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

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 imp...

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Autores principales:	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, Federico Zambelli
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Galaxy Cloud computing Bioinformatics Laniakea Software environment NGS Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/e5ee31659111446fa3d69e4960d6a9ee
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spelling	oai:doaj.org-article:e5ee31659111446fa3d69e4960d6a9ee2021-11-14T12:13:19ZLaniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service10.1186/s12859-021-04401-31471-2105https://doaj.org/article/e5ee31659111446fa3d69e4960d6a9ee2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12859-021-04401-3https://doaj.org/toc/1471-2105Abstract 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.Marco Antonio TangaroPietro MandreoliMatteo ChiaraGiacinto DonvitoMarica AntonacciAntonio ParisiAngelica BiancoAngelo RomanoDaniela Manila BianchiDavide CangelosiPaolo UvaIvan MolinerisVladimir NosiRaffaele A. CalogeroLuca AlessandriElena PedriniMarina MordentiEmanuele BonettiLuca SangiorgiGraziano PesoleFederico ZambelliBMCarticleGalaxyCloud computingBioinformaticsLaniakeaSoftware environmentNGSComputer applications to medicine. Medical informaticsR858-859.7Biology (General)QH301-705.5ENBMC Bioinformatics, Vol 22, Iss S15, Pp 1-21 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Galaxy Cloud computing Bioinformatics Laniakea Software environment NGS Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
spellingShingle	Galaxy Cloud computing Bioinformatics Laniakea Software environment NGS Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5 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 Federico Zambelli Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
description	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.
format	article
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 Federico Zambelli
author_facet	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 Federico Zambelli
author_sort	Marco Antonio Tangaro
title	Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
title_short	Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
title_full	Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
title_fullStr	Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
title_full_unstemmed	Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
title_sort	laniakea@recas: exploring the potential of customisable galaxy on-demand instances as a cloud-based service
publisher	BMC
publishDate	2021
url	https://doaj.org/article/e5ee31659111446fa3d69e4960d6a9ee
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Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

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