano Bagnasco, In-Kwon Yoo, Jun Takahashi, Sandra Moretto, Tomas Vanat, Peter Christiansen, Gines Martinez Garcia, Peter Hristov, Stefano Piano, Ivonne Alicia Maldonado Cervantes, Valentina Zaccolo, Mario Rodriguez Cahuantzi, Peter Papcun, Barbara Guerzoni, Paolo Camerini, A. J. Rubio-Montero, Cristina Terrevoli, Lidia Goerlich, Alessandro Grelli, Massimo Masera, Alberto Martín Gago Medina, Giacomo Volpe, Marek Kowalski, Otwinowski Jacek, Laurent Aphecetche, Mikhail Zhalov, DEEPIKA JENA, Michael Weber, Charalampos Kouzinopoulos, Sabyasachi Siddhanta, Sean Murray, Kenta Shigaki, Ian Bearden, Małgorzata Janik, Jeewon Seo, Piotr Gasik, Adela Kravcakova, Francesco Riggi, Marcello Lunardon, Marta Verweij, and Francesco Prino

Subjects
Nuclear reaction, Physics, Particle physics, Meson, 010308 nuclear & particles physics, Nuclear Theory, Hadron, Elementary particle, Bose–Einstein correlations, 01 natural sciences, Nuclear physics, Pion, 0103 physical sciences, Quark–gluon plasma, High Energy Physics::Experiment, Impact parameter, Nuclear Experiment, 010306 general physics
Abstract

We report on the measurement of freeze-out radii for pairs of identical-charge pions measured in Pb-Pb collisions at √sNN = 2.76 TeV as a function o

Published
2016

32. One-dimensional pion, kaon, and proton femtoscopy in Pb-Pb collisions atsNN=2.76TeV

Author

Christian Klein-Boesing, Podist Kurashvili, Marek Bombara, Diego Stocco, Rinaldo Rui, Łukasz Kamil Graczykowski, Mauro Cosentino, Yvonne Pachmayer, Toru Sugitate, Paolo Bartalini, Subhasis Chattopadhyay, Ivan Kisel, Leonid Vinogradov, Martin Schulc, Ron Soltz, Janka Vrlakova, Juan Carlos Cabanillas Noris, Muhammad Umair Naru, Jihyun Bhom, Caio Alves Garcia Prado, Yaroslav Berdnikov, Lee Barnby, Alexandre Suaide, Amalia Pop, Alexey Kurepin, Pasquale Di Nezza, Laure Massacrier, Alessandro Feliciello, Dr. Biswarup Paul, Ali OKATAN, Salvatore De Pasquale, Sara Vallero, Boris Teyssier, Prabhat Ranjan Pujahari, Elena Rocco, Ketil Røed, Nikolay Zaviyalov, Michal Křelina, Daniel Felea, Jovan Milosevic, Sumit Basu, Mirko Planinic, Jiri A. Mares, Paola Gianotti, Ashim Roy, Janusz Oleniacz, Professor David Evans, Salvatore Aiola, Marco Antonio Tangaro, Ciprian Mihai MITU, Smbat Grigoryan, Sergey Nikolaev, Andrew Lowe, Claude Pruneau, Leticia Cunqueiro, Borge S Nielsen, Ramona Lea, Renu Bala, Stefania Beole', Valery Kondratiev, Fedor Guber, Vito Manzari, Maximiliano Puccio, Jeremy Wilkinson, Jens-Jorgen Gaardhoje, Mais Suleymanov, Christoph Mayer, Alexander Akindinov, Andres Gomez Ramirez, Igor Pshenichnov, Krzysztof Redlich, Thomas Peitzmann, Kristjan Gulbrandsen, Christine Nattrass, Daniel Tapia Takaki, Elena Botta, Francesca Bellini, Vladimir Kovalenko, Antonio Ortiz, Debasish Das, Carlos A. Salgado, Yuri Kharlov, Antonio Uras, Domenico Di Bari, Arild Velure, Mohd Danish Azmi, Tiziano Virgili, Jan Čepila, Indranil Das, Andrzej Rybicki, Andrea Festanti, Raphael Tieulent, Fernando Scarlassara, Federico Ronchetti, David Silvermyr, Victor Riabov, Kai Schweda, Gábor Gyula Kiss, Christian Christensen, Jan Figiel, Adrian Sevcenco, Paolo Giubellino, Kenneth Read, Ewa Gładysz-Dziaduś, Ashutosh Kumar Pandey, Jens Erik Brücken, Francesca Soramel, Timo Hilden, Vladimir Vechernin, Lukas Nellen, Sang Un Ahn, Elena G. Ferreiro, Catia Maria Annunziata Petta, Nikola Poljak, Ayben Karasu Uysal, Ion-Sorin ZGURA, Eleuterio Spiriti, Raimond Snellings, Markus Keil, Guillaume Batigne, Nirbhay Kumar Behera, Andrea Alici, Mikael Mieskolainen, Satyajit Jena, Carlos Eugenio Perez Lara, Michal Sumbera, Chinorat Kobdaj, Luciano Ramello, Arturo Fernandez Tellez, Marielle Chartier, Sergey Fokin, Roy Lemmon, Roberto Barbera, Sami Räsänen, Michael Winn, Grzegorz Stefanek, Daniele De Gruttola, Piero Giubilato, Marie Germain, Michele Floris, Sergey Gorbunov, Arturo Fernández Téllez, Gianluca Usai, Marco Van Leeuwen, Livio BIANCHI, Muhammad Ajaz, David Chinellato, Giacomo Margagliotti, Mario Iván Martínez Hernández, Dmitry Blau, Somnath Kar, Javier Castillo Castellanos, Néstor Armesto, Enrico Scomparin, Yevgen Martynov, Anju Bhasin, Fiorella Maria Celeste Fionda, Petr Závada, Hector Bello Martinez, Anton Alkin, Roberto Preghenella, Elisa Meninno, Friederike Bock, Adam Kisiel, Grigory Feofilov, You Zhou, Stefano Bagnasco, In-Kwon Yoo, Jun Takahashi, Sandra Moretto, Tomas Vanat, Peter Christiansen, Gines Martinez Garcia, Peter Hristov, Stefano Piano, Ivonne Alicia Maldonado Cervantes, Valentina Zaccolo, Mario Rodriguez Cahuantzi, Peter Papcun, Barbara Guerzoni, Paolo Camerini, A. J. Rubio-Montero, Cristina Terrevoli, Lidia Goerlich, Alessandro Grelli, Massimo Masera, Alberto Martín Gago Medina, Giacomo Volpe, Marek Kowalski, Otwinowski Jacek, Laurent Aphecetche, Mikhail Zhalov, DEEPIKA JENA, Michael Weber, Charalampos Kouzinopoulos, Sabyasachi Siddhanta, Sean Murray, Kenta Shigaki, Ian Bearden, Małgorzata Janik, Jeewon Seo, Piotr Gasik, Adela Kravcakova, Francesco Riggi, Marcello Lunardon, Marta Verweij, and Francesco Prino

Subjects
Physics, Nuclear and High Energy Physics, 010308 nuclear & particles physics, Phonon, Differential equation, 01 natural sciences, symbols.namesake, Nonlinear system, Normal mode, Quantum mechanics, Lattice (order), 0103 physical sciences, symbols, Exponential decay, 010306 general physics, Hamiltonian (quantum mechanics), Linear equation
Abstract

We prove the existence of exponentially localised and time-periodic solutions in general nonlinear Hamiltonian lattice systems. Like normal modes, these localised solutions are characterised by collective oscillations at the lattice sites with a uniform time-dependence. The proof of existence uses the comparison principle for differential equations to demonstrate that at each lattice site every half of the fundamental period of oscillations, contributing to localised solutions of the nonlinear lattice, is sandwiched between two oscillatory states of auxiliary linear equations. For soft (hard) on-site potentials the allowed frequencies of the in-phase (out-of-phase) localised periodic solutions lie below (above) the lower (upper) value of the linear spectrum of phonon frequencies. By varying a control parameter the exponential decay of the localised states can be tuned continuously.

Published
2015

33. Two-pion femtoscopy inp-Pb collisions atsNN=5.02TeV

Author

Christian Klein-Boesing, Podist Kurashvili, Marek Bombara, Diego Stocco, Rinaldo Rui, Łukasz Kamil Graczykowski, Mauro Cosentino, Yvonne Pachmayer, Toru Sugitate, Paolo Bartalini, Ivan Kisel, Leonid Vinogradov, Martin Schulc, Ron Soltz, Janka Vrlakova, Muhammad Umair Naru, Jihyun Bhom, Caio Alves Garcia Prado, Yaroslav Berdnikov, Lee Barnby, Alexandre Suaide, Amalia Pop, Alexey Kurepin, Pasquale Di Nezza, Ijaz Ahmed, Alessandro Feliciello, Dr. Biswarup Paul, Ali OKATAN, Salvatore De Pasquale, Sara Vallero, Boris Teyssier, Vahedeh Razazi, Prabhat Ranjan Pujahari, Ketil Røed, Nikolay Zaviyalov, Elena Bruna, Michal Křelina, Daniel Felea, Jovan Milosevic, Sumit Basu, Mirko Planinic, Jiri A. Mares, Paola Gianotti, Ashim Roy, Janusz Oleniacz, Professor David Evans, Salvatore Aiola, Marco Antonio Tangaro, Ciprian Mihai MITU, Smbat Grigoryan, Sergey Nikolaev, Andrew Lowe, Claude Pruneau, Leticia Cunqueiro, Borge S Nielsen, Ramona Lea, Renu Bala, Stefania Beole', Valery Kondratiev, Fedor Guber, Vito Manzari, Maximiliano Puccio, Jeremy Wilkinson, Jens-Jorgen Gaardhoje, Mais Suleymanov, Christoph Mayer, Alexander Akindinov, Andres Gomez Ramirez, Igor Pshenichnov, Krzysztof Redlich, Thomas Peitzmann, Kristjan Gulbrandsen, Christine Nattrass, Daniel Tapia Takaki, Elena Botta, Francesca Bellini, Vladimir Kovalenko, Antonio Ortiz, Debasish Das, Carlos A. Salgado, Yuri Kharlov, Antonio Uras, Domenico Di Bari, Arild Velure, Mohd Danish Azmi, Tiziano Virgili, Jan Čepila, Indranil Das, Andrzej Rybicki, Andrea Festanti, Raphael Tieulent, Fernando Scarlassara, Federico Ronchetti, David Silvermyr, Victor Riabov, Antonin MAIRE, Tahir Hussain, Kai Schweda, Christian Christensen, Jan Figiel, Adrian Sevcenco, Paolo Giubellino, Kenneth Read, Ewa Gładysz-Dziaduś, Jens Erik Brücken, Francesca Soramel, Timo Hilden, Vladimir Vechernin, Lukas Nellen, Sang Un Ahn, Elena G. Ferreiro, Catia Maria Annunziata Petta, Nikola Poljak, Ayben Karasu Uysal, Ion-Sorin ZGURA, Enrichetta Maria Fiore, Eleuterio Spiriti, Raimond Snellings, Markus Keil, Guillaume Batigne, Nirbhay Kumar Behera, Andrea Alici, Mikael Mieskolainen, Satyajit Jena, Carlos Eugenio Perez Lara, Michal Sumbera, Chinorat Kobdaj, Luciano Ramello, Arturo Fernandez Tellez, Marielle Chartier, Sergey Fokin, Roy Lemmon, Roberto Barbera, Sami Räsänen, Michael Winn, Grzegorz Stefanek, Daniele De Gruttola, Piero Giubilato, Marie Germain, Michele Floris, Sergey Gorbunov, Arturo Fernández Téllez, Gianluca Usai, Marco Van Leeuwen, Livio BIANCHI, Muhammad Ajaz, David Chinellato, Giacomo Margagliotti, Mario Iván Martínez Hernández, Dmitry Blau, Somnath Kar, Javier Castillo Castellanos, Néstor Armesto, Enrico Scomparin, Yevgen Martynov, Anju Bhasin, Fiorella Maria Celeste Fionda, Petr Závada, Hector Bello Martinez, Anton Alkin, Roberto Preghenella, Elisa Meninno, Friederike Bock, Adam Kisiel, Grigory Feofilov, You Zhou, Stefano Bagnasco, In-Kwon Yoo, Jun Takahashi, Sandra Moretto, Tomas Vanat, Peter Christiansen, Gines Martinez Garcia, Peter Hristov, Stefano Piano, Ivonne Alicia Maldonado Cervantes, Valentina Zaccolo, Mario Rodriguez Cahuantzi, Barbara Guerzoni, Paolo Camerini, A. J. Rubio-Montero, Cristina Terrevoli, Lidia Goerlich, Alessandro Grelli, Massimo Masera, Alberto Martín Gago Medina, Giacomo Volpe, Marek Kowalski, Otwinowski Jacek, Laurent Aphecetche, Mikhail Zhalov, DEEPIKA JENA, Michael Weber, Charalampos Kouzinopoulos, Sabyasachi Siddhanta, Sean Murray, Kenta Shigaki, Ian Bearden, Małgorzata Janik, Jeewon Seo, Piotr Gasik, Adela Kravcakova, Francesco Riggi, Marcello Lunardon, Marta Verweij, and Francesco Prino

Subjects
Physics, Nuclear and High Energy Physics, Particle physics, Large Hadron Collider, 010308 nuclear & particles physics, Bose–Einstein correlations, High multiplicity, 01 natural sciences, Gluon, Nuclear physics, Pion, 0103 physical sciences, Quark–gluon plasma, Transverse momentum, Multiplicity (chemistry), Nuclear Experiment, 010306 general physics
Abstract

We report the results of the femtoscopic analysis of pairs of identical pions measured in p-Pb collisions at root(NN)-N-S = 5.02 TeV. Femtoscopic radii are determined as a function of event multiplicity and pair momentum in three spatial dimensions. As in the pp collision system, the analysis is complicated by the presence of sizable background correlation structures in addition to the femtoscopic signal. The radii increase with event multiplicity and decrease with pair transverse momentum. When taken at comparable multiplicity, the radii measured in p-Pb collisions, at high multiplicity and low pair transverse momentum, are 10%-20% higher than those observed in pp collisions but below those observed in A-A collisions. The results are compared to hydrodynamic predictions at large event multiplicity as well as discussed in the context of calculations based on gluon saturation.

Published
2015

34. ExclusiveJ/ψPhotoproduction off Protons in Ultraperipheralp-Pb Collisions atsNN=5.02 TeV

Author

Christian Klein-Boesing, Podist Kurashvili, Marek Bombara, Diego Stocco, Rinaldo Rui, Łukasz Kamil Graczykowski, Mauro Cosentino, Yvonne Pachmayer, Toru Sugitate, Subhasis Chattopadhyay, Ivan Kisel, Leonid Vinogradov, Martin Schulc, Ron Soltz, Janka Vrlakova, Jihyun Bhom, Caio Alves Garcia Prado, Yaroslav Berdnikov, Lee Barnby, Alexandre Suaide, Amalia Pop, Alexey Kurepin, Ginevra D'Erasmo, Pasquale Di Nezza, Ijaz Ahmed, Alessandro Feliciello, Ali OKATAN, Salvatore De Pasquale, Igor Altsybeev, Sara Vallero, Vahedeh Razazi, Prabhat Ranjan Pujahari, Ketil Røed, Nikolay Zaviyalov, Elena Bruna, Michal Křelina, Daniel Felea, Jovan Milosevic, Sumit Basu, Mirko Planinic, Jiri A. Mares, Paola Gianotti, Ashim Roy, Janusz Oleniacz, Professor David Evans, Salvatore Aiola, Marco Antonio Tangaro, Ciprian Mihai MITU, Smbat Grigoryan, Sergey Nikolaev, Claude Pruneau, Leticia Cunqueiro, Borge S Nielsen, Ramona Lea, Renu Bala, Fernando Sanchez, Stefania Beole', Valery Kondratiev, Vito Manzari, Jeremy Wilkinson, Jens-Jorgen Gaardhoje, Mais Suleymanov, Christoph Mayer, Alexander Akindinov, Andres Gomez Ramirez, Igor Pshenichnov, Krzysztof Redlich, Thomas Peitzmann, Kristjan Gulbrandsen, Christine Nattrass, Daniel Tapia Takaki, Elena Botta, Francesca Bellini, Vladimir Kovalenko, Antonio Ortiz, Debasish Das, Carlos A. Salgado, Yuri Kharlov, Antonio Uras, Domenico Di Bari, Arild Velure, Mohd Danish Azmi, Tiziano Virgili, Jan Čepila, Indranil Das, Andrzej Rybicki, Andrea Festanti, Raphael Tieulent, Fernando Scarlassara, Federico Ronchetti, David Silvermyr, Victor Riabov, Kai Schweda, Gábor Gyula Kiss, Christian Christensen, Jan Figiel, Adrian Sevcenco, Jochen Thaeder, Andrey Zarochentsev, Paolo Giubellino, Kenneth Read, Ewa Gładysz-Dziaduś, Francesca Soramel, Timo Hilden, Vladimir Vechernin, Sang Un Ahn, Elena G. Ferreiro, Catia Maria Annunziata Petta, Vincenzo Paticchio, Nikola Poljak, Ayben Karasu Uysal, Ion-Sorin ZGURA, Enrichetta Maria Fiore, Eleuterio Spiriti, Raimond Snellings, Guillaume Batigne, Nirbhay Kumar Behera, Andrea Alici, Satyajit Jena, Carlos Eugenio Perez Lara, Michal Sumbera, Chinorat Kobdaj, Luciano Ramello, Arturo Fernandez Tellez, Sergey Fokin, Roy Lemmon, Roberto Barbera, Sami Räsänen, Michael Winn, Grzegorz Stefanek, Daniele De Gruttola, Marie Germain, Michele Floris, Sergey Gorbunov, Arturo Fernández Téllez, Gianluca Usai, Marco Van Leeuwen, Livio BIANCHI, Muhammad Ajaz, Rosario Turrisi, David Chinellato, Giacomo Margagliotti, Dmitry Blau, Somnath Kar, Javier Castillo Castellanos, Néstor Armesto, Enrico Scomparin, Yevgen Martynov, Anju Bhasin, Fiorella Maria Celeste Fionda, Andrea Dainese, Petr Závada, Anton Alkin, Roberto Preghenella, Elisa Meninno, Friederike Bock, Mariana Petris, Adam Kisiel, Grigory Feofilov, You Zhou, Stefano Bagnasco, In-Kwon Yoo, Jun Takahashi, Sandra Moretto, Peter Christiansen, Gines Martinez Garcia, Peter Hristov, Stefano Piano, Ivonne Alicia Maldonado Cervantes, Valentina Zaccolo, Mario Rodriguez Cahuantzi, Barbara Guerzoni, Paolo Camerini, A. J. Rubio-Montero, Cristina Terrevoli, Lidia Goerlich, Alessandro Grelli, Massimo Masera, Alberto Martín Gago Medina, Giacomo Volpe, Marek Kowalski, Otwinowski Jacek, Laurent Aphecetche, Mikhail Zhalov, DEEPIKA JENA, Michael Weber, Sabyasachi Siddhanta, Sean Murray, Kenta Shigaki, Ian Bearden, Małgorzata Janik, Jeewon Seo, Adela Kravcakova, Francesco Riggi, Marcello Lunardon, Marta Verweij, and Francesco Prino

Subjects
Quantum chromodynamics, Physics, Particle physics, Large Hadron Collider, Proton, Meson, 010308 nuclear & particles physics, General Physics and Astronomy, HERA, 7. Clean energy, 01 natural sciences, Gluon, Nuclear physics, 0103 physical sciences, Rapidity, Center of mass, 010306 general physics
Abstract

We present the first measurement at the LHC of exclusive J/ψ photoproduction off protons, in ultraperipheral proton-lead collisions at √sNN=5.02 TeV. Events are selected with a dimuon pair produced either in the rapidity interval, in the laboratory frame, 2.5

Published
2014

35. Two- and three-pion quantum statistics correlations in Pb-Pb collisions atsNN=2.76 TeV at the CERN Large Hadron Collider

Author

Christian Klein-Boesing, Podist Kurashvili, Marek Bombara, Diego Stocco, Rinaldo Rui, Łukasz Kamil Graczykowski, Mauro Cosentino, Yvonne Pachmayer, Toru Sugitate, Ramon Gomez Jimenez, Subhasis Chattopadhyay, Ivan Kisel, Leonid Vinogradov, Martin Schulc, Ron Soltz, Janka Vrlakova, Jihyun Bhom, Caio Alves Garcia Prado, Yaroslav Berdnikov, Lee Barnby, Alexandre Suaide, Amalia Pop, Alexey Kurepin, Ginevra D'Erasmo, Pasquale Di Nezza, Ijaz Ahmed, Alessandro Feliciello, Ali OKATAN, Salvatore De Pasquale, Igor Altsybeev, Vipul Bairathi, Sara Vallero, Oleksii Ivanytskyi, Vahedeh Razazi, Prabhat Ranjan Pujahari, Ketil Røed, Nikolay Zaviyalov, Elena Bruna, Michal Křelina, Daniel Felea, Jovan Milosevic, Sumit Basu, Mirko Planinic, Jiri A. Mares, Paola Gianotti, Ashim Roy, Janusz Oleniacz, Professor David Evans, Salvatore Aiola, Marco Antonio Tangaro, Ciprian Mihai MITU, Smbat Grigoryan, Sergey Nikolaev, Claude Pruneau, Leticia Cunqueiro, Ramona Lea, Renu Bala, Stefania Beole', Valery Kondratiev, Vito Manzari, Jeremy Wilkinson, Jens-Jorgen Gaardhoje, Mais Suleymanov, Christoph Mayer, Alexander Akindinov, Igor Pshenichnov, Krzysztof Redlich, Thomas Peitzmann, Christine Nattrass, Elena Botta, Francesca Bellini, Vladimir Kovalenko, Antonio Ortiz, Debasish Das, Carlos A. Salgado, Sandeep Sharma, Yuri Kharlov, Antonio Uras, Domenico Di Bari, Mohd Danish Azmi, Tiziano Virgili, Jan Čepila, Indranil Das, Andrzej Rybicki, Andrea Festanti, Raphael Tieulent, Fernando Scarlassara, Federico Ronchetti, David Silvermyr, Victor Riabov, Kai Schweda, Gábor Gyula Kiss, Christian Christensen, Jan Figiel, Adrian Sevcenco, Jochen Thaeder, Andrey Zarochentsev, Paolo Giubellino, Kenneth Read, Ewa Gładysz-Dziaduś, Francesca Soramel, Vladimir Vechernin, Sang Un Ahn, Elena G. Ferreiro, Catia Maria Annunziata Petta, Vincenzo Paticchio, Nikola Poljak, Ayben Karasu Uysal, Ion-Sorin ZGURA, Enrichetta Maria Fiore, Raimond Snellings, Guillaume Batigne, Nirbhay Kumar Behera, Andrea Alici, Satyajit Jena, Carlos Eugenio Perez Lara, Michal Sumbera, Chinorat Kobdaj, Luciano Ramello, Dr. Rakesh Mazumder, Arturo Fernandez Tellez, Sergey Fokin, Roy Lemmon, Roberto Barbera, Sami Räsänen, Michael Winn, Grzegorz Stefanek, Daniele De Gruttola, Marie Germain, Michele Floris, Sergey Gorbunov, Arturo Fernández Téllez, Gianluca Usai, Marco Van Leeuwen, Livio BIANCHI, Muhammad Ajaz, Rosario Turrisi, David Chinellato, Giacomo Margagliotti, Dmitry Blau, Somnath Kar, Javier Castillo Castellanos, Néstor Armesto, Enrico Scomparin, Yevgen Martynov, Anju Bhasin, Fiorella Maria Celeste Fionda, Andrea Dainese, Anton Alkin, Roberto Preghenella, Friederike Bock, Mariana Petris, Adam Kisiel, Grigory Feofilov, You Zhou, Stefano Bagnasco, In-Kwon Yoo, Jun Takahashi, Sandra Moretto, Peter Christiansen, Peter Hristov, Stefano Piano, Ivonne Alicia Maldonado Cervantes, Valentina Zaccolo, Mario Rodriguez Cahuantzi, Barbara Guerzoni, Paolo Camerini, A. J. Rubio-Montero, Cristina Terrevoli, Lidia Goerlich, Alessandro Grelli, Massimo Masera, Alberto Martín Gago Medina, Giacomo Volpe, Marek Kowalski, Otwinowski Jacek, Laurent Aphecetche, Mikhail Zhalov, DEEPIKA JENA, Michael Weber, Sabyasachi Siddhanta, Sean Murray, Kenta Shigaki, Ian Bearden, Małgorzata Janik, Jeewon Seo, Adela Kravcakova, Francesco Riggi, Marcello Lunardon, Marta Verweij, and Francesco Prino

Subjects
Physics, Nuclear and High Energy Physics, Particle physics, Large Hadron Collider, 010308 nuclear & particles physics, Nuclear Theory, Bose–Einstein correlations, 01 natural sciences, law.invention, Nuclear physics, Pion, law, 0103 physical sciences, Coherent states, High Energy Physics::Experiment, Nuclear Experiment, 010306 general physics, Quantum statistical mechanics, Bose–Einstein condensate, Coherence (physics)
Abstract

Correlations induced by quantum statistics are sensitive to the spatiotemporal extent as well as dynamics of particle-emitting sources in heavy-ion collisions. In addition, such correlations can be used to search for the presence of a coherent component of pion production. Two- and three-pion correlations of same and mixed charge are measured at low relative momentum to estimate the coherent fraction of charged pions in Pb-Pb collisions at √sNN=2.76 TeV at the CERN Large Hadron Collider with ALICE. The genuine three-pion quantum statistics correlation is found to be suppressed relative to the two-pion correlation based on the assumption of fully chaotic pion emission. The suppression is observed to decrease with triplet momentum. The observed suppression at low triplet momentum may correspond to a coherent fraction in charged-pion emission of 23%±8%.

Published
2014

37. CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

Author

David S. Horner, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, Graziano Pesole, and Matteo Chiara

Subjects
Statistics and Probability, 0303 health sciences, AcademicSubjects/SCI01060, Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), 030302 biochemistry & molecular biology, Computational biology, Genome Analysis, Biochemistry, Genome, Computer Science Applications, Applications Note, 03 medical and health sciences, Computational Mathematics, Annotation, Tree (data structure), Computational Theory and Mathematics, Functional annotation, Molecular Biology, 030304 developmental biology
Abstract

Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

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