ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community

• Published in: BMC bioinformatics 2020-08, Vol.21 (Suppl 10), p.352-352, Article 352
• Main Authors: Castrignanò, Tiziana, Gioiosa, Silvia, Flati, Tiziano, Cestari, Mirko, Picardi, Ernesto, Chiara, Matteo, Fratelli, Maddalena, Amente, Stefano, Cirilli, Marco, Tangaro, Marco Antonio, Chillemi, Giovanni, Pesole, Graziano, Zambelli, Federico
• Format: Article
• Language: English
• Subjects: Algorithms; Analysis; Animals; Annotations; Automation; Bioinformatics; Biomedical materials; Cell Line; Computation; Computational Biology; Compute service; Computer applications; Computing Methodologies; Data analysis; Data storage; Databases, Genetic; Datasets; Digital archives; Gene Fusion; Genome; Genomes; High performance computing; HPC; Humans; Information storage and retrieval; Infrastructure; Life sciences; Line interfaces; Medical research; Next-generation sequencing; NGS data analysis; Provisioning; Prunus persica - genetics; Random access memory; Rankings; Research projects; RNA Editing; Software; Software environment; Supercomputers; Swallows - genetics; User services; Work environment
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-020-03565-8

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. 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. 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 effect