ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
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ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community Tiziana Castrignanò1*, Silvia Gioiosa2,3, Tiziano Flati2,3, Mirko Cestari2, Ernesto Picardi3,4, Matteo Chiara3,5, Maddalena Fratelli6, Stefano Amente7, Marco Cirilli8, Marco Antonio Tangaro3, Giovanni Chillemi3,9, Graziano Pesole3,4* and Federico Zambelli3,5* From 13th Bioinformatics and Computational Biology Conference - BBCC 2018 Naples, Italy. 19-21 November 2018
* Correspondence: tiziana. [email protected]; graziano. [email protected]; federico.zambelli@ unimi.it 1 Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy 3 Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (IBIOM-CNR), Bari, Italy Full list of author information is available at the end of the article
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. (Continued on next page)
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