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4 results on '"Cuccuru, G."'

1. Training Infrastructure as a Service.

Author

Rasche H, Hyde C, Davis J, Gladman S, Coraor N, Bretaudeau A, Cuccuru G, Bacon W, Serrano-Solano B, Hillman-Jackson J, Hiltemann S, Zhou M, Grüning B, and Stubbs A

Subjects
Humans, Europe, Computational Biology, Software, Learning
Abstract

Background: Hands-on training, whether in bioinformatics or other domains, often requires significant technical resources and knowledge to set up and run. Instructors must have access to powerful compute infrastructure that can support resource-intensive jobs running efficiently. Often this is achieved using a private server where there is no contention for the queue. However, this places a significant prerequisite knowledge or labor barrier for instructors, who must spend time coordinating deployment and management of compute resources. Furthermore, with the increase of virtual and hybrid teaching, where learners are located in separate physical locations, it is difficult to track student progress as efficiently as during in-person courses., Findings: Originally developed by Galaxy Europe and the Gallantries project, together with the Galaxy community, we have created Training Infrastructure-as-a-Service (TIaaS), aimed at providing user-friendly training infrastructure to the global training community. TIaaS provides dedicated training resources for Galaxy-based courses and events. Event organizers register their course, after which trainees are transparently placed in a private queue on the compute infrastructure, which ensures jobs complete quickly, even when the main queue is experiencing high wait times. A built-in dashboard allows instructors to monitor student progress., Conclusions: TIaaS provides a significant improvement for instructors and learners, as well as infrastructure administrators. The instructor dashboard makes remote events not only possible but also easy. Students experience continuity of learning, as all training happens on Galaxy, which they can continue to use after the event. In the past 60 months, 504 training events with over 24,000 learners have used this infrastructure for Galaxy training., (© The Author(s) 2023. Published by Oxford University Press GigaScience.)

Published
2022
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2. Orione, a web-based framework for NGS analysis in microbiology.

Author

Cuccuru G, Orsini M, Pinna A, Sbardellati A, Soranzo N, Travaglione A, Uva P, Zanetti G, and Fotia G

Subjects
High-Throughput Nucleotide Sequencing, Internet, Metagenomics, Microbiological Techniques, Reproducibility of Results, Software
Abstract

Unlabelled: 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., (© The Author 2014. Published by Oxford University Press.)

Published
2014
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3. The PARIGA server for real time filtering and analysis of reciprocal BLAST results.

Author

Orsini M, Carcangiu S, Cuccuru G, Uva P, and Tramontano A

Subjects
Databases, Genetic, Databases, Protein, Internet, Time Factors, Computational Biology methods, Software
Abstract

BLAST-based similarity searches are commonly used in several applications involving both nucleotide and protein sequences. These applications span from simple tasks such as mapping sequences over a database to more complex procedures as clustering or annotation processes. When the amount of analysed data increases, manual inspection of BLAST results become a tedious procedure. Tools for parsing or filtering BLAST results for different purposes are then required. We describe here PARIGA (http://resources.bioinformatica.crs4.it/pariga/), a server that enables users to perform all-against-all BLAST searches on two sets of sequences selected by the user. Moreover, since it stores the two BLAST output in a python-serialized-objects database, results can be filtered according to several parameters in real-time fashion, without re-running the process and avoiding additional programming efforts. Results can be interrogated by the user using logical operations, for example to retrieve cases where two queries match same targets, or when sequences from the two datasets are reciprocal best hits, or when a query matches a target in multiple regions. The Pariga web server is designed to be a helpful tool for managing the results of sequence similarity searches. The design and implementation of the server renders all operations very fast and easy to use.

Published
2013
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4. Tools and data services registry: a community effort to document bioinformatics resources

Author

Callum Smith, Paolo Uva, Thomas Gatter, Peter Løngreen, Peter Juvan, Hans Ienasescu, Giuseppe Profiti, Aleksandra Nenadic, Kristoffer Rapacki, Chris Morris, Paola Roncaglia, Steffen Möller, Laura Emery, Søren Brunak, Maria Maddalena Sperotto, Heinz Stockinger, Kristian Davidsen, Federico Zambelli, Helen Parkinson, Olivia Doppelt-Azeroual, Luana Licata, Tatyana Goldberg, Andrea Schafferhans, Elisabeth Gasteiger, Emil Karol Rydza, Camille Laibe, Victor De La Torre, Marie Grosjean, Manuela Helmer-Citterich, Hervé Ménager, Radka Svobodová Vařeková, Rafael C. Jimenez, Martin Closter Jespersen, Anthony Bretaudeau, Jan Brezovsky, Tunca Doğan, Matúš Kalaš, Peter M. Rice, Ivan Mičetić, Rune Møllegaard Friborg, Maximilian Koch, Silvio C. E. Tosatto, Nick Juty, Björn Grüning, Gianmauro Cuccuru, Frederik Coppens, Gianni Cesareni, Jon Ison, Rabie Saidi, Sébastien Moretti, Rita Casadio, Gert Vriend, Guy Yachdav, Niall Beard, Timothy F. Booth, Michael Cornell, Piotr Jaroslaw Chmura, Veit Schwämmle, Karel Berka, Dan Bolser, Vassilios Ioannidis, Jing-Woei Li, Burkhard Rost, Gianluca Della Vedova, Fabien Mareuil, Hedi Peterson, Allegra Via, Paolo Romano, Christian Anthon, Technical University of Denmark [Lyngby] (DTU), Institut Pasteur de Madagascar, Réseau International des Instituts Pasteur (RIIP), University of Bergen (UIB), University of Copenhagen = Københavns Universitet (KU), University of Manchester, Palacky University, European Bioinformatics Institute, NEBC Wallingford, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Masaryk University, University of Bologna, Università degli Studi di Roma Tor Vergata [Roma], Ghent University [Belgium] (UGENT), Flanders Institute for Biotechnology, CRS4 Bioinformat, Università degli studi di Milano-Bicocca, Swiss Institute of Bioinformatics, Universität Bielefeld = Bielefeld University, Tumor Biology Center, Centre National de la Recherche Scientifique (CNRS), University of Freiburg, University of Ljubljana, The Chinese University of Hong Kong [Hong Kong], Universita degli Studi di Padova, Bioinformatics Research Centre, Université de Lausanne, CCLRC Daresbury Laboratory, Universität zu Lübeck [Lübeck] - University of Lübeck [Lübeck], Universität Rostock, University of Tartu, Imperial College London, IRCCS Azienda Ospedaliera Universitaria Integrata San Martino (IRCCS AOU San Martino), University of Southern Denmark (SDU), WTCHG, Central European Institute of Technology [Brno] (CEITEC), Instituto Nacional de Bioinformática, Sapienza University of Rome (DIAG), Consiglio Nazionale delle Ricerche, University of Milan, Radboud University Nijmegen, Ison, J, Rapacki, K, Ménager, H, Kalaš, M, Rydza, E, Chmura, P, Anthon, C, Beard, N, Berka, K, Bolser, D, Booth, T, Bretaudeau, A, Brezovsky, J, Casadio, R, Cesareni, G, Coppens, F, Cornell, M, Cuccuru, G, Davidsen, K, DELLA VEDOVA, G, Dogan, T, Doppelt Azeroual, O, Emery, L, Gasteiger, E, Gatter, T, Goldberg, T, Grosjean, M, Grüning, B, Helmer Citterich, M, Ienasescu, H, Ioannidis, V, Jespersen, M, Jimenez, R, Juty, N, Juvan, P, Koch, M, Laibe, C, Li, J, Licata, L, Mareuil, F, Mičetić, I, Friborg, R, Moretti, S, Morris, C, Möller, S, Nenadic, A, Peterson, H, Profiti, G, Rice, P, Romano, P, Roncaglia, P, Saidi, R, Schafferhans, A, Schwämmle, V, Smith, C, Sperotto, M, Stockinger, H, Vařeková, R, Tosatto, S, de la Torre, V, Uva, P, Via, A, Yachdav, G, Zambelli, F, Vriend, G, Rost, B, Parkinson, H, Løngreen, P, Brunak, S, University of Bergen (UiB), Palacky University Olomouc, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Masaryk University [Brno] (MUNI), Universiteit Gent = Ghent University [Belgium] (UGENT), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Swiss Institute of Bioinformatics [Lausanne] (SIB), Université de Lausanne (UNIL), Universität zu Lübeck [Lübeck], Central European Institute of Technology [Brno] (CEITEC MU), Brno University of Technology [Brno] (BUT), Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Danmarks Tekniske Universitet = Technical University of Denmark (DTU), University of Copenhagen = Københavns Universitet (UCPH), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, University of Bologna/Università di Bologna, Universiteit Gent = Ghent University (UGENT), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Université de Lausanne = University of Lausanne (UNIL), Università degli Studi di Padova = University of Padua (Unipd), Universität zu Lübeck = University of Lübeck [Lübeck], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), Università degli Studi di Milano = University of Milan (UNIMI), Ison, Jon, Rapacki, Kristoffer, Ménager, Hervé, Kalaš, Matúš, Rydza, Emil, Chmura, Piotr, Anthon, Christian, Beard, Niall, Berka, Karel, Bolser, Dan, Booth, Tim, Bretaudeau, Anthony, Brezovsky, Jan, Casadio, Rita, Cesareni, Gianni, Coppens, Frederik, Cornell, Michael, Cuccuru, Gianmauro, Davidsen, Kristian, Vedova, Gianluca Della, Dogan, Tunca, Doppelt-Azeroual, Olivia, Emery, Laura, Gasteiger, Elisabeth, Gatter, Thoma, Goldberg, Tatyana, Grosjean, Marie, Grüning, Björn, Helmer-Citterich, Manuela, Ienasescu, Han, Ioannidis, Vassilio, Jespersen, Martin Closter, Jimenez, Rafael, Juty, Nick, Juvan, Peter, Koch, Maximilian, Laibe, Camille, Li, Jing-Woei, Licata, Luana, Mareuil, Fabien, Mičetić, Ivan, Friborg, Rune Møllegaard, Moretti, Sebastien, Morris, Chri, Möller, Steffen, Nenadic, Aleksandra, Peterson, Hedi, Profiti, Giuseppe, Rice, Peter, Romano, Paolo, Roncaglia, Paola, Saidi, Rabie, Schafferhans, Andrea, Schwämmle, Veit, Smith, Callum, Sperotto, Maria Maddalena, Stockinger, Heinz, Vařeková, Radka Svobodová, Tosatto, Silvio C E, de la Torre, Victor, Uva, Paolo, Via, Allegra, Yachdav, Guy, Zambelli, Federico, Vriend, Gert, Rost, Burkhard, Parkinson, Helen, Løngreen, Peter, and Brunak, Søren

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], registry, Bioinformatics, computer.software_genre, Matematikk og naturvitenskap: 400::Informasjons- og kommunikasjonsvitenskap: 420::Systemutvikling og -arbeid: 426 [VDP], Task (project management), Documentation, Data and Information, Database Issue, Registries, bioinformatique, Data Curation, base de données, Settore BIO/11, gestion de données, tool, SOFTWARE-DEVELOPMENT, bioinformatics, ddc, outil informatique, Tools and data services registry, SEQANSWERS, Web service, MOLECULAR-BIOLOGY, Biology, Ecology and Environment, 03 medical and health sciences, SDG 3 - Good Health and Well-being, Genetics, Implementation, Dissemination, Bioinformatikk / Bioinformatics, Data curation, bioinformatic, business.industry, Computational Biology, Software, Software development, bioinformatics, tools, registry, elixir, Biology and Life Sciences, Mathematics and natural scienses: 400::Information and communication science: 420::System development and design: 426 [VDP], FRAMEWORK, ELIXIR, Settore BIO/18 - Genetica, 030104 developmental biology, tools, Data as a service, COMPILATION, business, COLLECTION, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], computer, WEB SERVICES, LIFE SCIENCES
Abstract

Contains fulltext : 171819.pdf (Publisher’s version ) (Open Access) Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

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