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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2021
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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. |
format | Online Article Text |
id | pubmed-7906312 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
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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