{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T09:23:09Z","timestamp":1775985789820,"version":"3.50.1"},"reference-count":36,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T00:00:00Z","timestamp":1614211200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>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\u2014the 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.<\/jats:p>\n                  <jats:p>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\u2019 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.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008622","type":"journal-article","created":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T13:28:03Z","timestamp":1614259683000},"page":"e1008622","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":27,"title":["Using prototyping to choose a bioinformatics workflow management system"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1765-8234","authenticated-orcid":true,"given":"Michael","family":"Jackson","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9167-7145","authenticated-orcid":true,"given":"Kostas","family":"Kavoussanakis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8025-6361","authenticated-orcid":true,"given":"Edward W. J.","family":"Wallace","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,2,25]]},"reference":[{"issue":"11","key":"pcbi.1008622.ref001","doi-asserted-by":"crossref","first-page":"e1002303","DOI":"10.1371\/journal.pbio.1002303","article-title":"Computing Workflows for Biologists: A Roadmap","volume":"13","author":"A Shade","year":"2015","journal-title":"PLoS Biol"},{"key":"pcbi.1008622.ref002","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1038\/d41586-019-02619-z","article-title":"Workflow systems turn raw data into scientific knowledge","volume":"573","author":"JM Perkel","year":"2019","journal-title":"Nature"},{"key":"pcbi.1008622.ref003","article-title":"The three technologies bioinformaticians need to be using right now","author":"M. Watson","year":"2019","journal-title":"Opiniomics"},{"issue":"3","key":"pcbi.1008622.ref004","first-page":"530","article-title":"A review of bioinformatic pipeline frameworks","volume":"18","author":"J. Leipzig","year":"2017","journal-title":"Brief Bioinform"},{"issue":"461","key":"pcbi.1008622.ref005","first-page":"18","article-title":"Plotkin JB, Shah P. riboviz: analysis and visualization of ribosome profiling datasets. BMC Bioinform","volume":"25","author":"O Carja","year":"2017"},{"issue":"19","key":"pcbi.1008622.ref006","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake\u2013A scalable bioinformatics workflow engine","volume":"28","author":"J. K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"pcbi.1008622.ref007","article-title":"Common Workflow Language, v1.0. Specification","author":"P Amstutz","year":"2016","journal-title":"Database: figshare"},{"issue":"4","key":"pcbi.1008622.ref008","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1038\/nbt.3772","article-title":"Toil enables reproducible, open source, big biomedical data analyses","volume":"35","author":"J Vivian","year":"2017","journal-title":"Nat Biotechnol"},{"issue":"4","key":"pcbi.1008622.ref009","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nbt.3820","article-title":"Nextflow enables reproducible computational workflows","volume":"35","author":"P Di Tommaso","year":"2017","journal-title":"Nat Biotechnol"},{"key":"pcbi.1008622.ref010","article-title":"Options for RiboViz workflow management","author":"M Jackson","year":"2020","journal-title":"Database: figshare"},{"key":"pcbi.1008622.ref011","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.3317","article-title":"HISAT: a fast spliced aligner with low memory requirements","volume":"12","author":"D Kim","year":"2015","journal-title":"Nat Methods"},{"issue":"1","key":"pcbi.1008622.ref012","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","author":"M. Martin","year":"2011","journal-title":"EMBnet J."},{"issue":"16","key":"pcbi.1008622.ref013","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"6","key":"pcbi.1008622.ref014","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"pcbi.1008622.ref015","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1101\/gr.209601.116","article-title":"UMI-tools: Modelling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy","volume":"27","author":"T Smith","year":"2017","journal-title":"Genome Res"},{"issue":"3","key":"pcbi.1008622.ref016","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007358","article-title":"Seven quick tips for analysis scripts in neuroimaging","volume":"16","author":"M. van Vliet","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"1","key":"pcbi.1008622.ref017","doi-asserted-by":"crossref","first-page":"e1001745","DOI":"10.1371\/journal.pbio.1001745","article-title":"Best Practices for Scientific Computing","volume":"12","author":"G Wilson","year":"2014","journal-title":"PLoS Biol"},{"key":"pcbi.1008622.ref018","article-title":"Awesome Pipeline","author":"P Di Tommaso","year":"2014","journal-title":"GitHub"},{"key":"pcbi.1008622.ref019","article-title":"Computational Data Analysis Workflow Systems","author":"P Amstutz","year":"2016","journal-title":"GitHub"},{"issue":"457","key":"pcbi.1008622.ref020","article-title":"Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics","volume":"19","author":"S Baichoo","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"pcbi.1008622.ref021","article-title":"Given the experience of others writing bioinformatic pipelines, what are the pros\/cons of Toil vs Snakemake vs Nextflow?","author":"zeekawla99ii","year":"2018","journal-title":"Reddit"},{"key":"pcbi.1008622.ref022","article-title":"Which Bioinformatics Workflow Manager \/ Tool \/ Platform \/ Language \/ Specification \/ Standard do you use or prefer?","author":"A. Vilella","year":"2018","journal-title":"Twitter"},{"key":"pcbi.1008622.ref023","first-page":"1381","article-title":"Full-stack genomics pipelining with GATK4 + WDL + Cromwell [version 1; not peer reviewed]","volume":"6","author":"K Voss","year":"2017","journal-title":"F1000Res"},{"issue":"W1","key":"pcbi.1008622.ref024","doi-asserted-by":"crossref","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"E Afgan","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008622.ref025","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.future.2014.10.008","article-title":"Pegasus: a Workflow Management System for Science Automation","volume":"46","author":"E Deelman","year":"2015","journal-title":"Future Gener Comput Syst"},{"issue":"W1","key":"pcbi.1008622.ref026","doi-asserted-by":"crossref","first-page":"W557","DOI":"10.1093\/nar\/gkt328","article-title":"The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud","volume":"41","author":"K Wolstencroft","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"pcbi.1008622.ref027","volume-title":"Choosing the right open-source software for your project","author":"The Software Sustainability Institute","year":"2011"},{"key":"pcbi.1008622.ref028","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/B978-0-12-375114-0.00004-9","volume-title":"User Experience Re-Mastered: Your Guide to Getting the Right Design","author":"N. Nielsen","year":"2010"},{"key":"pcbi.1008622.ref029","article-title":"Common Workflow Language User Guide","author":"T Hodges","year":"2017","journal-title":"Database: zenodo"},{"key":"pcbi.1008622.ref030","article-title":"Collecting use cases for workflow level conditionals #725","author":"Common Workflow Language","year":"2018","journal-title":"GitHub"},{"key":"pcbi.1008622.ref031","unstructured":"Nextflow. Nextflow patterns. GitHub [Internet]. [cited 2020 Oct 19]. Available from: http:\/\/nextflow-io.github.io\/patterns\/index.html."},{"key":"pcbi.1008622.ref032","article-title":"Nextflow tutorial","author":"Nextflow","year":"2018","journal-title":"GitHub"},{"key":"pcbi.1008622.ref033","article-title":"suggestion: run -dry #31","author":"Nextflow","year":"2015","journal-title":"GitHub"},{"key":"pcbi.1008622.ref034","article-title":"riboviz: software for analysis and visualization of ribosome profiling datasets","author":"E Wallace","year":"2020","journal-title":"Database: figshare"},{"key":"pcbi.1008622.ref035","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"PA Ewels","year":"2020","journal-title":"Nat Biotechnol"},{"key":"pcbi.1008622.ref036","article-title":"Streamlining Data-Intensive Biology With Workflow Systems","author":"T Reiter","year":"2020","journal-title":"bioRxiv"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008622","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T13:28:29Z","timestamp":1614259709000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008622"}},"subtitle":[],"editor":[{"given":"Francis","family":"Ouellette","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,2,25]]},"references-count":36,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2021,2,25]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1008622","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.08.04.236208","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,2,25]]}}}