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Using prototyping to choose a bioinformatics workflow management system

Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can suppo...

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Detalles Bibliográficos
Autores principales: Jackson, Michael, Kavoussanakis, Kostas, Wallace, Edward W. J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906312/
https://www.ncbi.nlm.nih.gov/pubmed/33630841
http://dx.doi.org/10.1371/journal.pcbi.1008622
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author Jackson, Michael
Kavoussanakis, Kostas
Wallace, Edward W. J.
author_facet Jackson, Michael
Kavoussanakis, Kostas
Wallace, Edward W. J.
author_sort Jackson, Michael
collection PubMed
description Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental build and re-entrancy—the ability to selectively re-execute parts of a workflow in the presence of additional inputs or changes in configuration and to resume execution from where a workflow previously stopped. Many workflow management systems enhance portability by supporting the use of containers, high-performance computing (HPC) systems, and clouds. Most importantly, workflow management systems allow bioinformaticians to delegate how their workflows are run to the workflow management system and its developers. This frees the bioinformaticians to focus on what these workflows should do, on their data analyses, and on their science. RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, the authors reimplemented this workflow within a workflow management system. To select a workflow management system, a rapid survey of available systems was undertaken, and candidates were shortlisted: Snakemake, cwltool, Toil, and Nextflow. Each candidate was evaluated by quickly prototyping a subset of the RiboViz workflow, and Nextflow was chosen. The selection process took 10 person-days, a small cost for the assurance that Nextflow satisfied the authors’ requirements. The use of prototyping can offer a low-cost way of making a more informed selection of software to use within projects, rather than relying solely upon reviews and recommendations by others.
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spelling pubmed-79063122021-03-03 Using prototyping to choose a bioinformatics workflow management system Jackson, Michael Kavoussanakis, Kostas Wallace, Edward W. J. PLoS Comput Biol Education Workflow management systems represent, manage, and execute multistep computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental build and re-entrancy—the ability to selectively re-execute parts of a workflow in the presence of additional inputs or changes in configuration and to resume execution from where a workflow previously stopped. Many workflow management systems enhance portability by supporting the use of containers, high-performance computing (HPC) systems, and clouds. Most importantly, workflow management systems allow bioinformaticians to delegate how their workflows are run to the workflow management system and its developers. This frees the bioinformaticians to focus on what these workflows should do, on their data analyses, and on their science. RiboViz is a package to extract biological insight from ribosome profiling data to help advance understanding of protein synthesis. At the heart of RiboViz is an analysis workflow, implemented in a Python script. To conform to best practices for scientific computing which recommend the use of build tools to automate workflows and to reuse code instead of rewriting it, the authors reimplemented this workflow within a workflow management system. To select a workflow management system, a rapid survey of available systems was undertaken, and candidates were shortlisted: Snakemake, cwltool, Toil, and Nextflow. Each candidate was evaluated by quickly prototyping a subset of the RiboViz workflow, and Nextflow was chosen. The selection process took 10 person-days, a small cost for the assurance that Nextflow satisfied the authors’ requirements. The use of prototyping can offer a low-cost way of making a more informed selection of software to use within projects, rather than relying solely upon reviews and recommendations by others. Public Library of Science 2021-02-25 /pmc/articles/PMC7906312/ /pubmed/33630841 http://dx.doi.org/10.1371/journal.pcbi.1008622 Text en © 2021 Jackson et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Education
Jackson, Michael
Kavoussanakis, Kostas
Wallace, Edward W. J.
Using prototyping to choose a bioinformatics workflow management system
title Using prototyping to choose a bioinformatics workflow management system
title_full Using prototyping to choose a bioinformatics workflow management system
title_fullStr Using prototyping to choose a bioinformatics workflow management system
title_full_unstemmed Using prototyping to choose a bioinformatics workflow management system
title_short Using prototyping to choose a bioinformatics workflow management system
title_sort using prototyping to choose a bioinformatics workflow management system
topic Education
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7906312/
https://www.ncbi.nlm.nih.gov/pubmed/33630841
http://dx.doi.org/10.1371/journal.pcbi.1008622
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