Development and optimization of bioinformatics protocols and tools through high-performance computing techniques for use in processing large scale biological data

• Grant number: 16/04204-8
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: November 01, 2016
• End date: August 31, 2020
• Field of knowledge: Health Sciences - Medicine - Medical Clinics
• Principal Investigator: Iscia Teresinha Lopes Cendes
• Grantee: Wélliton de Souza
• Host Institution: Faculdade de Ciências Médicas (FCM). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 13/07559-3 - BRAINN - The Brazilian Institute of Neuroscience and Neurotechnology, AP.CEPID

Abstract

In the past five years, high-throughput sequencing became the main tool for genetic studies. The exponential increase in the volume of sequencing, allied with technology cost reduction, have created new challenges for computing. High-performance computing proposes solutions that are able to process large amount of data in a short amount of time. The evolution of this area led to the development of new architectures, such as cloud computing and heterogeneous computing. Cloud computing takes advantage of connectivity to the Internet to provide low-cost services; whereas heterogeneous computing combines high-performance computers with specialized devices to quickly process large volumes of data. To get the benefits of these new solutions in bioinformatics, it is necessary to optimize the tools and protocols that already exist or create new solutions. Besides the ability to analyze larger amount of genetic data sets, it is necessary to develop new methods for integrating results from different studies. Thus, this project aims to develop tools and automated pipelines for processing next-generation sequencing data, covering epigenetics, transcriptomics and genomics studies. The results of these studies will be integrated with public data bases of genomic information. We believe that high-performance computing will be the standard solution in -omics studies in a few years. Therefore, we want to anticipate and contribute positively in this area of knowledge, by providing tools that will be routinely used in research. Our work will also assist in the development of high-performance computing, since it will make this technology to be used more frequently by the scientific community.

Scientific publications

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

CENDES, LUCAS L.; DE SOUZA, WELLITON; LOPES-CENDES, ISCIA; CARVALHO, BENILTON S.. HPexome: An automated tool for processing whole-exome sequencing data. SOFTWAREX, v. 11, JAN-JUN 2020. (13/07559-3, 16/04204-8, 12/21548-1)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

SOUZA, Wélliton de. Development of scalable systems for genomic research at highperformance computing environments. 2020. Doctoral Thesis - Universidade Estadual de Campinas (UNICAMP). Faculdade de Ciências Médicas Campinas, SP.