ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
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 com...
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2020-08-01
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Series: | BMC Bioinformatics |
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Online Access: | http://link.springer.com/article/10.1186/s12859-020-03565-8 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
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 Federico Zambelli |
spellingShingle |
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 Federico Zambelli ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community BMC Bioinformatics HPC Compute service Bioinformatics Software environment NGS data analysis |
author_facet |
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 Federico Zambelli |
author_sort |
Tiziana Castrignanò |
title |
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community |
title_short |
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community |
title_full |
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community |
title_fullStr |
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community |
title_full_unstemmed |
ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community |
title_sort |
elixir-it hpc@cineca: high performance computing resources for the bioinformatics community |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2020-08-01 |
description |
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. |
topic |
HPC Compute service Bioinformatics Software environment NGS data analysis |
url |
http://link.springer.com/article/10.1186/s12859-020-03565-8 |
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doaj-fade78556bc14076b90853414e73b7e72020-11-25T03:43:50ZengBMCBMC Bioinformatics1471-21052020-08-0121S1011710.1186/s12859-020-03565-8ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics communityTiziana Castrignanò0Silvia Gioiosa1Tiziano Flati2Mirko Cestari3Ernesto Picardi4Matteo Chiara5Maddalena Fratelli6Stefano Amente7Marco Cirilli8Marco Antonio Tangaro9Giovanni Chillemi10Graziano Pesole11Federico Zambelli12Department of Ecological and Biological Sciences (DEB), University of TusciaCINECA, SuperComputing Applications and Innovation DepartmentCINECA, SuperComputing Applications and Innovation DepartmentCINECA, SuperComputing Applications and Innovation DepartmentInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR)Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR)IRCCS-Istituto di Ricerche Farmacologiche “Mario Negri”, MilanoDepartment of Molecular Medicine and Medical Biotechnologies, University of Naples ‘Federico II’Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy (DISAA), University of MilanInstitute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR)Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR)Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR)Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR)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.http://link.springer.com/article/10.1186/s12859-020-03565-8HPCCompute serviceBioinformaticsSoftware environmentNGS data analysis |