I am a bioinformatician and phylogenetics. I really love working on problems at the intersection of high-performance computing and scientific workflows applied to omics
SEEK ID: https://workflowhub.eu/people/296
Location: Brazil
ORCID: https://orcid.org/0000-0002-2151-7418
Joined: 23rd Jun 2022
Expertise: Bioinformatics, Scientific workflow developement, high-performance computing, phylogenomics
Tools: Not specified
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Here we introduce a scientific workflow implementing several open-source software executed by Parsl parallel scripting language in an high-performance computing environment. We have applied the workflow to a single-cardiomyocyte RNA-seq data retrieved from Gene Expression Omnibus database. The workflow allows for the analysis (alignment, QC, sort and count reads, statistics generation) of raw RNA-seq data and seamless integration of differential expression results into a configurable script code. ...
Space: Independent Teams
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Abstract (Expand)
Authors: Rafael Terra, Kary Ocaña, Carla Osthoff, Lucas Cruz, Philippe Navaux, Diego Carvalho
Date Published: 19th Oct 2022
Publication Type: InProceedings
DOI: 10.5753/wscad.2022.226366
Citation: Anais do XXIII Simpósio em Sistemas Computacionais de Alto Desempenho (WSCAD 2022),pp.73-84,Sociedade Brasileira de Computação
Abstract (Expand)
Authors: Rafael Terra, Kary Ocaña, Carla Osthoff, Diego Carvalho
Date Published: 18th Feb 2022
Publication Type: Master's Thesis
Citation: TERRA, R. S. Framework para execução de workflows de redes filogenéticas em ambientes de computação de alto desempenho. 2022. 71 f. Tese. (Programa de Pós-Graduação em Modelagem Computacional) - Laboratório Nacional de Computação Científica, Petrópolis, 2022.
Abstract (Expand)
Authors: Rafael Terra, Micaella Coelho, Lucas Cruz, Marco Garcia-Zapata, Luiz Gadelha, Carla Osthoff, Diego Carvalho, Kary Ocaña
Date Published: 18th Jul 2021
Publication Type: InProceedings
DOI: 10.5753/bresci.2021.15788
Citation: Anais do XV Brazilian e-Science Workshop (BRESCI 2021),pp.49-56,Sociedade Brasileira de Computação
RNAseq workflow UMG: Here we introduce a scientific workflow implementing several open-source software executed by Galaxy parallel scripting language in an high-performance computing environment. We have applied the workflow to a single-cardiomyocyte RNA-seq data retrieved from Gene Expression Omnibus database. The workflow allows for the analysis (alignment, QC, sort and count reads, statistics generation) of raw RNA-seq data and seamless integration of differential expression results into a ...
RNA-seq Scientific Workflow
Workflow for RNA sequencing using the Parallel Scripting Library - Parsl.
Reference: Cruz, L., Coelho, M., Terra, R., Carvalho, D., Gadelha, L., Osthoff, C., & Ocaña, K. (2021). Workflows Científicos de RNA-Seq em Ambientes Distribuídos de Alto Desempenho: Otimização de Desempenho e Análises de Dados de Expressão Diferencial de Genes. In Anais do XV Brazilian e-Science Workshop, p. 57-64. Porto Alegre: SBC. DOI: https://doi.org/10.5753/bresci.2021.15789 ...
Type: Unrecognized workflow type
Creators: Lucas Cruz, Luiz Gadelha, Kary Ocaña
Submitter: Kary Ocaña