Palestra INRA e LNCC hoje às 10h - Developing Efficient Scientific Gateways for Bioinformatics in Supercomputer Environments Supported by Artificial Intelligence

Abstract:

This project aims to develop green and intelligent scientific gateways for bioinformatics supported by high-performance computing environments (HPC) and specialized technologies such as scientific workflows, data mining, machine learning, and deep learning. The efficient analysis and interpretation of Big Data open new challenges to explore molecular biology, genetics, biomedical, and healthcare to improve personalized diagnostics and therapeutics; then, it becomes necessary to availability of new avenues to deal with this massive amount of information. New paradigms in Bioinformatics and Computational Biology drive the storing, managing, and accessing of data. HPC and Big Data advances in this domain represent a vast new field of opportunities for bioinformatics researchers and a significant challenge. The BioinfoPortal (https://bioinfo.lncc.br/) science gateway is a multiuser Brazilian infrastructure for bioinformatics applications, benefiting from the HPC infrastructure. We present several challenges for efficiently executing applications and discuss the findings on how to improve 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 carried out at Santos Dumont (SDumont, https://sdumont.lncc.br/), the largest supercomputer in Latin America that has 5.1 Petaflops and 36,472 computational cores distributed in 1,134 computational nodes.

Bios:
Carla Osthoff holds a degree in Electrical Engineering from the Pontifical Catholic University of Rio de Janeiro (1983), a Master's degree in Systems and Computer Engineering from the Federal University of Rio de Janeiro (1989), and a DSc. in Systems and Computer Engineering from the Federal University of Rio de Janeiro (2000). She has been working in the area of high-performance processing since 1985, initially in hardware development projects for distributed parallel multiprocessors and later as a researcher in Computer Architecture. Currently, she is a researcher in the area of High-Performance Computing at the National Laboratory for Scientific Computing (LNCC), is a professor at the Multidisciplinary Postgraduate Program at the National Laboratory for Scientific Computing and coordinates the National Center for High-Performance Processing (CENAPAD) at the LNCC., is a member of the Technical-Scientific body of the Santos Dumont Supercomputer Advisory Committee and coordinates the High-Performance Processing Sector of LNCC, which has several collaborative projects in the area of High-Performance Computing. Topics of interest are high-performance computing, distributed systems, parallel processing, parallel I/O systems, parallel programming models, and scientific computing.

Kary Ocaña is a Researcher in the Bioinformatics Laboratory (LABINFO) at the National Laboratory of Scientific Computing (LNCC). She was Post-Doc (2010–2015) of the Department of Computer Science at the COPPE Institute of the Federal University of Rio de Janeiro (Brazil) and was supported by a FAPERJ's grant "Post-Doc Note 10" (2013–2015). She received both her D.Sc. (2010) and M.Sc. (2006) in Cellular and Molecular Biology from the Oswaldo Cruz Institute (FIOCRUZ) (Rio de Janeiro, Brazil) and her B.Sc. (2002) in Pharmaceutical Biochemistry from the National University of San Marcos (Lima, Peru). In 2018 realized a scientific visit to the Center of Bioinformatics, Biostatistics, and Integrative Biology at Institut Pasteur (Paris, France), and in 2020 realized a second scientific visit to the Institute of Clinical Informatics at the University of Gottingen (Gottingen, Germany), reinforcing collaborative research. She was awarded in 2018 as Young Scientist of Our State, by FAPERJ (it is an award for prominent young researchers in the State of Rio de Janeiro, Brazil) for the project "Computational Support for Genomic Analysis of Neglected Tropical Diseases through Data Mining and Machine Learning".
Her main research interests covered areas in bioinformatics and computer science, working on the following topics: evolutionary and comparative genomics, phylogenomics, development of software applications for bioinformatics and computational biology, e-Science, scientific workflows for bioinformatics, parallel and distributed computation and cloud computing. She participates in research projects in those areas, with funding from Brazilian government agencies such as CNPq, CAPES, and FAPERJ, and is a member of IEEE, ACM, and the Brazilian Computer Society