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Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service.
Tangaro, Marco Antonio; Mandreoli, Pietro; Chiara, Matteo; Donvito, Giacinto; Antonacci, Marica; Parisi, Antonio; Bianco, Angelica; Romano, Angelo; Bianchi, Daniela Manila; Cangelosi, Davide; Uva, Paolo; Molineris, Ivan; Nosi, Vladimir; Calogero, Raffaele A; Alessandri, Luca; Pedrini, Elena; Mordenti, Marina; Bonetti, Emanuele; Sangiorgi, Luca; Pesole, Graziano; Zambelli, Federico.
  • Tangaro MA; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
  • Mandreoli P; National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy.
  • Chiara M; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
  • Donvito G; Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy.
  • Antonacci M; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy.
  • Parisi A; Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy.
  • Bianco A; National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy.
  • Romano A; National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy.
  • Bianchi DM; Istituto Zooprofilattico Sperimentale Della Puglia e Della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy.
  • Cangelosi D; Istituto Zooprofilattico Sperimentale Della Puglia e Della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy.
  • Uva P; National Reference Laboratory for Coagulase-Positive Staphylococci Including Staphylococcus Aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, Italy.
  • Molineris I; National Reference Laboratory for Coagulase-Positive Staphylococci Including Staphylococcus Aureus, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Via Bologna 148, 10154, Turin, Italy.
  • Nosi V; Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy.
  • Calogero RA; Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy.
  • Alessandri L; Italian Institute of Technology, Via Morego 30, 16163, Genova, Italy.
  • Pedrini E; Department of Life Science and System Biology, University of Turin, Via Accademia Albertina, 13-1023, Turin, Italy.
  • Mordenti M; Department of Computer Science, University of Turin, Via Pessinetto 12, 10049, Turin, Italy.
  • Bonetti E; Department of Molecular Biotechnology and Health Sciences, Via Nizza 52, 10126, Turin, Italy.
  • Sangiorgi L; Department of Molecular Biotechnology and Health Sciences, Via Nizza 52, 10126, Turin, Italy.
  • Pesole G; Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy.
  • Zambelli F; Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy.
BMC Bioinformatics ; 22(Suppl 15): 544, 2021 Nov 08.
Article in English | MEDLINE | ID: covidwho-1506889
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Cloud Computing / COVID-19 Limits: Humans Language: English Journal: BMC Bioinformatics Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: S12859-021-04401-3

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Cloud Computing / COVID-19 Limits: Humans Language: English Journal: BMC Bioinformatics Journal subject: Medical Informatics Year: 2021 Document Type: Article Affiliation country: S12859-021-04401-3