ArticlePLoS computational biology2021
Using prototyping to choose a bioinformatics workflow management system.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed.
- A scoping review of approaches to evaluating workflow management systems for bioinformatics users.Briefings in bioinformatics · 2026Article
- Playbook workflow builder: Interactive construction of bioinformatics workflows.PLoS computational biology · 2025Article
- zAMP and zAMPExplorer: reproducible scalable amplicon-based metagenomics analysis and visualization.Bioinformatics advances · 2025Article
- Article
- polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.Genome biology and evolution · 2023Article
- Big Data in Gastroenterology Research.International journal of molecular sciences · 2023Review
- A Drug Repurposing Pipeline Based on Bladder Cancer Integrated Proteotranscriptomics Signatures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Metaphor-A workflow for streamlined assembly and binning of metagenomes.GigaScience · 2022Article
- A simple guide to de novo transcriptome assembly and annotation.Briefings in bioinformatics · 2022Review
- Design considerations for workflow management systems use in production genomics research and the clinic.Scientific reports · 2021Article
- Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers.Nature methods · 2021Review
- pyrpipe: a Python package for RNA-Seq workflows.NAR genomics and bioinformatics · 2021Article
- Geniac: Automatic Configuration GENerator and Installer for nextflow pipelines.Open research Europe · 2021Article
- RNAflow: An Effective and Simple RNA-Seq Differential Gene Expression Pipeline Using Nextflow.Genes · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
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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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.