ReviewComputational and structural biotechnology journal2023
Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems.
Review in Computational and structural biotechnology journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Mapping the path to clinical implementation of multi-omics.Nature genetics · 2026Review
- SNPio: a Python interface for population genomic data processing.BMC bioinformatics · 2026Article
- A scoping review of approaches to evaluating workflow management systems for bioinformatics users.Briefings in bioinformatics · 2026Article
- Knowledge preservation in the era of big science and AI: strategies for sustainable scientific research.Nature communications · 2026Review
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- CAMP: a modular metagenomics analysis system for integrated multistep data exploration.NAR genomics and bioinformatics · 2026Article
- Genomic and functional characterization of a novel halophilic bacteriophage targeting carbapenem-resistant Klebsiella pneumoniae.PloS one · 2026Article
- PhIP-Seq: unveiling the complexity of antibody repertoires in health and disease.Frontiers in immunology · 2026Review
- Article
- Recommendations for Successful Development and Implementation of Digital Health Technology Tools.Journal of medical Internet research · 2025Article
- Improving the reliability, quality, and maintainability of bioinformatics pipelines with nf-test.GigaScience · 2025Article
- Gain efficiency with streamlined and automated data processing: Examples from high-throughput monoclonal antibody production.PloS one · 2025Article
- KiNext: a portable and scalable workflow for the identification and classification of protein kinases.BMC bioinformatics · 2024Article
- BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization.NAR genomics and bioinformatics · 2024Article
- Scalable and versatile container-based pipelines for de novo genome assembly and bacterial annotation.F1000Research · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Data analysis pipelines are now established as an effective means for specifying and executing bioinformatics data analysis and experiments. While scripting languages, particularly Python, R and notebooks, are popular and sufficient for developing small-scale pipelines that are often intended for a single user, it is now widely recognized that they are by no means enough to support the development of large-scale, shareable, maintainable and reusable pipelines capable of handling large volumes of data and running on high performance computing clusters. This review outlines the key requirements for building large-scale data pipelines and provides a mapping of existing solutions that fulfill them. We then highlight the benefits of using scientific workflow systems to get modular, reproducible and reusable bioinformatics data analysis pipelines. We finally discuss current workflow reuse practices based on an empirical study we performed on a large collection of workflows.
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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.