inria brasil - RISC2 Project https://www.risc2-project.eu Fri, 01 Sep 2023 13:50:06 +0000 en-US hourly 1 https://wordpress.org/?v=6.6.2 Latin American researchers present greener gateways for Big Data in INRIA Brazil Workshop https://www.risc2-project.eu/2023/05/03/latin-american-researchers-present-greener-gateways-for-big-data-in-inria-brazil-workshop/ Wed, 03 May 2023 13:29:03 +0000 https://www.risc2-project.eu/?p=2802 In the scope of the RISC2 Project, the State University of Sao Paulo and INRIA (Institut National de Recherche en Informatique et en Automatique), a renowned French research institute, held a workshop, on  that set the stage for the presentation of the results accomplished under the work Developing Efficient Scientific Gateways for Bioinformatics in Supercomputer […]

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]]> In the scope of the RISC2 Project, the State University of Sao Paulo and INRIA (Institut National de Recherche en Informatique et en Automatique), a renowned French research institute, held a workshop, on  that set the stage for the presentation of the results accomplished under the work Developing Efficient Scientific Gateways for Bioinformatics in Supercomputer Environments Supported by Artificial Intelligence.

The goal of the investigation is to provide users with simplified access to computing structures through scientific solutions that represent significant developments in their fields. In the case of this project, it is intended to develop intelligent green scientific solutions for BioinfoPortal (a multiuser Brazilian infrastructure)supported by High-Performance Computing environments.

Technologically, it includes areas such as scientific workflows, data mining, machine learning, and deep learning. The outlook, in case of success, is the analysis and interpretation of Big Data allowing new paths in molecular biology, genetics, biomedicine, and health— so it becomes necessary tools capable of digesting the amount of information, efficiently, which can come.

The team performed several large-scale bioinformatics experiments that are considered to be computationally intensive. Currently, artificial intelligence is being used to generate models to analyze computational and bioinformatics metadata to understand how automatic learning can predict computational resources efficiently. The workshop was held from April 10th to 11th, and took place in the University of Sao Paulo.

RISC2 Project, which aims to explore the HPC impact in the economies of Latin America and Europe, relies on the interaction between researchers and policymakers in both regions. It also includes 16 academic partners such as the University of Buenos Aires, National Laboratory for High Performance Computing of Chile, Julich Supercomputing Centre, Barcelona Supercomputing Center (the leader of the consortium), among others.

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]]> Developing Efficient Scientific Gateways for Bioinformatics in Supercomputer Environments Supported by Artificial Intelligence https://www.risc2-project.eu/2023/03/20/developing-efficient-scientific-gateways-for-bioinformatics-in-supercomputer-environments-supported-by-artificial-intelligence/ Mon, 20 Mar 2023 09:37:46 +0000 https://www.risc2-project.eu/?p=2781 Scientific gateways bring enormous benefits to end users by simplifying access and hiding the complexity of the underlying distributed computing infrastructure. Gateways require significant development and maintenance efforts. BioinfoPortal[1], through its CSGrid[2]  middleware, takes advantage of Santos Dumont [3] heterogeneous resources. However, task submission still requires a substantial step regarding deciding the best configuration that […]

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]]> Scientific gateways bring enormous benefits to end users by simplifying access and hiding the complexity of the underlying distributed computing infrastructure. Gateways require significant development and maintenance efforts. BioinfoPortal[1], through its CSGrid[2]  middleware, takes advantage of Santos Dumont [3] heterogeneous resources. However, task submission still requires a substantial step regarding deciding the best configuration that leads to efficient execution. This project aims to develop green and intelligent scientific gateways for BioinfoPortal supported by high-performance computing environments (HPC) and specialised technologies such as scientific workflows, data mining, machine learning, and deep learning. The efficient analysis and interpretation of Big Data opens new challenges to explore molecular biology, genetics, biomedical, and healthcare to improve personalised diagnostics and therapeutics; finding new avenues to deal with this massive amount of information becomes necessary. New Bioinformatics and Computational Biology paradigms drive storage, management, and data access. HPC and Big Data advanced in this domain represent a vast new field of opportunities for bioinformatics researchers and a significant challenge. the BioinfoPortal science gateway is a multiuser Brazilian infrastructure. We present several challenges for efficiently executing applications and discuss the findings on improving the use of computational resources. We performed several large-scale bioinformatics experiments that are considered computationally intensive and time-consuming. We are currently coupling artificial intelligence to generate models to analyze computational and bioinformatics metadata to understand how automatic learning can predict computational resources’ efficient use. The computational executions are conducted at Santos Dumont, the largest supercomputer in Latin America, dedicated to the research community with 5.1 Petaflops and 36,472 computational cores distributed in 1,134 computational nodes.

By:

Carneiro, B. Fagundes, C. Osthoff, G. Freire, K. Ocaña, L. Cruz, L. Gadelha, M. Coelho, M. Galheigo, and R. Terra are with the National Laboratory of Scientific Computing, Rio de Janeiro, Brazil.

Carvalho is with the Federal Center for Technological Education Celso Suckow da Fonseca, Rio de Janeiro, Brazil.

Douglas Cardoso is with the Polytechnic Institute of Tomar, Portugal.

Boito and L, Teylo is with the University of Bordeaux, CNRS, Bordeaux INP, INRIA, LaBRI, Talence, France.

Navaux is with the Informatics Institute, the Federal University of Rio Grande do Sul, and Rio Grande do Sul, Brazil.

References:

Ocaña, K. A. C. S.; Galheigo, M.; Osthoff, C.; Gadelha, L. M. R.; Porto, F.; Gomes, A. T. A.; Oliveira, D.; Vasconcelos, A. T. BioinfoPortal: A scientific gateway for integrating bioinformatics applications on the Brazilian national high-performance computing network. Future Generation Computer Systems, v. 107, p. 192-214, 2020.

Mondelli, M. L.; Magalhães, T.; Loss, G.; Wilde, M.; Foster, I.; Mattoso, M. L. Q.; Katz, D. S.; Barbosa, H. J. C.; Vasconcelos, A. T. R.; Ocaña, K. A. C. S; Gadelha, L. BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments. PeerJ, v. 1, p. 1, 2018.

Coelho, M.; Freire, G.; Ocaña, K.; Osthoff, C.; Galheigo, M.; Carneiro, A. R.; Boito, F.; Navaux, P.; Cardoso, D. O. Desenvolvimento de um Framework de Aprendizado de Máquina no Apoio a Gateways Científicos Verdes, Inteligentes e Eficientes: BioinfoPortal como Caso de Estudo Brasileiro In: XXIII Simpósio em Sistemas Computacionais de Alto Desempenho – WSCAD 2022 (https://wscad.ufsc.br/), 2022.

Terra, R.; Ocaña, K.; Osthoff, C.; Cruz, L.; Boito, F.; Navaux, P.; Carvalho, D. Framework para a Construção de Redes Filogenéticas em Ambiente de Computação de Alto Desempenho. In: XXIII Simpósio em Sistemas Computacionais de Alto Desempenho – WSCAD 2022 (https://wscad.ufsc.br/), 2022.

Ocaña, K.; Cruz, L.; Coelho, M.; Terra, R.; Galheigo, M.; Carneiro, A.; Carvalho, D.; Gadelha, L.; Boito, F.; Navaux, P.; Osthoff, C. ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression. In: Latin America High-Performance Computing Conference (CARLA), 2022, Rio Grande do Sul, Brazil. Proceedings of the Latin American High-Performance Computing Conference – CARLA 2022 (http://www.carla22.org/), 2022.

[1] https://bioinfo.lncc.br/

[2] https://git.tecgraf.puc-rio.br/csbase-dev/csgrid/-/tree/CSGRID-2.3-LNCC

[3] https://https://sdumont.lncc.br

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]]> Inria Brasil Workshops https://www.risc2-project.eu/events/inria-brasil-workshops/ Tue, 14 Mar 2023 12:55:49 +0000 https://www.risc2-project.eu/?post_type=mec-events&p=2779

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The post Inria Brasil Workshops first appeared on RISC2 Project.

]]> RISC2 virtual workshop on High-Performance Computing (HPC), data science and scientific computing https://www.risc2-project.eu/2022/07/05/risc2-virtual-workshop-on-high-performance-computing-hpc-data-science-and-scientific-computing/ Tue, 05 Jul 2022 11:12:24 +0000 https://www.risc2-project.eu/?p=2193