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31 Publications visible to you, out of a total of 31
Framework para a Construção de Redes Filogenéticas em Ambiente de Computação de Alto Desempenho

Abstract (Expand)

No presente artigo é apresentado uma avaliação de desempenho de um Framework de Redes Filogenéticas no ambiente do supercomputador Santos Dumont. O trabalho reforça os benefícios de paralelizar o … paralelizar o framework usando abordagens paralelas baseadas em Computação de Alta Vazão (CAV), e Computação de Alto Desempenho (CAD). Os resultados da execução paralela do framework proposto, demonstram que este tipo de experimento da bioinformática é apropriado para ser executado em ambientes de CAD; apesar de que nem todas as tarefas e programas componentes do framework tenham sido criados para usufruir de escalabilidade em ambientes de CAD, ou de técnicas de paralelismo em diferentes níveis. A análise comparativa da execução dos cinco pipelines de forma sequencial (como desenhado e usado originalmente por bioinformatas) apresentou um tempo estimado de 81, 67 minutos. Já a execução do mesmo experimento por meio do framework executa os cinco pipelines de forma paralela e usufruindo de um melhor gerenciamento das tarefas, gerando um tempo total de execução de 38,73 minutos. Essa melhora é de aproximadamente 2, 11 vezes em tempo de execução sugere que a utilização de um framework otimizado leva à diminuição do tempo computacional, à melhora de alocação de recursos e ao tempo de espera na alocação.

Authors: Rafael Terra, Kary Ocaña, Carla Osthoff, Lucas Cruz, Philippe Navaux, Diego Carvalho

Date Published: 19th Oct 2022

Publication Type: InProceedings

Framework para execução de workflows de redes filogenéticas em ambientes de computação de alto desempenho

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In the last years, the development of technologies, such as next-generation sequencing and high-performance computing allowed the execution of Bioinformatics experiments of high complexity and … computationally intensives. Different Bioinformatics fields need to use high-performance computing platforms to take advantage of the parallelism and tasks distribution, through specialized technologies of scientific workflows management systems. One of the Bioinformatics fields that need high-performance computing is phylogeny, a field that expresses the evolutive relations between genes and organisms, establishing which of them are most related evolutively. The phylogeny is used in several approaches, such as in the species classification; in the discovery of individuals’ kinship; in the identification of pathogens origins, and even in conservation biology. A way of representing these phylogenetic relations is using phylogenetic networks. However, the construction of these networks uses computationally intensive algorithms that require the constant manipulation of different input data. This work aims the development of a framework for construction of explicit phylogenetic networks, modeling a scientific workflow that adds different methods for the construction of the networks and the required input data treatment. The framework was developed to allow the use of multiple flows from the workflow in an automated, parallel, and distributed manner in a single execution and also to be executable in high- performance computing environments, constituting a challenging task, once the tools used are not developed focused in this environment. To orchestrate the workflow tasks, the scalable parallel programing library Parsl was used, allowing to do optimizations in the workflow’s tasks execution, performing better management of the resources. Two versions of the framework were developed, called Single Partition and Multi Partition, differing in the manner in which the resources are used. In tests performed, there was an improvement in the execution time of about five times when compared to the sequential execution of a flow without the optimizations. The framework was validated using public data of Dengue virus genomes, which were processed, annotated, and executed in the framework using the Santos Dumont supercomputer. The construction of the genomes’ explicit phylogenetic networks indicates that the framework is a functional, efficient, and easy to use tool.

Authors: Rafael Terra, Kary Ocaña, Carla Osthoff, Diego Carvalho

Date Published: 18th Feb 2022

Publication Type: Master's Thesis

Gerência e Análises de Workflows aplicados a Redes Filogenéticas de Genomas de Dengue no Brasil

Abstract (Expand)

Processos evolutivos e dispersão de genomas de Dengue no Brasil são relevantes na direção do impacto e vigilância endemo-epidêmico e social de arboviroses emergentes. Árvores e redes filogenéticas … filogenéticas permitem exibir eventos evolutivos e reticulados em vírus originados pela alta diversidade e taxa de mutação de recombinação homóloga frequente. Apresentamos um workflow científico paralelo e distribuído para redes filogenéticas desenhado para trabalhar com a diversidade de ferramentas e recursos em experimentos da biologia computacional e acoplados a ambientes de computação de alto desempenho. Apresentamos uma melhoria no tempo de execução de aproximadamente 5 vezes em comparação com a execução sequencial em análises de genomas de dengue e com identificação de eventos de recombinação.

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

INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance

Abstract (Expand)

Background A new era of flu surveillance has already started based on the genetic characterization and exploration of influenza virus evolution at whole-genome scale. Although this has been prioritized …d by national and international health authorities, the demanded technological transition to whole-genome sequencing (WGS)-based flu surveillance has been particularly delayed by the lack of bioinformatics infrastructures and/or expertise to deal with primary next-generation sequencing (NGS) data. Results We developed and implemented INSaFLU (“INSide the FLU”), which is the first influenza-oriented bioinformatics free web-based suite that deals with primary NGS data (reads) towards the automatic generation of the output data that are actually the core first-line “genetic requests” for effective and timely influenza laboratory surveillance (e.g., type and sub-type, gene and whole-genome consensus sequences, variants’ annotation, alignments and phylogenetic trees). By handling NGS data collected from any amplicon-based schema, the implemented pipeline enables any laboratory to perform multi-step software intensive analyses in a user-friendly manner without previous advanced training in bioinformatics. INSaFLU gives access to user-restricted sample databases and projects management, being a transparent and flexible tool specifically designed to automatically update project outputs as more samples are uploaded. Data integration is thus cumulative and scalable, fitting the need for a continuous epidemiological surveillance during the flu epidemics. Multiple outputs are provided in nomenclature-stable and standardized formats that can be explored in situ or through multiple compatible downstream applications for fine-tuned data analysis. This platform additionally flags samples as “putative mixed infections” if the population admixture enrolls influenza viruses with clearly distinct genetic backgrounds, and enriches the traditional “consensus-based” influenza genetic characterization with relevant data on influenza sub-population diversification through a depth analysis of intra-patient minor variants. This dual approach is expected to strengthen our ability not only to detect the emergence of antigenic and drug resistance variants but also to decode alternative pathways of influenza evolution and to unveil intricate routes of transmission. Conclusions In summary, INSaFLU supplies public health laboratories and influenza researchers with an open “one size fits all” framework, potentiating the operationalization of a harmonized multi-country WGS-based surveillance for influenza virus.

Authors: Vítor Borges, Miguel Pinheiro, Pedro Pechirra, Raquel Guiomar, João Paulo Gomes

Date Published: 1st Dec 2018

Publication Type: InProceedings

Landscape Analysis for the Specimen Data Refinery

Abstract (Expand)

This report reviews the current state-of-the-art applied approaches on automated tools, services and workflows for extracting information from images of natural history specimens and their labels. We … consider the potential for repurposing existing tools, including workflow management systems; and areas where more development is required. This paper was written as part of the SYNTHESYS+ project for software development teams and informatics teams working on new software-based approaches to improve mass digitisation of natural history specimens.

Authors: Stephanie Walton, Laurence Livermore, Olaf Bánki, Robert W. N. Cubey, Robyn Drinkwater, Markus Englund, Carole Goble, Quentin Groom, Christopher Kermorvant, Isabel Rey, Celia M Santos, Ben Scott, Alan Williams, Zhengzhe Wu

Date Published: 14th Aug 2020

Publication Type: Journal

Large-Scale Protein Interactions Prediction by Multiple Evidence Analysis Associated With an In-Silico Curation Strategy

Abstract (Expand)

Predicting the physical or functional associations through protein-protein interactions (PPIs) represents an integral approach for inferring novel protein functions and discovering new drug targets … during repositioning analysis. Recent advances in high-throughput data generation and multi-omics techniques have enabled large-scale PPI predictions, thus promoting several computational methods based on different levels of biological evidence. However, integrating multiple results and strategies to optimize, extract interaction features automatically and scale up the entire PPI prediction process is still challenging. Most procedures do not offer an in-silico validation process to evaluate the predicted PPIs. In this context, this paper presents the PredPrIn scientific workflow that enables PPI prediction based on multiple lines of evidence, including the structure, sequence, and functional annotation categories, by combining boosting and stacking machine learning techniques. We also present a pipeline (PPIVPro) for the validation process based on cellular co-localization filtering and a focused search of PPI evidence on scientific publications. Thus, our combined approach provides means to extensive scale training or prediction of new PPIs and a strategy to evaluate the prediction quality. PredPrIn and PPIVPro are publicly available at https://github.com/YasCoMa/predprin and https://github.com/YasCoMa/ppi_validation_process.

Authors: Yasmmin Côrtes Martins, Artur Ziviani, Marisa Fabiana Nicolás, Ana Tereza Ribeiro de Vasconcelos

Date Published: 6th Sep 2021

Publication Type: Journal

Making Canonical Workflow Building Blocks interoperable across workflow languages

Abstract (Expand)

We here introduce the concept of Canonical Workflow Building Blocks (CWBB), a methodology of describing and wrapping computational tools, in order for them to be utilized in a reproducible manner from … multiple workflow languages and execution platforms. We argue such practice is a necessary requirement for FAIR Computational Workflows [Goble 2020] to improve widespread adoption and reuse of a computational method across workflow language barriers.

Authors: Stian Soiland-Reyes, Genís Bayarri, Pau Andrio, Robin Long, Douglas Lowe, Ania Niewielska, Adam Hospital

Date Published: 7th Mar 2021

Publication Type: Journal

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data

Abstract (Expand)

While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a … activity of a microbiome. RNA-Seq data provides the possibility to determine active genes in the community and how their expression levels depend on external conditions. Although the field of metatranscriptomics is relatively young, the number of projects related to metatranscriptome analysis increases every year and the scope of its applications expands. However, there are several problems that complicate metatranscriptome analysis: complexity of microbial communities, wide dynamic range of transcriptome expression and importantly, the lack of high-quality computational methods for assembling meta-RNA sequencing data. These factors deteriorate the contiguity and completeness of metatranscriptome assemblies, therefore affecting further downstream analysis. Here we present MetaGT, a pipeline for de novo assembly of metatranscriptomes, which is based on the idea of combining both metatranscriptomic and metagenomic data sequenced from the same sample. MetaGT assembles metatranscriptomic contigs and fills in missing regions based on their alignments to metagenome assembly. This approach allows to overcome described complexities and obtain complete RNA sequences, and additionally estimate their abundances. Using various publicly available real and simulated datasets, we demonstrate that MetaGT yields significant improvement in coverage and completeness of metatranscriptome assemblies compared to existing methods that do not exploit metagenomic data. The pipeline is implemented in NextFlow and is freely available from https://github.com/ablab/metaGT .

Authors: Daria Shafranskaya, Varsha Kale, Rob Finn, Alla L. Lapidus, Anton Korobeynikov, Andrey D. Prjibelski

Date Published: 28th Oct 2022

Publication Type: Journal

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Abstract (Expand)

A widely used standard for portable multilingual data analysis pipelines would enable considerable benefits to scholarly publication reuse, research/industry collaboration, regulatory cost control, and … to the environment. Published research that used multiple computer languages for their analysis pipelines would include a complete and reusable description of that analysis that is runnable on a diverse set of computing environments. Researchers would be able to easier collaborate and reuse these pipelines, adding or exchanging components regardless of programming language used; collaborations with and within the industry would be easier; approval of new medical interventions that rely on such pipelines would be faster. Time will be saved and environmental impact would also be reduced, as these descriptions contain enough information for advanced optimization without user intervention. Workflows are widely used in data analysis pipelines, enabling innovation and decision-making for the modern society. In many domains the analysis components are numerous and written in multiple different computer languages by third parties. However, lacking a standard for reusable and portable multilingual workflows, then reusing published multilingual workflows, collaborating on open problems, and optimizing their execution would be severely hampered. Moreover, only a standard for multilingual data analysis pipelines that was widely used would enable considerable benefits to research-industry collaboration, regulatory cost control, and to preserving the environment. Prior to the start of the CWL project, there was no standard for describing multilingual analysis pipelines in a portable and reusable manner. Even today / currently, although there exist hundreds of single-vendor and other single-source systems that run workflows, none is a general, community-driven, and consensus-built standard. Preprint, submitted to Communications of the ACM (CACM).

Authors: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Carole Goble

Date Published: 14th May 2021

Publication Type: Unpublished

MGnify: the microbiome analysis resource in 2020

Abstract (Expand)

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in … particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline with multiple analysis pipelines that are tailored according to the input data, and that are formally described using the Common Workflow Language, enabling greater provenance, reusability, and reproducibility. MGnify's new analysis pipelines offer additional approaches for taxonomic assertions based on ribosomal internal transcribed spacer regions (ITS1/2) and expanded protein functional annotations. Biochemical pathways and systems predictions have also been added for assembled contigs. MGnify's growing focus on the assembly of metagenomic data has also seen the number of datasets it has assembled and analysed increase six-fold. The non-redundant protein database constructed from the proteins encoded by these assemblies now exceeds 1 billion sequences. Meanwhile, a newly developed contig viewer provides fine-grained visualisation of the assembled contigs and their enriched annotations.

Authors: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Date Published: 7th Nov 2019

Publication Type: Journal

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