Phyloinformatics Lab

New Events with Dr. Kary Ocaña

Denis Jacob Machado July 14, 2023
virologyepidemiologyphylogeneticsOne HealthHPCcomputing

The Phyloinformatics Lab is receiving the visit of Dr. Kary Ocaña from July 9 to July 25, 2023. Dr. Ocaña is a researcher at the Brazilian National Laboratory of Scientific Computing (LNCC), which is a part of Brazilian The Ministry of Science, Technology and Innovation (MCTI). Her main interests are phylogenomics, high-performance computing, data analytics in bioinformatics, and machine learning.

We want to make the most of Dr. Ocaña’s time with us. To helpo with that, we are putting together a few special events. Please see the details below.

Event 1 - Roundtable Discussion

Topic

Phyloinformatics, high-performance computing, and One Health: A roundtable with Dr. Kary Ocaña

Other details

Event 2 - Seminar

Title

Phylogenetic and evolutionary analysis of dengue virus serotypes in Brazil: User-steering in large-scale phylogenomic workflows

Abstract

Scientific workflows that construct phylogenetic trees have been proposed to manage the complex interplay of multiple bioinformatics applications. The exploratory nature of phylogenetic analyses is considered a computing-intensive process and demands monitoring high-performance computing (HPC) executions. This talk describes the development of a workflow implementation named PhyloHPC which allows for the remote execution of pipelines for phylogenetic analyses while benefiting from the parallel processing power of HPC environments. PhyloHPC is coupled to the Parsl Python library which contributes to the management of tasks executions in a HPC environment. Computational speedup and total execution time of the workflow show significant performance improvements and demonstrate that the Parsl model definition brings advantages of large-scale parallelism and the provenance support allows for runtime monitoring. We also explore the performance and scalability of RAxML in HPC environments. Phylogenetic tools included in PhyloHPC cover a wide yet selected range of programs and packages such as PHYLIP, PhyML, Weighbor, Tree-Puzzle, RAxML, Garli, IQ-TREE, and MrBayes. RAxML is a popular maximum likelihood software for processing large amounts of data in HPC environments. RAxML implements several phylogenetic likelihood function kernel variants (SSE3, AVX, AVX2) and offers coarsegrain/fine-grain parallelism via Hybrid and MPI/PThread versions. The circulation of new dengue virus lineages was described in Brazil and the Americas, but the precise classification of genotypes and lineages (clades) has been controversial. Here we perform phylogenetic and nucleotide-distance analyses of high-quality complete DENV1-4 genomes. DENV1 genotype V is representative of Latino America, and isolates in Brazil were organized into three distinct lineages, named clades I, II, and III. Sequence alignment was performed using MAFFT and phylogenetic trees were estimated using RAxML under the GTR nucleotide substitution model, which was inferred as the best-fit model by ModelFinder. The robustness of the tree topology was determined using 1,000 bootstrap replicates and visualized using FigTree v1.4.4. Due to the connectivity between the potential circulation of arboviruses, this investigation will be of value to scientists and public health officials dealing with the control and prevention of infections by this arboviral pathogen.

Other details

Dr. Ocaña’s Contact Information

Dr. Ocaña is one of the nicest people you will ever met. You can find her using the contact information below.

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