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

BMC Bioinformatics

Software

Davide Cangelosi¹  Paolo Uva²  Vladimir Nosi³  Ivan Molineris⁴  Raffaele A. Calogero⁵  Luca Alessandri⁵  Marina Mordenti⁶  Elena Pedrini⁶  Luca Sangiorgi⁶  Emanuele Bonetti⁷  Graziano Pesole⁸  Federico Zambelli⁹  Matteo Chiara⁹  Pietro Mandreoli⁹  Marco Antonio Tangaro^1,10  Angelica Bianco^1,11  Antonio Parisi^1,11  Giacinto Donvito^1,12  Marica Antonacci^1,12  Daniela Manila Bianchi^1,13  Angelo Romano^1,13 

[1] Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy;Clinical Bioinformatics Unit, Scientific Direction, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147, Genova, Italy;Italian Institute of Technology, Via Morego 30, 16163, Genova, Italy;Department of Computer Science, University of Turin, Via Pessinetto 12, 10049, Turin, Italy;Department of Life Science and System Biology, University of Turin, Via Accademia Albertina, 13-1023, Turin, Italy;Department of Molecular Biotechnology and Health Sciences, Via Nizza 52, 10126, Turin, Italy;Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy;Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Via di Barbiano 1/10, 40136, Bologna, Italy;Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy;Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy;Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona 4, 70126, Bari, Italy;Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy;Department of Biosciences, University of Milan, Via Celoria 26, 20133, Milano, Italy;Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Giovanni Amendola 122/O, 70126, Bari, Italy;National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy;Istituto Zooprofilattico Sperimentale Della Puglia e Della Basilicata, Via Manfredonia 20, 71121, Foggia, Italy;National Institute for Nuclear Physics (INFN), Section of Bari, Via Orabona 4, 70126, Bari, Italy;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;

关键词: Galaxy;    Cloud computing;    Bioinformatics;    Laniakea;    Software environment;    NGS;    ELIXIR;    Covid-19;    SARS-Cov-2;   

DOI  :  10.1186/s12859-021-04401-3

 received in 2021-09-12, accepted in 2021-09-24,  发布年份 2021

来源: Springer

【 摘 要 】

BackgroundImproving 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.ConclusionsDuring 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.

【 授权许可】

CC BY   
© The Author(s) 2021

【 图 表 】

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Fig. 2