BioCARLA

BioCARLA

Agenda | Tuesday October 5, 2021

Time of Guadalajara (GMT -5)

  • 10:45 - 11:00
    Opening BioCarla Workshop,
    Kary Ocaña and Francisco Martinez. BioCarla Chairs.
  • 11:00 - 11:20
    Laureant Dardenne, Laboratório Nacional de Computação Científica, LNCC, Brazil (dardenne@lncc.br).
    "DockThor-VS: A high-throughput virtual screening molecular docking platform coupled to the Brazilian supercomputer Santos Dumont"
  • 11:20 - 11:40
    Denis Jacob Machado, University of North Carolina at Charlotte, UNC, EE.UU. (dmachado@uncc.edu). "The HPC bottlenecks in the genomic surveillance of SARS-CoV-2"
  • 11:40 - 12:00
    Cristian Enrique Cadena Caballero, Universidad Industrial de Santander, Colombia (cadena.1405@gmail.com).
    “High Performance Computing applied to viral genomic diagnosis and sequencing for epidemiological surveillance”
  • 12:00 - 12:15
    Break
  • 12:15 - 12:35
    Nicole de Miranda Scherer, Instituto Nacional do Câncer, INCA, Brazil (nscherer@inca.gov.br).
    "The Red Queen dynamics of a bioinformatics platform"
  • 12:35 - 12:55
    Dante Travisany, Universidad de las Américas, Chile (dtravisany@udla.cl)
    "Towards a bioinformatics platform for Chilean SARS-CoV-2 genomes"
  • 12:55 - 13:15
    Fabricio Alves Barbosa da Silva, Fundação Oswaldo Cruz, FIOCRUZ, Brazil (fabricio.silva@fiocruz.br).
    "​​CellHeap: a Workflow for Processing COVID-19 Single-Cell RNA-seq Datasets in Supercomputers"
  • 13:15 - 13:35
    Marcela María Mecado Reyes, Instituto Nacional de Salud, INS, Colombia (mercado.marcela10@gmail.com).
    "Creation of the National SARS-CoV-2 Genomic Characterization Program in Colombia"
  • 13:35 - 14:00
    Cierre y mesa redonda:
    "Supercomputación en la Nueva Realidad Biológica y Médica en el Contexto Latinoamericano"
  • 14:15 - 14:25
    Presentación de trabajo 1: "Experiences in Executing Data-Intensive Bioinformatics Experiments in the Santos Dumont Supercomputer"
    Kary Ocaña1, Rafael Terra1, Lucas Cruz1,2, Guilherme Freire1,3, Marco Cabral1,4, Micaella Coelho1, Marcelo Galheigo1, Andre Carneiro1, Bruno Fagundes1, Diego Carvalho2, Douglas Cardoso2, Alexandre Cleim1, Luiz Gadelha1, Francieli Zanon-Boito5, Carla Osthoff1, Philippe Navaux6
    1LNCC, Rio de Janeiro - RJ, Brazil
    2CEFET-RJ, Rio de Janeiro - RJ, Brazil
    3FAETEC, Rio de Janeiro - RJ, Brazil
    4UFRJ, Rio de Janeiro - RJ, Brazil
    5LaBRI, Bordeaux, Inria, France
    6UFRGS, Rio Grande do Sul - RS, Brazil
  • 14:25 - 14:35
    Presentación de trabajo 2: "Algoritmo de clasificación para el diagnóstico de valvulopatías"
    Santiago I. Flores-Alonso1, René Luna-García1, Blanca Tovar-Corona2
    1IPN, CIC, Mexico, rlunag@ipn.mx}@puc-rio.br, sfloresa2010@alumno.ipn.mx
    2UPIITA, Mexico, btovar@ipn.mx
  • 14:35 - 14:45
    Presentación de trabajo 3:
    "Genome variant calling workflow implementation and deployment in HPC infrastructure".
    Elvismary Molina de Armas1, Nicole de Miranda Scherer2, Sergio Lifschitz1, and Mariana Boroni2.
    1PUC-RIO, Rio de Janeiro - RJ, Brasil, {earmas,sergio}@puc-rio.br.
    2INCA, Rio de Janeiro - RJ, Brasil {mariana.boroni,nscherer}@inca.br

Registration for this event.

Notice: Fundamental Tutorials registration is closed now.

Synopsis:

There has been a revolution in the way biology research is driven by the intensive use of computing resources from supercomputers to specialized high-performance environments. New high-throughput laboratory methods such as DNA microarray or Next-generation sequencing (NGS) produce several complex genomic data that describe gene expression levels, protein-protein interactions, and other information about how genes and proteins interact in living cells. They require an HPC vision and direction for leveraging on-demand management HPC bioinformatics systems.

This workshop will cover topics related to the interoperability of supercomputing and bioinformatics technologies that are being leveraged by real use cases and research infrastructure with a goal to improve the performance and efficiency of extreme-scale scientific workflows in several areas of bioinformatics and computational biology.

Emerging requirements from bioinformatics applications supported by HPC technologies offer new opportunities for engagement between the Latinoamerican bioinformatics communities.

Invited Speaker:
Marcela Mercado Reyes

Chair(s):
  • Francisco José Martínez Pérez
  • Kary Ann del Carmen Ocaña Gautherot